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  • RFLP  (237)
  • Springer  (237)
  • American Institute of Physics (AIP)
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • Wien : Geolog. Bundesanst.
  • 2005-2009
  • 2000-2004  (36)
  • 1990-1994  (201)
Collection
Publisher
  • Springer  (237)
  • American Institute of Physics (AIP)
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • Wien : Geolog. Bundesanst.
Years
Year
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 100 (2000), S. 564-568 
    ISSN: 1432-2242
    Keywords: Key words Triticum aestivum ; Tritiam timopheevii ; Pm6 ; Introgression lines ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Pm6 in bread wheat (Triticum aestivum L.), which was transferred from Triticum. timopheevii L., is a gene conferring resistance to the powdery mildew disease caused by Erysiphe graminis f. sp. tritici. Six near-isogenic lines ( NILs ) of Pm6 in a cultivar ’Prins’ background were analyzed to map this gene using restriction fragment length polymorphism (RFLP). Each of the six NILs possessed a T. timopheevii-derived segment, varying in length, and associated with powdery mildew resistance. Lines IGV1–465 (FAO163b/ 7*Prins) and IGV1–467 (Idaed 59B/7*Prins) had the shortest introgressed segments, which were detected only by DNA probes BCD135 and PSR934, respectively. The polymorphic loci detected by both probes were mapped to the long arm of chromosome 2B. Lines IGV1–458 (CI13250/7*Prins) and IGV1–456 (CI12559/8*Prins) contained the longest T. timopheevii segments involving both arms of donor chromosome 2G across the centromere. All these introgressed segments had an overlapping region flanked by the loci xpsr934 and xbcd135 on 2BL. Thus, Pm6 was located in this region since the powdery mildew resistance in all the NILs resulted from the introgressed fragments. Using the F2 mapping population from a cross of IGV1–463 (PI170914/7*Prins)×Prins, Pm6 was shown to be closely linked to the loci xbcd135 and xbcd266 at a genetic distance of 1.6 cM and 4.8 cM, respectively. BCD135 was successfully used in detecting the presence of Pm6 in different genetic backgrounds.
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  • 2
    ISSN: 1432-2242
    Keywords: Key words Chloroplast DNA ; Genetic diversity ; Ipomoeabatatas ; ISSR ; RFLP ; Sweetpotato
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Genetic diversity and relationships of 40 accessions of Ipomoea, representing ten species of series Batatas, were examined using ISSR markers and restriction-site variation in four non-coding regions of chloroplast DNA. A total of 2071 ISSR fragments were generated with 15 primers in these accessions and, on average, 52 bands per accession were amplified. Most of the primers contained dinucleotide repeats. The ISSR fragments were highly polymorphic (62.2%) among the 40 accessions studied. Restriction analysis of chloroplast (cp) DNA revealed 47 informative restriction-site and length mutations. Phylogenetic analyses of ISSR and cpDNA datasets generally revealed similar relationships at the interspecific level, but the high polymorphism of ISSRs resulted in a better separation of intraspecific accessions. However, the combined ISSR and cpDNA dataset appeared to be appropriate in resolving both intra- and interspecific relationships. Of the species examined, I. trifida was found to be the most closely related to cultivated sweetpotato, the hexaploid I. batatas, while I. ramosissima and I. umbraticola were the most distantly related to I. batatas within the series. Ipomoea triloba, hitherto considered to be one of the ancestors of sweetpotato, was only distantly related to sweetpotato based on ISSR similarity index.
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  • 3
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    Springer
    Theoretical and applied genetics 100 (2000), S. 899-905 
    ISSN: 1432-2242
    Keywords: Key words Petunia ; RFLP ; Genetic map ; Genome ; Segregation distortion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Due in large part to the data accumulated from years of classic genetic analysis, petunia (Petunia hybrida Vilm) has remained a useful model system, particularly for studies of gene regulation and genome structure. We have used three segregating populations of petunia, including those serving as the source of an earlier actin gene RFLP map, for RFLP mapping of several additional genes. Twenty-seven loci have been merged with 11 previously mapped morphological and biochemical markers. Our results contribute additional evidence to reports of a high degree of genome plasticity and segregation distortion in this species and suggest that petunia may be a useful plant system for detailed analysis of plant genome organization, activity and evolution.
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  • 4
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    Theoretical and applied genetics 100 (2000), S. 1018-1024 
    ISSN: 1432-2242
    Keywords: Key words cpDNA ; Cytoplasmic male sterility ; mtDNA ; Olea europaea ; Inheritance ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The olive tree is usually hermaphrodite but self-incompatible. In the Western Mediterranean some cultivars are totally male-sterile. Three different male-sterile phenotypes have been recognised. To infer the genetic basis of male sterility we studied its inheritance and cytoplasmic diversity in wild (oleaster) and cultivated Mediterranean olive. In the cross Olivière×Arbequina, the male-sterile trait was maternally inherited and affected all progenies. We also checked that both chloroplast and mitochondrial DNAs are maternally inherited. RFLP studies on chloroplast and mitochondrial DNAs revealed several cytotypes: two chlorotypes and four mitotypes in cultivars and oleaster (wild or feral Mediterranean olive). Furthermore, a total linkage desequilibrium between the CCK chlorotype and the MCK mitotype in cultivars and oleaster from different regions supports the fact that paternal leakage of organelles was not observed. The male sterility (ms 2) displayed by Olivière, plus six other cultivars and three oleaster was strictly associated with the CCK chlorotype and the MCK mitotype. These facts suggest that Olivière carries cytoplasmic male sterility. Male-fertile and male-sterile oleasters carrying this cytotype showed the presence of restorer alleles. This CMS might be due to a distant cross between olive taxa. The two other male-sterile phenotypes displayed by Lucques (ms 1) and Tanche (ms 3) were associated with the ME1 mitotype but we have not demonstrated CMS.
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  • 5
    ISSN: 1432-2242
    Keywords: Key words Triticum aestivum ; Aegilops speltoides ; Chromosome addition ; C-banding ; In situ hybridization ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Aegilops speltoides Tausch (2n = 2x = 14, SS) is considered as the closest living relative of the B and G genomes of polyploid wheats. A complete set of Triticum aestivum L. cv Chinese Spring-Ae. speltoides whole chromosomes and seven telosomic addition lines was established. A low pairing accession was selected for the isolation of the chromosome addition lines. Except for chromosomes 3S and 6S, which are presently only available as monosomic additions, all other lines were recovered as disomic or ditelosomic additions. The individual Ae. speltoides chromosomes isolated in the wheat background were assayed for their genetic effects on plant phenotype and cytologically characterized in terms of chromosome length, arm ratio, distribution of marker C-bands, and FISH sites using a Ae. speltoides-specific repetitive element, Gc1R-1, as a probe. The homoeology of the added Ae. speltoides chromosomes was established by using a standard set of RFLP probes. No chromosomal rearrangements relative to wheat were detected.
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  • 6
    ISSN: 1432-2242
    Keywords: Keywords Alfalfa ; Post-meiotic cytokinesis ; RFLP ; 4n pollen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The objective of this research was to map the jumbo-pollen trait in diploid alfalfa. Homozygous recessive (jpjp) plants are characterized by the complete failure of post-meiotic cytokinesis during microsporogenesis resulting in 100% 4n-pollen formation. Three F1 segregating populations were produced and analyzed for pollen-grain production and the segregation of RFLP markers. The first cross combination did not segregate for the jumbo-pollen trait, but showed a clear segregation for multinucleate (bi-, tri- and tetra-nucleate)-microspore formation. Cytological analysis showed that few plants produced 100% normal (uninucleate) microspores, whereas most of them produced multinucleate microspores at a variable frequency (0–75%). Plants with multinucleate microspores always showed a prevalence of binucleated microspores, even though some plants showed a background presence of tri- and tetra-nucleate microspores. QTL analysis based on ANOVA I and Stepwise Multiple Regression identified three QTLs with a highly significant effect on multinucleate-microspore formation. Two cross combinations, subsequently executed, showed Mendelian segregation for the jumbo-pollen trait and were effective in locating the jp gene on linkage group 6 close to the Vg1G1b RFLP locus. Interestingly, this RFLP locus was also linked to one QTL for multinucleate-microspore formation. Genetic models are discussed concerning the presence in linkage group 6 of a cluster of genes involved in multinucleate-microspore formation together with possible relationships between the jp gene and the Vg1G1b QTL.
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  • 7
    ISSN: 1432-2242
    Keywords: Key words Acacia ; RFLP ; Restriction enzymes ; Genome mapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Random genomic probes were used to assess levels of restriction fragment length polymorphism (RFLP) in two 2-generation outbred pedigrees of Acacia mangium Willd. Probes were evaluated for their ability to detect polymorphic loci in each pedigree and to determine the relative efficiency of different restriction enzymes in revealing polymorphisms. Sixty two percent of the probes which detected single- or low-copy number sequences revealed polymorphisms with at least one restriction enyzme. HpaII was the most efficient in detecting polymorphism among first-generation individuals. The recognition sequence of HpaII contains a CpG dimer, suggesting that cytosines in the CpG sequence may be hotspots for mutation in plant genomes, as previously reported in bacterial and mammalian genomes. Mendelian inheritance of 230 loci was demonstrated based on single-locus segregation in second-generation individuals. Less than 5% of loci showed evidence of segregation distortion. The proportion of fully informative loci (15%) was lower than previously reported in eucalypts reflecting the lower level of genetic diversity in A. mangium. The RFLP probes are suitable for the construction of a high-density genetic linkage map in A. mangium. Cross-hybridisation of the A.mangium RFLPs to DNA from species representing the three subgenera of the genus Acacia indicates that these markers could be used in breeding programs of other diploid acacias, for comparative studies of genome organisation, and for phylogenetic studies.
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  • 8
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    Theoretical and applied genetics 100 (2000), S. 602-606 
    ISSN: 1432-2242
    Keywords: Key words Triticum ; Hexaploid ; Mapping ; RFLP ; RSL ; Spelt
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A dominant allele at the Q locus on chromosome 5A is believed to be the principal factor responsible for free-threshing, square-head spikes with a non-fragile rachis in bread wheat, Triticum aestivum ssp. aestivum. The spelt syndrome, resulting in pyramidal spikes with a brittle rachis and hulled grain in T. aestivum, is believed to be principally caused by the q allele. Chromosome 5A of European and Iranian spelt was substituted for 5A of bread wheat and the lines were characterized with molecular markers. The substitution of bread wheat chromosome 5A by 5A of European spelt resulted in weakly hulled, pyramidal spikes with a non-brittle rachis, whereas and the substitution of 5A by 5A of Iranian spelt did not alter spike morphology at all. It is concluded that the expression of the spelt syndrome depends, to a large extent, on the interactions of q with genes controlling glume tenacity and rachis fragility on other chromosomes. The genetic basis for the spelt syndrome and the apparent presence of the Q allele in Iranian spelt are discussed.
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  • 9
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    Theoretical and applied genetics 100 (2000), S. 934-941 
    ISSN: 1432-2242
    Keywords: Key words Zea mays L ; Maize ; Sugarcane mosaic virus ; SCMV ; Scm1 ; Scm2 ; AFLP ; RFLP ; SSR ; Pedigree relationship
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Sugarcane mosaic virus (SCMV) causes serious losses of grain and forage yield of maize (Zea mays L.) in Europe. Two dominant genes, Scm1 and Scm2, have been identified to confer resistance to SCMV. Scm1 is located on the short arm of chromosome 6 and Scm2 near the centromere region of chromosome 3. In the present study,resistant, partially resistant, and susceptible maize inbred lines, together with their ancestral lines, were evaluated with molecular markers to trace back the origin of Scm1 and Scm2. The banding patterns indicated that the Scm1 region, originally identified in resistant European line FAP1360A, was derived from its ancestral line FAP954A. The other two resistant European lines, D21 and D32, most likely carry the same Scm1 region, which originated from their common ancestral line A632. This Scm1 region was also present in three partially resistant lines, D09, FAP1396A and FAP693A, but not in the resistant U.S. inbred Pa405. Apart from FAP954A and A632, none of the remaining ancestral lines and none of the susceptible lines harbored the Scm1 region. The Scm2 region present in FAP1360A was obviously transmitted from its ancestral line Co125. However, the presence of the respective Scm2 region was not confirmed in the other three resistant lines (D21, D32 and Pa405), the remaining ancestral lines, and all partially resistant lines by using closely linked markers.
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  • 10
    ISSN: 1432-2242
    Keywords: Key words Map-based cloning ; RFLP ; YAC
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  An ethylene-inducing xylanase (EIX) from Tricohoderma viride is a potent elicitor of ethylene biosynthesis, localized cell death and other defense responses in specific cultivars of tobacco (Nicotiana tabacum) and tomato (Lycopersicon esculentum). Wild species of tomato, such as Lycopersicon cheesmanii and Lycopersicon pennellii, do not respond to EIX treatment. The F1 progeny of a L. esculentum×L. cheesmanii and a L. esculentum×L. pennellii cross responded to EIX treatment with an increase in ethylene biosynthesis and the induction of localized cell death. The F2 progeny of the above mentioned crosses segregated 3:1 (responding:non-responding). We mapped the EIX-responding locus (Eix) to the short arm of chromosome 7 using a population of introgression lines (ILs), containing small RFLP-defined chromosome segments of L. pennellii introgressed into L. esculentum. RFLP analysis of 990 F2 plants that segregated for the introgressed segment mapped the Eix locus 0.1 cM and 0.9 cM from the flanking markers TG61 and TG131, respectively. Using the marker TG61 we isolated a yeast artificial chromosome (YAC) clone that carries 300-kb DNA segments derived from the Eix region. By mapping the ends of this YAC clone we show that it spans the Eix locus. Thus, positional cloning of the Eix locus appears feasible.
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  • 11
    ISSN: 1432-2242
    Keywords: Keywords Resistance ; Tomato powdery mildew ; Tomato ; Mapping ; Oidium lycopersicum ; RFLP ; Sequence characterised amplified region (SCAR)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Lycopersicon hirsutum G1.1560 is a wild accession of tomato that shows resistance to Oidium lycopersicum, a frequently occurring tomato powdery mildew. This resistance is largely controlled by an incompletely dominant gene Ol-1 near the Aps-1 locus in the vicinity of the resistance genes Mi and Cf-2/Cf-5. Using a new F2 population (n=150) segregating for resistance, we mapped the Ol-1 gene more accurately to a location between the RFLP markers TG153 and TG164. Furthermore, in saturating the Ol-1 region with more molecular markers using bulked segregant analysis, we were able to identify five RAPDs associated with the resistance. These RAPDs were then sequenced and converted into SCAR markers: SCAB01 and SCAF10 were L. hirsutum-specific; SCAE16, SCAG11 and SCAK16 were L. esculentum-specific. By linkage analysis a dense integrated map comprising RFLP and SCAR markers near Ol-1 was obtained. This will facilitate a map-based cloning approach for Ol-1 and marker-assisted selection for powdery mildew resistance in tomato breeding.
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  • 12
    ISSN: 1432-2242
    Keywords: Key words Genomic map ; Acacia mangium ; Recombination rate ; Microsatellites ; RFLP ; Legumes ; Polyads
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  An integrated genetic linkage map, comprised of 219 RFLP and 33 microsatellite loci in 13 linkage groups, was constructed using two outbred pedigrees of Acacia mangium Willd. The linkage groups ranged in size from 23 to 103 cM and the total map length was 966 cM. Individual maps were made for each pedigree and the ordering of loci was consistent with the integrated map. The use of two independent pedigrees allowed a comparison of recombination rates between linked loci in male and female meioses as well as between parents. Differences were confined to specific regions and were not uniform across the male and female genomes or between genotypes. The heterogeneity in recombination frequencies did not result in major differences in the ordering of loci between pedigrees; hence, the integrated map provides a sound basis for QTL detection, leading to marker-assisted selection in A. mangium. It also provides a reference map for comparative genome analysis in acacias. The co-dominant markers used for mapping provide a useful resource in population studies and for quality control in acacia breeding programs. Detection of a relatively high proportion of selfs in pods derived from flowers which were not emasculated (30%), compared with emasculated flowers (0.01%), indicates that emasculation is desirable for efficient delivery of control-crossed seed in acacia breeding programs.
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  • 13
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    Theoretical and applied genetics 101 (2000), S. 613-624 
    ISSN: 1432-2242
    Keywords: Keywords Melon (Cucumis melo L.) ; Fruit ripening ; Ethylene production rate ; Postharvest fruit decay ; Shelf-life ; ACC oxidase ; ACC synthase ; SSR ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Sixty three cultigens from eight market types of the melon (Cucumis melo L. subsp. melo) groups Cantaloupensis and Inodorus were evaluated for ethylene production rate, shelf-life (postharvest decay), and RFLP polymorphisms. The ethylene production rates of melon fruits at maturity and (after) postharvest decay were measured on individual genotypes. The ethylene production rates of individual genotypes ranged from undetectable to 103 nl/g per h. The mean ethylene production rates of the eight market types, ranked from highest to lowest, were Eastern U.S. type, Charentais, Western U.S. type, Long Shelf-Life cantaloupes (LSL), Galia, Ananas, Honeydew, and Casaba. Ethylene production and postharvest decay rating were positively significantly correlated (r 2=0.87, P=0.05). Orange-fleshed melon fruits produced significantly (P=0.05) more ethylene than did green- or white-fleshed types. Melon fruits with a netted rind had significantly (P=0.05 for orange-flesh fruits and 0.01 for green- or white-flesh fruits) higher ethylene production than did smooth-type fruits. Using probes made from cDNAs encoding ACC oxidase (MEL1) or ACC synthase (MEACS1) genes, RFLPs were detected melon cultigens of the eight marker types showing varying ethylene production rates and different flesh colors. Low ethylene production and green- and white-flesh color were associated (r 2=0.91; P=0.05) with the presence of a putative RFLP-MEL1 allele A 0 (15-kb), whereas high ethylene production and orange-flesh color were associated with allele B 0 (8.5-kb) in the homozygous condition, after probing MEL1 with EcoRV-digested genomic DNA. Also, after probing MEACS1 with NdeI-digested genomic DNA, RFLP polymorphism revealed five fragments denoted as A, B, C, D and E, with molecular sizes of 5.2-, 4.2-, 3.8-, 3.0- and 1.0-kb, respectively. A two-fragment pattern, AB, and a three-fragment pattern, ACE, the two predominant RFLP patterns, were also associated with low and high ethylene production, respectively. The ACE fragment pattern was also associated with orange-flesh melons. Scoring of both probes allowed for the unique classification of most melon market types consistent with ethylene production and the postharvest decay phenotypes. Therefore, these RFLPs might have utility in marker-assisted selection for the development of melons with enhanced postharvest keeping ability.
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  • 14
    ISSN: 1432-2242
    Keywords: Keywords Oryza sativa L. ; Gene mapping ; Magna porthe grisea ; Pyricularia grisea ; Disease resistance ; Complete resistance ; Resistance genes ; Pyramiding ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A framework linkage map was developed using 284 F10 recombinant inbred lines (RILs) from a ’Lemont’×’Teqing’ rice cultivar cross. Evaluation of a subset of 245 of these RILs with five races of the rice blast pathogen permitted RFLP mapping of three major resistance genes from Teqing and one major gene from Lemont. All mapped genes were found to confer resistance to at least two blast races, but none conferred resistance to all five races evaluated. RFLP mapping showed that the three resistance genes from Teqing, designated Pi-tq5, Pi-tq1 and Pi-tq6, were present on chromosomes 2, 6 and 12, respectively. The resistance gene from Lemont, Pi-lm2, was located on chromosome 11. Pi-tq1 is considered a new gene, based on its reaction to these five races and its unique map location, while the other three genes may be allelic with previously reported genes. Lines with different gene combinations were evaluated for disease reaction in field plots. Some gene combinations showed both direct effects and non-linear interaction. The fact that some of the lines without any of the four tagged genes exhibited useful levels of resistance in the field plots suggests the presence of additional genes or QTLs affecting the blast reaction segregating in this population.
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  • 15
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    Theoretical and applied genetics 100 (2000), S. 519-527 
    ISSN: 1432-2242
    Keywords: Key words Wheat ; Triticum aestivum ; Physical mapping ; Deletion lines ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Extended physical maps of chromosomes 6A, 6B and 6D of common wheat (Triticum aestivum L. em Thell., 2n=6x=42, AABBDD) were constructed with 107 DNA clones and 45 homoeologous group-6 deletion lines. Two-hundred and ten RFLP loci were mapped, including three orthologous loci with each of 34 clones, two orthologous loci with each of 31 clones, one locus with 40 clones, two paralogous loci with one clone, and four loci, including three orthologs and one paralog, with one clone. Fifty five, 74 and 81 loci were mapped in 6A, 6B and 6D, respectively. The linear orders of the mapped orthologous loci in 6A, 6B and 6D appear to be identical and 65 loci were placed on a group-6 consensus physical map. Comparison of the consensus physical map with eight linkage maps of homoeologous group-6 chromosomes from six Triticeaespecies disclosed that the linear orders of the loci on the maps are largely, if not entirely, conserved. The relative distributions of loci on the physical and linkage maps differ markedly, however. On most of the linkage maps, the loci are either distributed relatively evenly or clustered around the centromere. In contrast, approximately 90% of the loci on the three physical maps are located either in the distal one-half or the distal two-thirds of the six chromosome arms and most of the loci are clustered in two or three segments in each chromosome.
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  • 16
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    Theoretical and applied genetics 101 (2000), S. 860-864 
    ISSN: 1432-2242
    Keywords: Key words Melon ; AFLP ; RFLP ; RAPD ; Genetic similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Three different types of molecular markers, RAPD, AFLP and RFLP were used to measure genetic diversity among six genotypes of Cucumis melo L. Each line represented a different melon genotype: Piel de Sapo, Ogen, PI161375, PI414723, Agrestis and C105. A number of polymorphic RAPD, AFLP and RFLP bands were scored on all materials and the genetic similarity measured. Clustering analysis performed with the three types of markers separated the genotypes into two main groups: (1) the sweet type, cultivated melons and (2) the exotic type, not cultivated melons. While the data obtained suggest that all three types of markers are equally informative, AFLPs showed the highest efficiency in detecting polymorphism.
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  • 17
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    Theoretical and applied genetics 101 (2000), S. 948-955 
    ISSN: 1432-2242
    Keywords: Key words Theobroma cacao L. ; AFLP ; Microsatellites ; RFLP ; High-density genetic map
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The first linkage map established by Lanaud et al. (1995) was used as a starting point to produce a high-density molecular linkage map. A mapping population of 181 progenies resulting from a cross between two heterozygous genotypes, a Forastero and a Trinitario (hybrid between Forastero and Criollo), was used for the linkage analysis. A new DNA isolation protocol was established, which allows enough good quality DNA to construct a genetic map with PCR-based markers. The map comprises 424 markers with an average spacing between markers of 2.1 cM. The marker types used were five isozymes, six loci from known function genes, 65 genomic RFLPs, 104 cDNA RFLPs, three telomeric probes, 30 RAPDs, 191 AFLPs and 20 microsatellites. The use of new marker types, AFLP and microsatellites, did not disturb the original order of the RFLP loci used on the previous map. The genetic markers were distributed over ten linkage groups and cover 885.4 cM. The maximum distance observed between adjacent markers was 16.2 cM, and 9.4% of all loci showed skewed segregation.
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  • 18
    ISSN: 1432-2242
    Keywords: Key words Sugarcane ; Rust resistance gene ; Comparative mapping ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A major rust resistance gene has been identified in a self-progeny of the sugarcane cultivar R570. Until now, this gene was known to be linked to a marker revealed by the sugarcane probe CDSR29 but unassigned to any linkage group of the current genetic map. We used synteny relationships between sugarcane and three other grasses in an attempt to saturate the region around this rust resistance gene. Comparison of sugarcane, sorghum, maize and rice genetic maps led to the identification of homoeologous chromosome segments at the extremity of sorghum linkage group D, rice linkage group 2, maize linkage group 4 and in the centromeric region of maize linkage group 5. One hundred and eighty-four heterologous probes were selected and tested for cross-hybridization with sugarcane DNA; 106 produced a good hybridization signal and were hybridized on 88 individuals of the R570 selfed progeny. Two hundred and seventeen single-dose markers were added to the R570 genetic map, of which 66% mapped to linkage group VII, together with the rust resistance gene. This gene has now been mapped to the end of a co-segregating group consisting of 19 RFLP markers. None of the mapped loci were located closer to the gene than CDSR29. The gene thus appears to reside at the edge of a ’’synteny cluster’’ used to describe the different grass genomes.
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  • 19
    ISSN: 1432-2242
    Keywords: Key words Genetic relationship ; Maize ; Pedigree ; RFLP ; SSR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The genetic relationship between inbreds i and j can be estimated from pedigree or from molecular marker data. The objectives of this study were to: (1) determine whether pedigree, restriction fragment length polymorphism (RFLP), and simple sequence repeat (SSR) data give similar estimates of parental contribution and coefficient of coancestry (f ij ) among a set of maize (Zea mays L.) inbreds, and (2) compare the usefulness of RFLP and SSR markers for estimating genetic relationship. We studied 13 maize inbreds with known pedigrees. The inbreds were genotyped using 124 RFLP and 195 SSR markers. For each type of marker, parental contributions were estimated from marker similarity among an inbred and both of its parents, and were subsequently used to estimate f ij . Estimates of parental contribution differed significantly (α〈0.05) between pedigree data and either type of marker, but not between the marker systems. The RFLP estimates of parental contribution failed to sum to 1.0, reflecting a higher frequency of non-parental bands with RFLP than with SSR markers. The f ij estimated from pedigree, RFLP, and SSR data were highly correlated (r=0.87–0.97), although significant differences were found among the three sets of f ij estimates. We concluded that pedigree and marker data often lead to different estimates of parental contribution and f ij , and that SSR markers are superior to RFLP markers for estimating genetic relationship. A relevant question is whether or not the inbreds previously genotyped with an older marker system (e.g., RFLP) need to be re-analyzed with a newer marker system (e.g., SSR) for the purpose of estimating genetic relationship. Such re-analysis seems unnecessary if data for the same type of marker are available for a given inbred and both of its parents.
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  • 20
    ISSN: 1432-2242
    Keywords: Key words Karnal bunt ; Repetitive elements ; Genome diversity ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Neovossia indica (Tilletia indica), causing Karnal bunt of wheat, affects major wheat growing regions all over the world. Karnal bunt ranks as one of the major diseases of wheat causing quality losses and monetary losses due to international quarantine regulations. The present work is the first report of a genetic diversity analysis of Indian isolates of N. indica. A library of N. indica isolate Ni7 was constructed in a λZAPII system, and three repetitive elements were identified for molecular analysis. These repetitive elements generated complex hybridization profiles producing fingerprint patterns of all seven isolates. Copy-number estimation of these three elements, pNiR9, pNiR12 and pNiR16, indicated the presence of 32, 61 and 64 copies, respectively. Cluster analysis based on hybridization patterns grouped together moderately virulent isolates Ni1, Ni7 and Ni8, thus suggesting a positive correlation between virulence typing and cluster analysis based on molecular data. Variability analysis of N. indica isolates will aid in checking new resistant sources in host germplasm.
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  • 21
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    Molecular genetics and genomics 263 (2000), S. 925-933 
    ISSN: 1617-4623
    Keywords: Key words S-like RNase ; Phosphate starvation ; Senescence ; RFLP ; Almond
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cDNA for an S-like RNase (RNase PD2) has been isolated from a pistil cDNA library of Prunus dulcis cv. Ferragnés. The cDNA encodes an acidic protein of 226 amino acid residues with a molecular weight of 25 kDa. A potential N-glycosylation site is present at the N-terminus in RNase PD2. A signal peptide of 23 amino acid residues and a transmembrane domain are predicted. The two active-site histidines present in enzymes of the T2/S RNase superfamily were detected in RNase PD2. Its amino acid sequence shows 71.2% similarity to RNS1 of Arabidopsis and RNase T2 of chickpea, respectively. Northern blotting and RT-PCR analyses indicate that PD2 is expressed predominantly in petals, pistils of open flowers and leaves of the almond tree. Analyses of shoots cultured in vitro suggested that the expression of RNase PD2 is associated with phosphate starvation. Southern analysis detected two sequences related to RNase PD2 in the P. dulcis genome. RFLP analysis showed that S-like RNase genes are polymorphic in different almond cultivars. The PD2 gene sequence was amplified by PCR and two introns were shown to interrupt the coding region. Based on sequence analysis, we have defined three classes of S-like RNase genes, with the PD2 RNase gene representing a distinct class. The significance of the structural divergence of S-like RNase genes is further discussed.
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  • 22
    ISSN: 1572-9788
    Keywords: mapping ; morphology ; QTL ; RFLP ; spike density ; Triticeae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Quantitative trait loci (QTLs) for three traits related to ear morphology (spike length, number of spikelets, and compactness as the ratio between number of spikelets and spike length) in wheat (Triticum aestivum L.) were mapped in a doubled-haploid (DH) population derived from the cross between the cultivars Courtot and Chinese Spring. A molecular marker linkage map of this cross that had previously been constructed based on 187 DH lines and 380 markers was used for QTL mapping. The genome was well covered (85%) except chromosomes 1D and 4D and a set of anchor loci regularly spaced (one marker each 15.5 cM) were chosen for marker regression analysis. The presence of a QTL was declared at a significance threshold α = 0.001. The population was grown in one location under field conditions during three years (1994, 1995 and 1998). For each trait, 4 to 6 QTLs were identified with individual effects ranging between 6.9% and 21.8% of total phenotypic variation. Several QTLs were detected that affected more than one trait. Of the QTLs 50% were detected in more than one year and two of them (number of spikelets on chromosome 2B, and compactness on chromosome 2D) emerged from the data from the three years. Only one QTL co-segregated with the gene Q known to be involved in ear morphology, namely the speltoid phenotype. However, this chromosome region explained only a minor part of the variation (7.5–11%). Other regions had a stronger effect, especially two previously unidentified regions located on chromosomes 1A and 2B. The region on the long arm of chromosome 1A was close to the locus XksuG34-1A and explained 12% of variation in spike length and 10% for compactness. On chromosome 2B, the QTL was detected for the three traits near the locus Xfbb121-2B. This QTL explained 9% to 22% of variation for the traits and was located in the same region as the gene involved in photoperiod response (Ppd2). Other regions were located at homoeologous positions on chromosomes 2A and 2D.
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  • 23
    ISSN: 1572-9788
    Keywords: late blight ; durable resistance ; RFLP ; AFLP ; SSR ; CAPS ; QTL mapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Six F1 populations produced from crosses between two Solanum microdontum genotypes and three S. tuberosum genotypes have been assessed for resistance to Phytophthora infestans (late blight; LB) in the field and proved to segregate for P. infestans resistance. The six populations were subjected to genetic mapping using AFLP markers in combination with a core map consisting of RFLPs and a few PCR-based markers. The two S. microdontum parents MCD167 and MCD178 harbour different alleles contributing to resistance. In the MCD167 set of populations a major QTL contributing to resistance was located on chromosome 4. This locus was not detected in the MCD178 set of populations. In the latter set of populations, a major QTL for resistance was detected on chromosome 10. This locus for resistance was not detected in the MCD167 set of populations. A third QTL contributing strongly to resistance was detected on chromosome 5. However, this locus was not consistently detected in all populations. For the loci on chromosome 5 and 10, segregation for resistance alleles from the susceptible parents was also observed. The results provide a starting point for future combinations of genes, to predict the value of each combination and finally to obtain potato germplasm carrying high levels of durable resistance to LB.
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  • 24
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    Molecular breeding 6 (2000), S. 105-111 
    ISSN: 1572-9788
    Keywords: carbohydrates ; genetic mapping ; oil ; protein ; QTL ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Sucrose is a primary constituent of soybean (Glycine max) seed; however, little information concerning the inheritance of seed sucrose in soybean is available. The objective of this research was to use molecular markers to identify genomic regions significantly associated with quantitative trait loci (QTL) controlling sucrose content in a segregating F2 population. DNA samples from 149 F2 individuals were analyzed with 178 polymorphic genetic markers, including RFLPs, SSRs, and RAPDs. Sucrose content was measured on seed harvested from each of 149 F2:3 lines from replicated field experiments in 1993 and 1995. Seventeen marker loci, mapping to seven different genomic regions, were significantly associated with sucrose variation at P〈0.01. Individually, these markers explained from 6.1% to 12.4% of the total phenotypic variation for sucrose content in this population. In a combined analysis these genomic regions; explained 53% of total variation for sucrose content. No significant evidence of epistasis among QTLs was observed. Comparison of our QTL mapping results for sucrose content and those previously reported for protein and oil content (the other major seed constituents in soybean), suggests that seed quality traits are inherited as clusters of linked loci or that `major' QTLs with pleiotropic effects may control all three traits. Of the seven genomic regions having significant effects on sucrose content, three were associated with significant variation for protein content and three were significantly associated with oil content.
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  • 25
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    European journal of plant pathology 106 (2000), S. 179-186 
    ISSN: 1573-8469
    Keywords: geminivirus ; RFLP ; PCR ; PAGE ; differentiation ; dot-blot
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Tomato yellow leaf curl disease is spreading in southern Europe, where it has quickly become a serious problem. In recent years, several virus isolates have been characterised. Although with some genetic variability, all isolates found in Europe belong to one of two species Tomato yellow leaf curl-Sardinia (TYLCV-Sar) or Tomato yellow leaf curl-Israel (TYLCV-Is). Several methods were tested to identify and type TYLCV isolates from field samples: (1) RFLP of a DNA fragment amplified from the coat protein gene; (2) PAGE of a fragment amplified from the C2 gene; (3) dot-blot hybridisation. All methods enabled the detection of the TYLCVs and provided good indications for attributing them to one species or the other. However, for typing purposes, the RFLP method was the most reliable, due to the easily recognisable pattern produced by the two virus species present in Europe. Dot-blot hybridisation is less expensive for identifying TYLCVs in large numbers of samples, particularly when a mixture of two probes is used. PAGE of the C2 fragment is the fastest of the methods tested.
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  • 26
    ISSN: 1573-5060
    Keywords: adaptedness ; morphological and genetic differentiation ; Oryza sativa L. ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Indica and Japonica differentiation under the species of Oryza sativa L. has been documented using morphological characters, isozyme and DNA markers. We illustrate marker assisted analysis of genetic differentiation with a sample of RFLP and isozyme data from 111 accessions of rice lines and compare it to morphological differentiation based on Cheng and Wang' morphological character index. The results lead to three main conclusions: (1) Among the 92 polymorphic cloned probes deliberately selected, 41 were highly associated with Indica-Japonica differentiation, suggesting such differentiation was an accumulative process of gene change at multiple loci; (2) There exist two main types of relationships between morphological and genetic differentiation. For well differentiated Indica and Japonica (as the case in the control subset), morphology and genomic constitutions are synchronously specialized. For incompletely differentiated rice lines (as the case in the subset of DH lines), morphological differentiation and genetic differentiation are asynchronous. (3)Synthetic or incompletely differentiated rice lines with different genomic constitutions are often adapted to specific environments. These results indicate that marker alleles provide applied breeders with effective ways to identify, track, and incorporate regions of chromosomes governing adaptedness to specific target environments into improved cultivars.
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  • 27
    ISSN: 1573-5060
    Keywords: agronomic characters ; geneticmapping ; quantitative trait loci ; QTL ; RFLP ; Secale cereale L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Using the marker information of 275 F2 plants quantitative traits determining morphological and yield characters were studied analyzing F3progenies grown in four different experiments at three sites. The map constructed contains 113 markers including the major dwarfing gene Ddw1 with an average distance of about 10 cM between adjacent markers. Of the 21 QTLs detected ten were found to map on chromosome 5RL in the region of Ddw1. Beside the expected effects on plant height and peduncle length that are most probably due to the presence of the major dwarfing gene, additional effects on yield characters and flowering time were discovered in that region which may be caused by pleiotropic effects of Ddw1. An additional supposed gene cluster consisting of four QTLs controlling flowering time and yield components was discovered in the centromere region of chromosome 2R. Further loci are distributed on chromosomes 1R (1), 4R (1) 6R (3) and 7R (1). The map positions of the quantitative trait loci detected in rye are discussed in relation to major genes or QTLs determining agronomically important traits in other cereals.
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  • 28
    ISSN: 1573-5060
    Keywords: gene diversity ; population genetics ; RFLP ; Theobroma cacao L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The genetic structure of 175 genotypes of Theobroma cacao L. was investigated using 27 RFLP/cDNA loci. The number of alleles per locus was never higher than four and a high genetic diversity was found. Criollo genotypes appeared differentiated from Forastero genotypes. A deficiency of heterozygotes was found in all populations and some alleles were fixed in some populations. Within population gene diversity was high. When four morphological groups were considered, Upper Amazon Forastero was the most polymorphic and diverse population. Almost all the alleles of the whole species could be found within this group. Observed heterozygosity was the highest within Criollo and Trinitario populations but a certain proportion of homozygous genotypes was present in all groups.
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  • 29
    ISSN: 1573-5109
    Keywords: Chinese landraces ; chloroplast ; mitochondria ; phylogeny ; RFLP ; soybean
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Restriction fragment-length polymorphism (RFLP) of chloroplast and mitochondrial DNA of many soybean landraces were analyzed to characterize their cytoplasmic genome and to consider the diversity and phylogeny of soybean in China. Three chloroplast and five mitochondrial types were distinguished, and seven cytoplasmic genome types were observed in different combinations in specimens collected from China. The cytoplasmic genome diversity was higher at the Yangtze River Valley. The main group of cytoplasmic genomes was composed of five types related phylogenetically and occurred in the southern region of China. Two unique types were very different in cytoplasmic genome constitution from each other and from the main group. They were considered to be derived from wild plants with the same cytoplasmic genome and to occur in two remote regions, the northern region and the Yangtze River Valley of China, respectively. Therefore, when considered with regard to the cytoplasmic genome of soybean landraces detected in China, seven genome types are distinguished, some types may be assumed to have arisen in wild soybean before domestication; and the Yangtze River Valley is the center of cytoplasmic diversity of the soybean.
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  • 30
    ISSN: 1572-9699
    Keywords: flor yeasts ; identification ; ITS ; RFLP ; ribosomal DNA ; Saccharomyces
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The PCR amplification and subsequent restriction analysis of the region spanning the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene was applied to the identification of yeasts belonging to the genus Saccharomyces. This methodology has previously been used for the identification of some species of this genus, but in the present work, this application was extended to the identification of new accepted Saccharomyces species (S. kunashirensis, S. martiniae, S. rosinii, S. spencerorum, and S. transvaalensis), as well as to the differentiation of an interesting group of Saccharomyces cerevisiae strains, known as flor yeasts, which are responsible for ageing sherry wine. Among the species of the Saccharomyces sensu lato complex, the high diversity observed, either in the length of the amplified region (ranged between 700 and 875 bp) or in their restriction patterns allows the unequivocal identification of these species. With respect to the four sibling species of the Saccharomyces sensu stricto complex, only two of them, S. bayanus and S. pastorianus, cannot be differentiated according to their restriction patterns, which is in accordance with the hybrid origin (S. bayanus × S. cerevisiae) of S. pastorianus. The flor S. cerevisiae strains exhibited restriction patterns different from those typical of the species S. cerevisiae. These differences can easily be used to differentiate this interesting group of strains. We demonstrate that the specific patterns exhibited by flor yeasts are due to the presence of a 24-bp deletion located in the ITS1 region and that this could have originated as a consequence of a slipped-strand mispairing during replication or be due to an unequal crossing-over. A subsequent restriction analysis of this region from more than 150 flor strains indicated that this deletion is fixed in flor yeast populations.
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  • 31
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    Experimental and applied acarology 24 (2000), S. 751-774 
    ISSN: 1572-9702
    Keywords: AFLP ; allozymes ; DALP ; DNA sequencing ; genetic structure ; microsatellites ; mitochondrial DNA ; mites ; molecular systematics ; PCR ; phylogeny ; RAPD ; RFLP ; ribosomal DNA ; ticks
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The application of molecular markers to the study of ticks and mites has recently yielded new insights into their population structures and taxonomic relationships. Ticks have been studied at individual, population and species level. Mites are a more diverse group and those that have been studied to the same degree as the ticks include the Tetranychidae (spider mites), Phytoseiidae (predatory mites) and the Eriophyidae. Population variation has also been studied in the important bee parasitic mite Varroa jacobsoni Oudemans. The methods used to study these organisms have much in common. At the individual level these range from general approaches, such as AFLP, RAPD or DALP, to highly specific microsatellite analysis. Although these markers also work at the population and species level, additional analysis of specific nuclear or mitochondrial genes has been conducted either by RFLP or sequencing. Molecular applications have had particular success in facilitating the identification of taxonomically difficult species, understanding population structures and elucidating phylogenetic relationships.
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  • 32
    ISSN: 1573-5109
    Keywords: Agrostis stoloniferaL. ; cultivar identification ; RFLP ; turfgrass
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The potential use of RFLP molecular markers for the identification of four creeping bentgrass (Agrostis stolonifera L.) cultivars and one variety of A. tenuis Sibth. used as control, was investigated. Seven probes out of the total 44 screened were able to differentiate all five cultivars at once. On the basis of their genetic similarity the varieties bred at the Pennsylvania State University were grouped closely together, whereas the variety Prominent and the A. tenuis control were more distantly related.
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  • 33
    ISSN: 1573-5060
    Keywords: Comparative genetics ; Hordeum bulbosum ; Hordeum vulgare ; mapping ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A restriction fragment length polymorphism (RFLP) based linkage map of a cross between two diploid Hordeum bulbosum (2n = 2x = 14) clones, PB1 and PB11, was constructed from 46 recombinant progeny clones. Since both parents are heterozygous, separate and combined parental maps were constructed. All of the RFLP markers screened had previously been mapped in barley (H. vulgare L.) so that comparative maps could be produced. The PB1 linkage map consists of 20 RFLP marker loci assigned to four linkage groups covering 94.3 cM. The PB11 linkage map consists of 27 RFLP marker loci assigned to six linkage groups covering 149.1 cM. Thirteen markers polymorphic in both parents were used as ‘anchors’ to create a combined linkage map consisting of 38 loci assigned to six linkage groups and covering a genetic distance of 198 cM. Marker order was highly conserved in a comparison with the linkage map of H. vulgare (Laurie etal., 1995). However, in contrast, the genetic distances for the same markers were very different being 649 cM and 198 cM respectively, a genetic distance ratio of 1: 3.3. Thus although the map was short, it can be presumed to cover half the genome of H. bulbosum. This study provides further confirmation of the close relationship between the two species and gives a basis for the development of marker mediated introgression through interspecific hybridisation between the two species.
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  • 34
    ISSN: 1573-5060
    Keywords: genetic diversity ; germplasm ; RFLP ; Triticum aestivum ; wheat breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A set of 292 accessions of common wheat (Triticum aestivum L.) representing 21 germplasm pools based on geographical or breeding program origins was assayed for RFLP diversity. Thirty cDNA and genomic DNA probes and the HindIII restriction enzyme were employed for RFLP analysis. About 61% of all 233 scored bands were present in 75% or more of the accessions. All but one of the 30 probes revealed polymorphism, and the average number of distinct patterns per probe over all accessions was 9.5.Polymorphic Information Content (PIC) values within a pool varied from 0 to 0.9 and depended on the identities of both the germplasm pool and the probe. Rare banding patterns with a relative frequency of ≤0.2 within a pool were detected. These rare patterns were more likely to occur in pools exhibiting high levels of heterogeneity. The highest level of polymorphism was observed in the Turkish landraces from Southwest Asia. The Eastern U.S. soft red winter wheat germplasm pool was more genetically diverse than the other advanced germplasm pools, and nearly as diverse as the Turkish landrace pool. RFLP-based genetic relationships between germplasm pools generally tracked expectations based on common geographical origin, breeding history and/or shared parentages. The Chinese wheat landraces from Sichuan, Tibet, and Yunnan provinces were distinct from other pools. Similarity matrices for among-pool genetic distance estimates based on either band frequencies or banding pattern frequencies showed good correlation with matrices derived from Nei and Li's mean genetic similarity estimates (r=−0.82** and r=−0.73**, respectively.
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  • 35
    ISSN: 1573-6857
    Keywords: genetic diversity ; Oryza ; retrotransposons ; RFLP ; wild rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To better understand the genetic diversity of the wild relatives of rice (Oryza sativa L.) in the O. officinalis species complex repetitive DNA markers were obtained from the diploid species of this complex. One cloned sequence from O. eichingeri gave intense hybridization signals with all species of the O. officinalis complex. This 242 bp clone, named pOe.49, has a copy number from 0.9 to 4.0 × 104 in diploid species of this complex. Analysis of the primary structure and database searches revealed homology of pOe.49 to a number of sequences representing part of the integrase coding domain of retroviruses and gypsy-like retrotransposons. Sequencing of specific PCR products confirmed that pOe.49 is part of a gypsy-like retrotransposon. RFLP analysis was used to study the genomic organisation of pOe.49 among 30 accessions of the O. officinalis complex using 10 restriction enzymes. Diversity analysis based on 120 polymorphic fragments obtained from the RFLP assay grouped the O. officinalis complex accessions by genome, species and eco-geographic groups. The results suggest that, with further characterization, this retrotransposon-like DNA sequence may be useful for phylogenetic analysis of species in the O. officinalis complex.
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  • 36
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    Journal of human genetics 45 (2000), S. 119-126 
    ISSN: 1435-232X
    Keywords: Key words Extra-embryonic tissue ; Methylation-sensitive endonuclease ; Phosphoglycerate kinase ; RFLP ; Skewing of X-chromosome inactivation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract To investigate X-chromosome inactivation (XCI) in human trophoblasts during early pregnancy, tropho-blast genomic DNA was extracted and analyzed for a Bst XI restriction endonuclease site polymorphism in the X-linked phosphoglycerate kinase gene, after digestion with methylation-sensitive Hpa II (control samples were digested instead with Afa I). Six villous trophoblast DNA samples were informative for the polymorphism (ie, heterozygous) and were derived from women homozygous for the polymorphism. These samples were then evaluated for XCI. In five of the six samples with Hpa II predigestion, the sizes of the two heterozygous band peaks differed; maternal X-chromosome (XM)-derived alleles showed smaller peak sizes than paternal X-chromosome (XP)-derived alleles, but the differences varied in degree. In samples obtained by microdissection from formalin-fixed, paraffin-embedded tissues (30 samples from different anchoring villi, and 38 samples from different branch villi), monoclonal band patterns of XP-derived alleles were observed more frequently than those of XM-derived alleles, but almost half of the samples showed polyclonal pat-terns. Our results suggest that a skewing of XCI exists in the human trophoblast; however, the degree of non-randomness due to predominant XP inactivation appears to be restricted. It is probable that transcription of the X inactivation center (XIC) begins earlier in mice than in humans.
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  • 37
    ISSN: 1432-2145
    Keywords: Gametophytic self incompatibilityself-compatibility ; Lycopersicon peruvianum Lycopersicon hirsutum ; S-associated proteins ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Self-compatibility was investigated separately in two species of tomato, Lycopersicon peruvianum and L. hirsutum. The codominant expression of self-compatibility (SC)/self incompatibility (SI) was established using intraspecific hybrids of SC and SI hybrids. In SC L. peruvianum, a major stylar protein of approximately 29 kDa cosegregates with self-compatibility in the progeny of SC/SI hybrids. The SC/SI hybrids are self-fertile, but only partially so, since the SI allele present in the hybrids is capable of eliminating certain genotypes in the resultant progeny. In L. hirsutum, the majority of hybrids between one accession of SI L. hirsutum f. hirsutum and one of SC L. hirsutum f. glabratum are self-fertile. Analysis of the progeny revealed that the SC and SI alleles are codominant in this species as well. A protein product for the SC allele is not obvious in style extracts of L. hirsutum f. glabratum. Segregating progeny from SC/SI hybrids of L. hirsutum were used to map the S locus against five RFLP markers on chromosome 1, and estimated map distances are given. In addition, evidence is presented that indicates that one of the DNA markers, CD15, is duplicated in L. hirsutum f. glabratum, and the duplication is not linked to the S locus.
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  • 38
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    Current genetics 26 (1994), S. 456-460 
    ISSN: 1432-0983
    Keywords: Parasitella parasitica ; Zygomycetes ; RAPD ; PCR ; RFLP ; Electrophoretic karyotype ; Molecular taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In addition to conventional methods for the identification of fungi, molecular techniques at the DNA level are increasingly being employed. In order to check the validity of such experimental approaches, we have analyzed the well-defined species Parasitella parasitica, which belongs to the family Mucoraceae (Mucorales, Zygometes). The seven strains of this species, which are available from international strain collections, were analyzed by several molecular methods: restriction fragment length polymorphism analysis (RFLP), the random primer-dependent polymerase chain reaction (RAPD-PCR), and electrophoretic karyotyping. Unexpectedly, these strains are highly diverse at the molecular level. By these techniques they can be divided consistently into two different groups. Nevertheless, all seven strains belong to a single species. They show no morphological differences and sexual spores (zygospores) were found in all possible combinations either within or between the two groups. Southern-blot analysis of genomic DNA of all P. parasitica strains with RAPD-PCR-derived labelled probes shows the existence of repetitive elements characteristic for only one group of P. parasitica. In addition, chromosome sizes, which were separated by rotating-field electrophoresis, were highly divergent, and ranged from 3 to 6.5 Mb in one group and between 2 and 4.5 Mb in the other. The RAPD-PCR patterns also discriminate both groups of P. parasitica. However, they are very similar if strains of a single group are compared. Therefore, we propose that the determination of fungal species by molecular techniques should be vetted at least by morphological and physiological parameters and, whenever possible, by mating experiments.
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  • 39
    ISSN: 1432-0983
    Keywords: Cytoplasmic male sterility ; Antisense RNA ; RFLP ; Cybrids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Asymmetric cell-fusion of the japonica cultivar ofOryza sativa (rice) with cytoplasmic-male-sterile (CMS) plants bearing cytoplasm derived from Chinsurah Boro II, resulted in two classes of cytoplasmic hybrids (cybrids), fertile and CMS. Southern-blot analysis of the mitochondrial DNA (mtDNA) indicates recombination events around a number of genes; however, the appearance of the CMS character is tightly correlated to reorganization around theatp6 gene, suggesting recombination downstream from theatp6 gene is involved in CMS. The nucleotide sequence downstream fromatp6 contains a pseudogene which was probably created by recombination of the mitochondrial genome. Sense and antisense transcripts of the downstream region ofatp6 were found in CMS-and restored CMS (fertile)-lines, but not in the normal (fertile) line. In the CMS line, several antisense transcripts of theatp6 gene were also found. However, in the restored line which contains a nuclear-encoded gene,Rf-1, the levels of these transcripts were lower than in the CMS line. These results suggest abnormal transcripts of theatp6 gene produced in the antisense direction may be involved in CMS, and that products of the nuclear-encoded restorer gene may reduce abnormal transcription in this region of the mitochondrial genome.
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  • 40
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    Plant molecular biology 26 (1994), S. 1065-1071 
    ISSN: 1573-5028
    Keywords: Brassica ; polyploid ; gene expression ; RT-PCR ; RFLP
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    Topics: Biology
    Notes: Abstract One of the essential issues regarding evolution of polyploid species is how duplicate genes are expressed. Most studies on gene expression in polyploids have been based on isozyme analyses; RNA analysis has not been widely used partially due to difficulties in distinguishing homologous transcripts which usually have the same length and similar or almost identical sequences. In this study, a method combining RT-PCR with RFLP was used to analyze transcripts of homologous genes in natural and synthetic Brassica amphidiploids. Sequences coding for several known genes were selected and used to synthesize gene-specific primers. Total RNAs were used as templates for RT-PCR to amplify homologous transcripts in three diploid parental species, three cultivated amphidiploid species and six synthetic amphidiploids. For each gene, initial PCR products amplified in all species had identical length; however, homologous transcripts in the diploid and amphidiploid species could be distinguished after digesting the PCR products with restriction enzymes. Preliminary results based on three genes indicated that both transcripts from the diploid parents were expressed in the synthetic and natural amphidiploids. This study represents the first application of RT-PCR and RFLP analysis to investigate expression of homologous genes in higher plants. The technique is a sensitive, simple and efficient method for distinguishing homologous transcripts in a mixed RNA population and can be applied to many types of studies on expression of homologous genes.
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  • 41
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    Theoretical and applied genetics 88 (1994), S. 273-278 
    ISSN: 1432-2242
    Keywords: RFLP ; Genetic linkage mapping ; Pinus taeda L.
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    Notes: Abstract A genetic linkage map for loblolly pine (Pinus taeda L.) was constructed using segregation data from a three-generation outbred pedigree consisting of four grandparents, two parents, and 95 F2 progeny. The map was based predominantly on restriction fragment length polymorphism (RFLP) loci detected by cDNA probes. Sixty-five cDNA and three genomic DNA probes revealed 90 RFLP loci. Six polymorphic isozyme loci were also scored. One-fourth (24%) of the cDNA probes detected more than 1 segregating locus, an indication that multigene families are common in pines. As many as six alleles were observed at a single segregating locus among grandparents and it was not unusual for the progeny to segregate for three or four alleles per locus. Multipoint linkage analysis placed 73 RFLP and 2 isozyme loci into 20 linkage groups; the remaining 17 RFLP and 4 isozyme loci were unlinked. The mapped RFLP probes provide a new set of codominant markers for genetic analyses in loblolly pine.
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  • 42
    ISSN: 1432-2242
    Keywords: Hevea brasiliensis ; RFLP ; Nuclear probes ; Isozyme ; Genetic diversity
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    Notes: Abstract Restriction fragment length polymorphism was assessed in wild and cultivated populations of Hevea brasiliensis using random probes from an Hevea nuclear library. One-hundred-and-sixty-four individuals were surveyed, and the results discussed in the light of previous work performed on isozyme variation. Both studies show that germplasm collections have led to an effective enrichment of the genetic resources available for Hevea breeding, and that cultivated clones have conserved a relatively high level of polymorphism, despite their narrow genetic base and their high level of inbreeding. An equivalent level of polymorphism is revealed by random nuclear probes and isozymes. However, the genetic structuring of the diversity appears more striking using RFLP markers. Wild accessions can be divided into three genetic groups according to their geographical origin. The present results are an essential guide to the incorporation of wild material in breeding schemes.
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  • 43
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    Theoretical and applied genetics 88 (1994), S. 383-394 
    ISSN: 1432-2242
    Keywords: Photosynthesis-related genes ; Copy numbers ; Chromosome assignments ; RFLP ; Origin of polyploid wheats
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    Topics: Biology
    Notes: Abstract Copy numbers of four photosynthesis-related genes, PhyA, Ppc, RbcS and Lhcb1 *1, in wheat genomes were estimated by slot-blot analysis, and these genes were assigned to the chromosome arms of common wheat by Southern hybridization of DNA from an aneuploid series of the cultivar Chinese Spring. The copy number of PhyA was estimated to be one locus per haploid genome, and this gene was assigned to chromosomes 4AL, 4BS and 4DS. The Ppc gene showed a low copy number of small multigenes, and was located on the short arm of homoeologous group 3 chromosomes and the long arm of chromosomes of homoeologous group 7. RbcS consisted of a multigene family, with approximately 100 copies in the common wheat genome, and was located on the short arm of group 2 chromosomes and the long arm of group 5 chromosomes. Lhcb1 *1 also consisted of a multigene family with about 50 copies in common wheat. Only a limited number of restriction fragments (approximately 15%) were used to determine the locations of members of this family on the long arm of group 1 chromosomes owing to the multiplicity of DNA bands. The variability of hybridized bands with the four genes was less in polyploids, but was more in the case of multigene families. RFLP analysis of polyploid wheats and their presumed ancestors was carried out with probes of the oat PhyA gene, the maize Ppc gene, the wheat RbcS gene and the wheat Lhcb1 *1 gene. The RFLP patterns of common wheat most closely resembled those of T. Dicoccum (Emmer wheat), T. urartu (A genome), Ae. speltoides (S genome) and Ae. squarrosa (D genome). Diversification of genes in the wheat complex appear to have occurred mainly at the diploid level. Based on RFLP patterns, B and S genomes were clustered into two major groups. The fragment numbers per genome were reduced in proportion to the increase of ploidy level for all four genes, suggesting that some mechanism(s) might operate to restrict, and so keep to a minimum, the gene numbers in the polyploid genomes. However, the RbcS genes, located on 2BS, were more conserved (double dosage), indicating that the above mechanism(s) does not operate equally on individual genes.
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  • 44
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    Theoretical and applied genetics 88 (1994), S. 472-478 
    ISSN: 1432-2242
    Keywords: RFLP ; PCR ; Chrysanthemum ; Genetic diversity ; Polyploidy
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    Topics: Biology
    Notes: Abstract In order to study genetic variability at the DNA level in chrysanthemum (Dendranthema grandiflora Tzvelev) PstI and HindIII genomic libraries were constructed. Probes from both libraries were tested for the presence of restriction fragment length polymorphisms (RFLPs). Of the probes from the PstI library 91% appeared to hybridize to low-copy genes, while only 35% of those from the HindIII library appeared to do so. The PstI probes were used in further analyses as 79% of them showed RFLPs, whereas the HindIII low-copy number probes gave only 14% polymorphic patterns. Because of the hexaploid character of chrysanthemum, complex patterns generally consisting of 6–12 fragments were visible on a Southern blot after hybridization. To simplify the genetic analysis, locus-specific polymerase chain reaction (PCR) primers were developed that gave simple polymorphic patterns in a number of cases. The RFLP probes and primers developed will be used in future marker-assisted selection in this polyploid crop.
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  • 45
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    Theoretical and applied genetics 89 (1994), S. 865-872 
    ISSN: 1432-2242
    Keywords: Comparative mapping ; RFLP ; Barley ; Triticum tauschii ; Genome evolution
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    Notes: Abstract Hordeum vulgare (barley) and Triticum tauschii are related, but sexually incompatible, species. This study was conducted to determine the extent of homology between the genomes of barley and T. tauschii using a common set of restriction fragment length polymorphism (RFLP) markers. Results showed that 〉95% of low-copy sequences are shared, but 42% of the conserved sequences showed copy-number differences. Sixty-three loci were mapped in T. tauschii using RFLP markers previously mapped in barley. A comparison of RFLP marker order showed that, in general, barley and T. tauschii have conserved linkage groups, with markers in the same linear orders. However, six of the seven linkage groups of T. tauschii contained markers which mapped to unrelated (i.e., non-homoeologous) barley chromosomes. Additionally, four of the T. tauschii linkage groups contained markers that were switched in order with respect to barley. All the chromosome segments differing between T. tauschii and barley contained markers that were detected by multi-copy probes. The results suggest that the observed differences between the T. tauschii and barley genomes were brought about by duplications or deletions of segments in one or both species. The implications of these findings for genetic mapping, breeding, and plant genome evolution are discussed.
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  • 46
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    Theoretical and applied genetics 88 (1994), S. 818-823 
    ISSN: 1432-2242
    Keywords: Diploid wheat ; Einkorn ; RFLP ; Taxonomy
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    Notes: Abstract To study the relationships between different species of the Einkorn group, 55 different accessions ofTriticum monococcum,T. boeoticum,T. urartu,T. sinskajae,T. thaoudar andT. aegilopoides were analyzed. Fifteen anonymous probes and four clones corresponding to storage protein genes were used for detecting restriction fragment length polymorphisms (RFLPs). The DNA was restricted with the restriction enzymesAluI,HaeIII,RsaI andTaqI. The 25 probe/enzyme combinations employed yielded a total of 488 polymorphic fragments. Statistical analyses were performed using Jaccard's coefficient of similarity and principal coordinate analysis. Different values of similarity within the three main taxa,monococcum,boeoticum andurartu, were obtained; the grouping at the species level was quite well reflected by the RFLP analysis done here. The coincidence between RFLP data and the subspecies classification of theT. monococcum group was only partial. OneT. urartu accession is clearly different from all of the other 54 accessions. The need for an RFLP based revision of the Einkorn taxonomy is evident.
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  • 47
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    Theoretical and applied genetics 88 (1994), S. 824-830 
    ISSN: 1432-2242
    Keywords: Pleurotus cornucopiae ; rDNA unit ; RFLP ; Ribosomal polymorphism
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    Notes: Abstract In the ribosomal DNA unit ofPleurotus cornucopiae, the rDNA coding regions are in the order 5′, 5S-18S-5.8S-25S, 3′, with the 5′ location of the 5S gene differing from its 3′ location found in other basidiomycetes. The most discriminating probe used to study the rDNA polymorphism consisted of a fragment that included the 5S, 18S and part of the 5.8S and 25S genes flanking three intergenic sequences. A high degree of rDNA polymorphism was observed in the sevenP. cornucopiae dikaryons studied. For the first time within a basidiomycete species, the restrictions maps distinguished two types of rDNA units (I and II). In each rDNA type, length variations in the external intergenic sequence IGS 1 located between the 25S and 5S genes allowed characterization of two different rDNA units in type I and four rDNA units in type II. This suggested that theP. cornucopiae rDNA units were derived from two kinds of ancestors (type I and II) by insertion or deletion events (100–700 bp) in the IGS 1. In four dikaryotic strains, two rDNA units of the same type (I or II) differing only by the IGS 1 length, were found in a similar number of copies, and presented a meiotic segregation in homokaryotic progeny. In one progeny, some homokaryotic strains possessed two different rDNA units: one with a high copy number and another with a lower one, showing that two different rDNA units could coexist in a single nucleus.
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  • 48
    ISSN: 1432-2242
    Keywords: DNA ; RFLP ; RAPD ; Brassica ; Genetic relationships
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    Notes: Abstract Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers are being used widely for evaluating genetic relationships of crop germplasm. Differences in the properties of these two markers could result in different estimates of genetic relationships among some accessions. Nuclear RFLP markers detected by genomic DNA and cDNA clones and RAPD markers were compared for evaluating genetic relationships among 18 accessions from six cultivated Brassica species and one accession from Raphanus sativus. Based on comparisons of genetic-similarity matrices and cophenetic values, RAPD markers were very similar to RFLP markers for estimating intraspecific genetic relationships; however, the two marker types gave different results for interspecific genetic relationships. The presence of amplified mitochondrial and chloroplast DNA fragments in the RAPD data set did not appear to account for differences in RAPD- and RFLP-based dendrograms. However, hybridization tests of RAPD fragments with similar molecular weights demonstrated that some fragments, scored as identical, were not homologous. In all these cases, the differences occurred at the interspecific level. Our results suggest that RAPD data may be less reliable than RFLP data when estimating genetic relationships of accessions from more than one species.
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  • 49
    ISSN: 1432-2242
    Keywords: Wheat ; Spelt ; RFLP ; Marker Genetic diversity
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    Notes: Abstract Fifty-two winter wheat (Triticum aestivum L.), nine spring wheat, and 20 spelt (Triticum spelta L.) lines representing part of the European breeding germplasm, were assayed for RFLPs (restriction fragment length polymorphisms) with 56 wheat DNA clones and two barley cDNA clones. Objectives of this study were to (1) determine the level of variation for RFLPs in the wheat and spelt breeding lines, (2) characterize the genetic diversity within the European winter wheat germplasm, and (3) evaluate the usefulness of RFLP markers for pedigree analysis and the grouping of wheat and spelt lines of various origins. Seventy-three of the 166 RFLP loci detected with 58 probes and one restriction enzyme were polymorphic for the 81 lines. The percentage of polymorphic loci was greatest for the B genome (58%) and smallest for the D genome (21%). Among the 81 lines, 271 different RFLP bands were detected. RFLP band frequencies of the winter wheat lines differed considerably (≥0.5) from those of the spring wheat lines at five loci, and from those of the spelt lines at 17 loci. Eight cultivars that had a major impact as progenitors on the development of improved winter wheat cultivars accounted for 93% of the observed RFLP bands in winter wheat. Genetic distance (GD) estimates between two lines ranged between 0.01 and 0.21. Mean GD estimates within winter wheat (0.083), within spring wheat (0.108) and within spelt (0.096) were smaller than between spring and winter wheat (0.114), and greatest between winter wheat and spelt (0.132) and spring wheat and spelt (0.148). Principal coordinate analysis performed on GD estimates revealed a clear separation of wheat and spelt germplasm. Novel spelt lines with various proportions of wheat germplasm were positioned between wheat and traditional spelt lines. The spring wheat lines formed a distinct group at the periphery of the distribution of the winter wheat lines. Subgroupings of the winter wheat lines according to the cluster analysis were in good agreement with their origin, and lines with common ancestors were grouped together.
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    Theoretical and applied genetics 89 (1994), S. 211-216 
    ISSN: 1432-2242
    Keywords: Hordeum vulgare ; RFLP ; Genetic map ; Recombination ; Crossover
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    Notes: Abstract The pattern of recombination in barley with regard to (1) the distribution of crossover points among whole gametes, (2) the distribution of crossover points among individual chromosomes and (3) the distribution of crossover points within chromosomes has been analysed using data sets underlying two recently published restriction fragment length polymorphism (RFLP) linkage maps representing male and female meiosis, respectively. The data indicated that the process of recombination had been random with no interference. The two data sets gave similar results, indicating that male and female meiosis in barley do no differ significantly. The possibility of using RFLP data in studies of crossover distribution is stressed.
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  • 51
    ISSN: 1432-2242
    Keywords: Evolution ; Tandemly repeated DNA sequences ; Phylogenetic relationships ; RFLP ; Poaceae
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    Notes: Abstract The recombinant plasmid dpTa1 has an insert of relic wheat DNA that represents a family of tandemly organized DNA sequences with a monomeric length of approximately 340 bp. This insert was used to investigate the structural organization of this element in the genomes of 58 species within the tribe Triticeae and in 7 species representing other tribes of the Poaceae. The main characteristic of the genomic organization of dpTa1 is a classical ladder-type pattern which is typical for tandemly organized sequences. The dpTa1 sequence is present in all of the genomes of the Triticeae species examined and in 1 species from a closely related tribe (Bromus inermis, Bromeae). DNA from Hordelymus europaeus (Triticeae) did not hybridize under the standard conditions used in this study. Prolonged exposure was necessary to obtain a weak signal. Our data suggest that the dpTa1 family is quite old in evolutionary terms, probably more ancient than the tribe Triticeae. The dpTa1 sequence is more abundant in the D-genome of wheat than in other genomes in Triticeae. DNA from several species also have bands in addition to the tandem repeats. The dpTa1 sequence contains short direct and inverted subrepeats and is homologous to a tandemly repeated DNA sequence from Hordeum chilense.
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  • 52
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    Theoretical and applied genetics 89 (1994), S. 259-264 
    ISSN: 1432-2242
    Keywords: RFLP ; Bootstrap ; Sampling variance ; Zea mays
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    Topics: Biology
    Notes: Abstract Knowledge of genetic relationships among genotypes is useful in a plant breeding program because it permits the organization of germplasm and provides for more efficient sampling. The genetic distance (GD) among genotypes can be estimated using random restriction fragment length polymorphisms (RFLPs) as molecular markers. Knowledge of the sampling variance associated with RFLP markers is needed to determine how many markers are required for a given level of precision in the estimate of GD. The sampling variance for GD among all pairs of 37 maize (Z. mays L.) inbred lines was estimated from 1202 RFLPs. The 1202 polymorphisms were generated from 251 enzyme-probe combinations (EPC). The sampling variance was used to determine how large a sample of RFLPs was required to provide a given level of precision. The coefficient of variation (CV) associated with GD has a nearly linear relationship between its expected standard deviation and mean. The magnitude of the decrease in the mean CV for GD with increasing numbers of bands was dependent upon the sampling unit; e.g., individual polymorphic bands vs EPC, and the degree of relatedness among the inbreds compared. The rate of reduction in mean CV with increasing sample size was the same regardless of the restriction enzyme used, BamHI, EcoRI or HindIII, when the bootstrap sampling units were individual polymorphic bands. In constrast, although the rate of reduction (slopes) was the same, the intercepts of the mean CVs were different when EPCs were used as the bootstrap sampling unit. This difference was due to the higher number of bands per EPC in BamHI (4.94) compared with EcoRI (4.83) and HindIII (4.63).
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    Theoretical and applied genetics 89 (1994), S. 265-270 
    ISSN: 1432-2242
    Keywords: Bamboo ; Phyllostachys ; RFLP ; Variation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic and taxonomic difficulties are common within the woody bamboos, due to their unique life cycle, which severely limits the availability of floral characters. To addresss some of these problems, 20 species of woody bamboos in the genus Phyllostachys were analyzed using nuclear restriction fragment length polymorphisms (RFLPs). The RFLP data were used to generate genetic distances between all pairs of taxa and to examine the degree of genetic variation within and among bamboo species. The genetic distances were also used to create dendrograms of accessions and species. These trees supported the current division of the genus into two sections and provided some information on the thorny taxonomic problems in this group. We show that RFLPs can be used for species identification and the delineation of species limits.
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  • 54
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    Theoretical and applied genetics 89 (1994), S. 271-275 
    ISSN: 1432-2242
    Keywords: RAPD ; RFLP ; Chloroplast DNA ; Natural hybrid ; Paulownia taiwaniana
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genomic DNA of Paulownia fortunei, P. kawakamii and P. taiwaniana were amplified with 10-base primers of arbitrary sequences using the polymerase chain reaction (PCR). A total of 351 DNA fragments were amplified from 23 primers and of these 265 fragments (75.5%) were polymorphic. Almost all of the PCR-amplified products of P. taiwaniana were shared by either P. fortunei or P. kawakamii, or both, and the number of polymorphic fragments shared by P. taiwaniana and P. fortunei was about equivalent to those shared by P. taiwaniana and P. kawakamii. Restriction fragments of chloroplast DNA (cpDNA) purified from Paulownia species and from reciprocal crosses between P. fortunei and P. kawakamii were analyzed. Restriction enzyme SalI-digested cpDNA showed an identical pattern in both P. kawakamii and P. taiwaniana. These results further support the hypothesis that P. taiwaniana is the natural hybrid between P. fortunei and P. kawakamii and that the maternal parent of P. taiwaniana is P. kawakamii.
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    Theoretical and applied genetics 89 (1994), S. 636-642 
    ISSN: 1432-2242
    Keywords: Apomixis ; Agamospermy ; Pearl Millet ; Interspecific hybrids ; RFLP ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two molecular markers, a RAPD (randomly amplified polymorphic DNA) and a RFLP/STS (restriction fragment length polymorphism/sequence-tagged site), previously were found associated with apomictic reproductive behavior in a backcross population produced to transfer apomixis from Pennisetum squamulatum to pearl millet. The occurrence of these molecular markers in a range of 29 accessions of Pennisetum comprising 11 apomictic and 8 sexual species was investigated. Both markers were specific for apomictic species in Pennisetum. The RFLP/STS marker, UGT 197, was found to be associated with all taxa that displayed apomictic reproductive behavior except those in section Brevivalvula. Neither UGT197 nor the cloned RAPD fragment OPC-04600 hybridized with any sexually reproducing representatives of the genus. The cloned C04600 was associated with 3 of the 11 apomictic species, P. ciliare, P. massaicum, and P. squamulatum. UGT197 was more consistently associated with apomictic reproductive behavior than OPC04600 or cloned C04600, thus it could be inferred that UGT197 is more closely linked to the gene(s) for apomixis than the cloned C04600. The successful use of these probes to survey other Pennisetum species indicates that apomixis is a trait that can be followed across species by using molecular means. This technique of surveying species within a genus will be useful in determining the relative importance of newly isolated markers and may facilitate the identification of the apomixis gene(s).
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    Theoretical and applied genetics 88 (1994), S. 441-448 
    ISSN: 1432-2242
    Keywords: RFLP ; Mitochondrial DNA ; Cytoplasmic male sterility ; Pearl millet
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    Topics: Biology
    Notes: Abstract Mitochondrial DNA (mtDNA) from 13 cytoplasmic male-sterile (cms) lines from diverse sources were characterized by Southern blot hybridization to pearl millet and maize mtDNA probes. Hybridization patterns of mtDNA digested with PstI, BamHI, SmaI or XhoI and probed with 13.6-, 10.9-, 9.7- or 4.7-kb pearl millet mtDNA clones revealed similarities among the cms lines 5141 A and ICMA 1 (classified as the S-A1 type of cytoplasm based on fertility restoration patterns), PMC 30A and ICMA 2. The remaining cms lines formed a distinct group, within which three subgroups were evident. Among the maize mitochondiral gene clones used, the coxI probe revealed two distinct groups of cytoplasms similar to the pearl millet mtDNA clones. The atp9 probe differentiated the cms line 81 A4, derived from P. glaucum subsp. monodii, while the coxII gene probe did not detect any polymorphism among the cms lines studied. MtDNA digested with BamHI, PstI or XhoI and hybridized to the atp6 probe revealed distinct differences among the cms lines. The maize atp6 gene clone identified four distinct cytoplasmic groups and four subgroups within a main group. The mtDNA fragments hybridized to the atp6 gene probe with differing intensities, suggesting the presence of more than one copy of the gene in different stoichiometries. Rearrangements involving the coxI and/or rrn18-rrn5 genes (mapped within the pearl millet clones) probably resulted in the S-A1 type of sterility. Rearrangements involving the atp6 gene (probably resulting in chimeric form) may be responsible for male sterility in other cms lines of pearl millet.
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  • 57
    ISSN: 1432-2242
    Keywords: RFLP ; Genetic mapping ; Triticum turgidum Recombinant substitution lines (RSLs) ; Mapmaker G-Mendel
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    Notes: Abstract RFLP-based genetic maps of chromosomes 6A and 6B of Triticum turgidum have been constructed using data obtained by the study of Triticum turgidum var ‘durum’ cv ‘Langdon’-T. t. var ‘dicoccoides’ recombinant substitution lines (RSLs) supplemented with data obtained from F3 families derived from ‘Langdon’ dicoccoides 6A and 6B disomic substitution lines. The average RFLP frequencies detected for the two chromosomes in a test of 45 DNA clones with six restriction enzymes were 56% and 53%, respectively, and a subset of 32 clones gave frequencies of 75% and 72%, respectively. Seventeen loci were mapped in 6A and 18 in 6B. With the possible exception of 5 loci in the centromeric region of 6A, all of the mapped 6A and 6B loci are located in the same arm as are homologous loci in hexaploid wheat, and the linear order of the loci is the same in the two chromosomes, except possibly close to the centromere. Major differences in genetic distances exist between homologous loci located in the proximal regions of the 6AL and 6BL linkage groups, however, the distances being much larger in the former than in the latter. The 6B maps that were constructed using data from both the RSL and the F2 populations and using data from the RSL population alone closely resemble one another, indicating that the 6B RSL population, composed of 85 lines, can be reliably used for genetic mapping. Additional studies must be conducted before the utility of the 6A RSL population, composed of 66 lines, can be adequately assessed.
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  • 58
    ISSN: 1432-2242
    Keywords: STS ; RFLP ; Rice ; Genetic map ; Coding region
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    Topics: Biology
    Notes: Abstract Generating sequence-tagged sites (STSs) is a prerequisite to convert a genetic map to a physical map. With the help of sequence information from these STSs one can also isolate specific genes. For these purposes, we have designed PCR primer sets, of 20 bases each, by reference to sequences of restriction fragment length polymorphism (RFLP) landmarkers consisting of rice genomic clones. These markers were evenly distributed over the 12 chromosomes and were shown to be single copy by Southern-blot analysis. With improved PCR protocols, 63 standard STS landmarkers in the rice genome were generated. Similarity searches of all partial sequences of RFLP landmarkers by the FASTA algorithm showed that 2 of the 63 RFLP landmarkers, G357 and G385, contained part of the ORFs of aspartate aminotransferase and protein kinase, respectively.
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    Theoretical and applied genetics 89 (1994), S. 775-782 
    ISSN: 1432-2242
    Keywords: Somatic hybrid ; Solanum etuberosum ; S. tuberosum ; S. berthaultii ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Electrofusion was used to obtain somatic hybrids between Solanum etuberosum (2n=2x=24) and two diploid potato lines. These hybridizations were conducted to determine if haploidxwild species hybrids are better fusion partners than conventional S. tuberosumGp. Tuberosum haploids. Restriction fragment length polymerase (RFLP) analyses of the putative somatic hybrids confirmed that each parental genome was present. The somatic hybrids between S. etuberosum and a haploid S. tuberosum clone, US-W730, were stunted and had curled, purple leaves. In contrast, somatic hybrids between S. etuberosum and a haploidxwild species hybrid (US-W 730 haploidx S. berthaultii), were vigorous and generally tuberized under field conditions. These hybrids were designated as E+BT somatic hybrids. Analyses of 23 E+BT somatic hybrids revealed a statistically significant bias towards the retention of S. etuberosum chloroplasts. Stylar incompatibilities were observed when the E+BT somatic hybrids were used as pollen donors in crosses with S. tuberosum cultivars. Reciprocal crosses did not show this incompatibility. The progeny were vigorous and had improved tuber traits when compared to the maternal E+BT parent. RFLP analyses of three sexual progeny lines confirmed the presence of all 12 S. etuberosum chromosomes. In two of these lines, RFLPs that marked each of the 24 chromosome arms of S. etuberosum were present. However, RFLP markers specific for regions on chromosomes 2, 7, and 11 were missing from the third clone. Because other markers for these chromosomes were present in the progeny line, these results indicated the likelihood of pairing and recombination between S. etuberosum and S. tuberosum chromosomes.
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  • 60
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    Theoretical and applied genetics 87 (1994), S. 821-828 
    ISSN: 1432-2242
    Keywords: RFLP ; Tissue culture ; Triticum aestivum ; Wheat
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    Topics: Biology
    Notes: Abstract Total DNAs of plants regenerated from immature embryo-derived 2-month-old embryogenic calli of wheat (cultivars Florida 302, Chris, Pavon, RH770019) were probed with six maize mitochondrial genes (atpA, atp6, apt9, coxI, coxII, rrn18-rrn5), three hypervariable wheat mitochondrial clones (K′, K3, X2), five random pearl millet mitochondrial clones (4A9, 4D1, 4D12, 4E1, 4E11) and the often-used wheat Nor locus probe (pTA71), in order to assess the molecular changes induced in vitro. In addition, protoplast-derived plants, and 24-month-old embryogenic and non-embryogenic calli and cell suspension cultures of Florida 302 were also analyzed. No variation was revealed by the wheat or millet mitochondrial clones. Qualitative variation was detected in the nonembryogenic suspension culture by three maize mitochondrial genes (coxI, rrn18-rrn5, atp6). A callus-specific 3.8-kb Hind III fragment was detected in all four cultivars after hybridization with the coxI gene. The organization of the Nor locus of the plants regenerated from Florida 302 and Chris was stable when compared to their respective control plants and calli. The Nor locus in regenerants of Pavon and RH, on the other hand, was found to be variable. However, Nor locus variability was not observed in 14 individual seed-derived control plants from either Pavon or RH sources. In Pavon, a 3.6-kb Taq I or a 5.6-kb Bam HI+ Eco RI fragment was lost after regeneration. In one of the RH regenerants, which lost a fragment, an additional fragment was observed.
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  • 61
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    Theoretical and applied genetics 87 (1994), S. 973-987 
    ISSN: 1432-2242
    Keywords: Potato ; Trichome ; Insect resistance ; RFLP ; QTL
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    Topics: Biology
    Notes: Abstract Genetic mapping of several components of a complex type of insect resistance has been undertaken as a means toward more efficient use of the valuable characteristics of a wild relative of potato. RFLP maps constructed on interspecific diploid progenies of Solanum tuberosum × S. berthaultii were used in conjunction with morphological, biochemical and biological phenotyping to identify quantitative trait loci (QTLs) contributing to trichome-mediated insect resistance. By superimposing QTL data for a wide range of phenotypes including biochemical assays, correlative and direct screens for insect resistance, and adaptation to the target environment on the genetic maps, we have addressed the organization, action and interaction of genes controlling the resistance mechanism. The outcome contributes to an understanding of the association between component traits and between desirable and undesirable features of the donor species generated in an applied breeding program. Research is proceeding toward the development of selectable markers for the introgression and transfer of this resistance among potato gene pools.
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  • 62
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    Theoretical and applied genetics 88 (1994), S. 65-69 
    ISSN: 1432-2242
    Keywords: Oryza sativa L. ; RFLP ; Wide compatibility ; Subspecies differentiation ; Heterosis
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    Topics: Biology
    Notes: Abstract Twenty-one wide compatibility varieties (WCVs) of rice together with three indica and three japonica testers were assayed with 160 DNA probes that were selected to represent the entire RFLP map at an average interval of 11 cM. On the basis of four enzyme digestion 125 probes detected polymorphisms among the WCVs and subspecies' testers. Among these polymorphic probes there were 68 that could distinguish the indica from the japonica testers. Two dendrograms were constructed on the basis of 398 polymorphic fragments of 125 probes and 139 polymorphic fragments of 68 subspecies' differentiating probes in combination with single enzymes, respectively. The reliability and representativeness of the testers and the levels of DNA variations among WCVs were estimated. The potential of WCVs in the utilization of intersubspecific heterosis is discussed.
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  • 63
    ISSN: 1432-2242
    Keywords: Leaf rust ; RAPD ; RFLP ; Triticum aestivum ; Triticum spelta
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    Notes: Abstract Near-isogenic lines (NILs) for the leaf rust resistance gene Lr9 were screened for polymorphisms at the molecular level. RAPD (random amplified polymorphic DNA) primers as well as RFLP (restriction fragment length polymorphism) markers were used. Out of 395 RAPD primers tested, three showed polymorphisms between NILs, i.e., an additional band was found in resistant lines. One of these polymorphic bands was cloned and sequenced. Specific primers were synthesized, and after amplification only resistant lines showed an amplified product. Thus, these primers define a sequence-tagged site that is specific for the translocated fragment carrying the Lr9 gene. A cross between a resistant NIL and the spelt (Triticum spelta) variety ‘Oberkulmer’ was made, and F2 plants were analyzed for genetic linkage. All three polymorphisms detected by the PCR (polymerase chain reaction) and one RFLP marker (cMWG684) showed complete linkage to the Lr9 gene in 156 and 133 plants analyzed, respectively. A second RFLP marker (PSR546) was closely linked (8±2.4 cM) to the Lr9 gene and the other four DNA markers. As this marker maps to the distal part of the long arm of chromosome 6B of wheat, Lr9 and the other DNA markers also map to the distal region of 6BL. All three PCR markers detected the Lr9 gene in independently derived breeding lines and varieties, thus proving their general applicability in wheat breeding programs.
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  • 64
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    Theoretical and applied genetics 88 (1994), S. 159-166 
    ISSN: 1432-2242
    Keywords: Mitochondrial DNA ; RFLP ; Asteraceae ; Cichorium
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    Topics: Biology
    Notes: Abstract Mitochondrial DNA polymorphism was employed to assess cytoplasmic diversity among cytoypes of the genus Cichorium and related genera of the tribe Lactuceae (Asteraceae). Hybridization patterns of total DNA using six restriction enzymes and five heterologous mtDNA probes were examined. From estimates of mtDNA diversity, Cichorium spinosum appeared as an ecotype of C. intybus rather than a separate species. Interspecific mtDNA polymorphism in the genus Cichorium was higher than that observed in Cicerbita Crepis, Lactuca and Tragopogon. Molecular data seemed to indicate that Catananche is very distant from the other genera examined. Intergeneric comparisons allowed the clustering of Cicerbita, Lactuca and Cichorium, genera which belong to different subtribes. However, further molecular investigations on a larger number of genera are needed to clarify the relationships among genera within and between subtribes of the tribe Lactuceae.
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  • 65
    ISSN: 1432-2242
    Keywords: RFLP ; mtDNA diversity ; Phaseolus coccineus ; P. polyanthus ; P. vulgaris ; cytoplasmic male sterility
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    Notes: Abstract Previous results have shown that cytoplasmic male sterility (CMS) in lines from Phaseolus coccineus and Phaseolus vulgaris contain the same CMS-specific sequence, raising the question of whether this sequence rearrangement arose before divergence of the two species or afterward with subsequent transfer by introgression. Hybridization patterns of total DNA from eight P. vulgaris lines with cytoplasm from P. coccineus and three P. vulgaris lines were examined in order to analyze the mitochondrial DNA (mtDNA) diversity within each species and to determine differences between CMS lines derived from the two species. Three restriction enzymes and 17 heterologous mtDNA sequences were used. The analysis of the different hybridization patterns revealed a considerable diversity in mtDNA organization particularly within P. coccineus. We obtained distinctive hybridization patterns for the five CMS lines tested. The resulting classification showed that mitochondrial genomes from P. coccineus CMS lines group with those of fertile P. coccineus but not with CMS lines from P. vulgaris. The groupings concur with the taxonomic classification of these lines. The results support the hypothesis of a single ancient origin of the CMS determinant and exclude the transfer of cytoplasm by introgression from P. vulgaris to P. coccineus and P. coccineus ssp polyanthus.
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  • 66
    ISSN: 1432-2242
    Keywords: RFLP ; Sr22 ; Triticum aestivum ; T. boeoticum ; Recombination
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    Notes: Abstract Analysis of the bread wheat variety Schomburgk, and related lines in its pedigree, identified RFLP markers associated with the segment of chromosome 7A carrying the Sr22 gene derived from the diploid species T. boeoticum. The distribution of the RFLP markers indicated that at least 50% of 7AS and 80% of 7AL in Schomburgk is of T. boeoticum origin. Evaluation of five sets of nearisogenic lines, backcross lines in 20 different genetic backgrounds and an F2 population segregating for Sr22 demonstrated a very low level of recombination between the 7A chromosomes of T. boeoticum and T. aestivum. Several recombinants carrying Sr22 but with a much reduced segment of T. boeoticum were identified and these may prove useful in the breeding of further varieties with Sr22.
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  • 67
    ISSN: 1432-2242
    Keywords: Sorghum ; RFLP ; Genetic diversity Cultivated ; Racial differentiation
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    Notes: Abstract Careful assessment of the comparative diversity for molecular markers and for potentially-useful morpho-agronomic traits is paramount to the analysis of a genome through the mapping of favorable genes. Sorghum (Sorghum bicolor ssp.bicolor) varieties are traditionally classified into five races on the basis of morphological traits, especially panicle and grain traits. Isozyme diversity has provided a new insight into genetic diversity, and showed a marked geographic structure. We performed RFLP analysis on 94 varieties, chosen to represent the main cross combinations (race × geographic origin), using 35 maize probes that detect polymorphism with at least one of the two restriction enzymesHindIII andXbaI. A total of 50 polymorphic probe-enzyme combinations yielded 158 polymorphic bands. The bicolor race appeared highly variable and included many rare markers. Among the other races multivariate analysis of the data differentiated six clusters corresponding, by decreasing magnitude of divergence, to: the margaritiferum types (a sub-race of race guinea); the guinea forms from western Africa; race caudatum; race durra; race kafir; and the guinea forms from southern Africa.The apparent geographic differentiation was related to the contrasting distribution of these races and to a higher similarity between races localized in southern Africa. The data agree with the current hypotheses on sorghum domestication but reveal associations between neutral markers and traits probably highly subjected to human selection. Whether such associations will be observed with other useful traits, and to what extent they are maintained by genetic linkage, is worth exploring.
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    Theoretical and applied genetics 88 (1994), S. 845-851 
    ISSN: 1432-2242
    Keywords: Tomato ; Lycopersicon esculentum ; GACA ; Genetic fingerprinting ; RFLP ; PCR
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract Simple sequence repeat oligonucleotides were used to probe the tomato genome for elements displaying variability amongst commercial cultivars. The oligonucleotide (GACA)4 was found to be particularly informative on genotype screening blots, hybridising to a highly polymorphic family of elements, and was used to clone one such member from a lambda library. The GACA-hybridisation was localised to a 1.3-kbHinfI fragment within the original 15-kb lambda insert. This 1,349-bp subclone (pT-GACA-2:1.3) was used to probe 27 Californian processing varieties and found to be capable of distinguishing all from each other, thus demonstrating its utility as a genetic fingerprinting probe for cultivar identification. Hybridisation occurred to approximately 10 major high molecular weight (〉 4-kb) bands, most of which segregated independently in F2 populations, as well as a large number of less clearly resolvable smaller fragments. Sequence analysis of the cloned element reveals that it is almost entirely composed of GACA or GATA repeats. These tetranucleotides are organised into distinct repetitive domains, consisting either of tandem arrays of each tetranucleotide or interspersions of GACA and GATA to form dodecanucleotides that are then further repeated. The boundaries between domains contain sufficient departures from the concensus repeat to allow construction of unique polymerase chain reaction (PCR) primers. Amplification from two such contiguous regions identifies length variation in both, thus yielding a genotype screen appropriate for high-throughput applications, such as assessment of purity in F1 hybrid seed lots.
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  • 69
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    Theoretical and applied genetics 89 (1994), S. 54-59 
    ISSN: 1432-2242
    Keywords: Rice ; Semidwarf gene (sd-1) ; RFLP ; Molecular marker ; Marker-assisted selection
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    Notes: Abstract To establish the location of the semidwarf gene, sd-1, the anthocyanin activator (A), purple node (Pn), purple auricle (Pau), and the isozyme locus, EstI-2, in relation to DNA markers on the molecular linkage map of rice, 20 RFLP markers, previously mapped to the central region of chromosome 1 (McCouch et al. 1988), were mapped onto an F2 population derived from the cross Taichung 65 (A,Pn,Pau)/Taichung 65 (sd-1). sd-1 and EstI-2 were determined to be linked most tightly to RFLP markers RG 109 and RG 220, which cosegregated with each other. The distance between these RFLP markers and sd-1 was estimated to be 0.8 cM, based on an observed recombination value of 0.8%. The order of genes and markers in this region of chromosome 1 was determined to be sd-1 — (EstI-2 — RG220 — RG109) — RG381 — A — Pn — Pau. To test the efficacy of selection for sd-1 based on these linked markers, 50-day-old F2 seedlings derived from another cross, Milyang 23/Gihobyeo, were analyzed for marker genotype. At this age, the semidwarf character could not be clearly detected based on phenotype. In addition, plant height was normally distributed in this population, making it difficult to unambiguously identify plants carrying sd-1. Thirteen seedlings homozygous for the sd-1-associated allele at EstI-2, RG220 and RG109, and 13 seedlings homozygous for the Sd-1-associated allele at all three marker loci were selected for further genetic analysis. At 20 days after heading, the culm lengths of these 26 plants were measured and the expected phenotype was confirmed in every case. These 26 plants were then selfed for four generations and F6 lines were again evaluated to determine whether any recombination among the three molecular markers, or between these markers and the sd-1 gene, could be detected. No recombinants were identified, confirming the tight linkage of these loci and the usefulness of genotypic selection for this recessive semidwarf character prior to the time when it can be evaluated based on phenotype.
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  • 70
    ISSN: 1432-2242
    Keywords: Triticum aestivum ; Agropyron cristatum ; Alien addition ; RFLP ; Non-radioactive labelling
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    Notes: Abstract A non-radioactive digoxigenin-labelled DNA method was used successfully to identify RFLP markers in 54 Triticum aestivum cv ‘Chinese Spring’ — Agropyron cristatum (2n=28, genome PPPP) P-genome monosomic addition lines. Southern analysis using a set of 14 DNA probes identifying each homoeologous chromosome arm, combined with two restriction enzymes HindIII and EcoRI, indicated that six A. cristatum chromosomes (1P, 2P, 3P, 4P, 5P and 6P) and five A. cristatum chromosome arms (2PS, 2PL, 5PL, 6PS and 6PL) have been individually added to the wheat genome. The added chromosomes of three lines were Agropyron translocated chromosomes. It was also found that two addition plants possessed an Agropyron-wheat translocation. These results showed that RFLP analysis using the set of assigned wheat probes was a powerful tool in detecting and establishing homoeology of alien A. cristatum chromosomes, or arms, added to wheat, as well as in screening the alien addition material. The creation of the monosomic addition lines should be useful for the transfer of disease-resistance genes from A. cristatum to wheat.
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  • 71
    ISSN: 1432-2242
    Keywords: Powdery mildew (Leveillula taurica) ; Tomato ; RAPD ; RFLP ; Lv
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    Notes: Abstract We report the tagging of a powdery mildew [Leveillula taurica (Lév.) Arnaud.] resistance gene (Lv) in tomato using RAPD and RFLP markers. DNA from a resistant (cv Laurica) and a susceptible cultivar were screened with 300 random primers that were used to amplify DNA of resistant and susceptible plants. Four primers yielded fragments that were unique to the resistant line and linked to the resistance gene in an F2 population. One of these amplified fragments, OP248, with a molecular weight of 0.7 kb, was subsequently mapped to chromosome 12, 1 cM away from CT134. Using RFLP markers located on chromosome 12, it was shown that approximately one half of chromosome 12 (about 42 cM), in the resistant variety is comprised of foreign DNA, presumably introgressed with the resistance gene from the wild species L. chilense. Further analysis of a backcross population revealed that the Lv gene lies in the 5.5-cM interval between RFLP markers, CT211 and CT219. As a prelude to map-based cloning of the Lv gene, we are currently enriching the density of markers in this region by a combination of RAPD primers and other techniques.
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  • 72
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    Theoretical and applied genetics 89 (1994), S. 590-598 
    ISSN: 1432-2242
    Keywords: Linkage map ; Brassica nigra ; RFLP ; RAPD
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    Notes: Abstract We constructed a genetic map on Brassica nigra based on a segregating population of 83 F2 individuals. Three different types of molecular markers were used to build the map including isozymes, restriction fragment length polymorphisms (RFLP), and random amplified polymorphic DNA (RAPD). The final map contained 124 markers distributed in 11 linkage groups. The map covered a total distance of 677 cM with the markers distributed within a mean distance of 5.5cM. Of the sequences found in the B. nigra map, 40% were duplicated and organized into three different types of arrangements. They were either scattered throughout the genome, organized in tandem, or organized in blocks of duplicated loci conserved in more than 1 linkage group.
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  • 73
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    Theoretical and applied genetics 89 (1994), S. 801-810 
    ISSN: 1432-2242
    Keywords: Hordeum ; Phylogeny ; Repetitive DNA sequences ; RFLP ; In situ hybridization
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. in situ hybridization experiments showed dispersed organization of the sequences over all chromosomes of H. vulgare and the wild barley species H. bulbosum, H. marinum and H. murinum. Southern blot hybridization revealed different levels of polymorphism among barley species and the RFLP data were used to generate a phylogenetic tree for the genus Hordeum. Our data are in a good agreement with the classification system which suggests the division of the genus into four major groups, containing the genomes I, X, Y, and H. However, our investigation also supports previous molecular studies of barley species where the unique position of H. bulbosum has been pointed out. In our experiments, H. bulbosum generally had hybridization patterns different from those of H. vulgare, although both carry the I genome. Based on our results we present a hypothesis concerning the possible origin and phylogeny of the polyploid barley species H. secalinum, H. depressum and the H. brachyantherum complex.
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  • 74
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    Theoretical and applied genetics 88 (1994), S. 193-198 
    ISSN: 1432-2242
    Keywords: Theobroma cacao ; RFLP ; diversity study seed cDNA
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    Topics: Biology
    Notes: Abstract The variability of the cocoa (Theobroma cacao) nuclear genome was investigated. A total of 203 cocoa clones was surveyed for restriction fragment length polymorphisms (RFLPs) using four restriction endonuclease and 31 seed cDNA probes. A high level of polymorphism has been found. This study points to a structuring of the species that fits with the distinction between the Criollo and Forastero populations. These results combined with previously obtained nuclear rDNA and mtDNA data allow us to propose new hypotheses on the origin and evolution of the different cocoa populations.
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    Theoretical and applied genetics 88 (1994), S. 215-219 
    ISSN: 1432-2242
    Keywords: Barley stripe rust ; RFLP ; QTL mapping ; Molecular marker-assisted backcrossing
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    Notes: Abstract Two genes conferring resistance to the barley stripe rust found in Mexico and South America, previously identified as race 24, were mapped to the M arms of barley chromosomes 7 and 4 in a doubled haploid population using molecular markers and the quantitative trait loci (QTL) mapping approach. The resistance gene on chromosome 7 had a major effect, accounting for 57% of the variation in disease severity. The resistance gene on chromosome 4 had a minor effect, accounting for 10% of the variation in trait expression. Two pairs of restriction fragment length polymorphism markers are being used to introgress the resistance genes to North American spring barley using molecular marker-assisted backcrossing.
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    Theoretical and applied genetics 88 (1994), S. 255-260 
    ISSN: 1432-2242
    Keywords: RFLP ; Hybrid variegation ; Plastid DNA ; Interspecific incompatibility ; Zantedeschia
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    Topics: Biology
    Notes: Abstract Plastid DNA (ptDNA) probes were used in RFLP analysis to determine ptDNA inheritance in interspecific hybrids in Zantedeschia. Biparental and maternal ptDNA inheritance was found in albino hybrids between the evergreen species Z. aethiopica and several winter-dormant species. From two albino hybrids, different types of ptDNA were detected in shoots derived from different parts of an embryo. This result indicates that plastids were sorted out during embryo development. Only maternal ptDNA was detected in the hybrids of Z. aethiopica × Z. odorata (a summer-dormant species) but paternal, biparental, and maternal ptDNA were found in the hybrids of the reciprocal cross. Z. odorata × Z. aethiopica. By correlating these ptDNA inheritance patterns with the leaf colour (albino, pale-green, and green) of the hybrids, it is suggested that the Z. odorata plastome is incompatible with the Z. aethiopica genome. The Z. aethiopica plastome is partially compatible with the Z. odorata genome but the development of Z. aethiopica plastids appears to be blocked by the presence of the Z. odorata plastids.
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  • 77
    ISSN: 1432-2242
    Keywords: Breeding ; Helminthosporium turcicum ; RFLP ; QTLs ; Disease-resistance ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RFLPs were used to investigate components of host-plant response to Exserohilum turcicum in 150 unselected F2∶3 lines of a B52/Mo17 maize population. Following inoculation with spore suspensions of the pathogen (race 0), components of disease development were measured and then quantitative trait mapping was performed to identify the location and effects of quantitative trait loci (QTLs) determining host-plant response. Components of interest were the average number of lesions per leaf, the average percent leaf tissue diseased (severity) and the average size of lesions (cm2). Based on a LOD threshold of 2.31 (P〈0.05), the number of lesions appears to be associated with QTLs on chromosomes 1S, 3L, 5S. Severity was associated with analogous regions and, in addition, QTLs on chromosomes 7L and 8L. Most QTLs, for either of these two components, involve additive gene action and partial dominance or overdominance. In contrast, lesion size was associated with QTLs on chromosomes 7L and 5L; recessive gene action may be involved at 7L.
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  • 78
    ISSN: 1432-2242
    Keywords: RFLP ; QTL ; Epistasis ; Soybean ; Recombinant inbreds
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Quantitative trait values for seed oil and protein content or for maturity were measured in recombinant inbred lines (RIL) of soybean derived from a cross between two soybean cultivars: ‘Minsoy’ PI 27890 and ‘Noir 1’ PI 290136. Seed oil was found to be inversely correlated to protein content. By analyzing DNA from plants with extreme phenotypes, we were able to identify quantitative trait loci (QTL) for these traits as being linked to several restriction fragment length polymorphism (RFLP) loci, including R183 for oil and protein content and R79 for maturity. Cumulative distributions of trait values were graphed for those RIL with ‘Minsoy’ alleles and for those with ‘Noir 1’ alleles. As already suggested by the alleles found associated with extreme phenotypes, the distributions were consistent with an independent and additive expression of the maturity QTL linked to R79. That is, the cumulative distributions for plants with ‘Minsoy’ alleles and for plants with ‘Noir 1’ alleles were similar in shape, but the entire ‘Noir 1’ curve had been shifted to later maturity dates. In contrast, the trait distributions for a locus affecting oil and protein content linked to R183 were not compatible with an additive model. These results suggest that this approach can be used for rapid identification of QTLs with epistatic expression.
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    Theoretical and applied genetics 88 (1994), S. 727-732 
    ISSN: 1432-2242
    Keywords: Mitochondria ; Larix ; RFLP ; Somatic embryogenesis ; Somaclonal variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract outhern hybridization analysis using wheat mitochondrial gene-specific probes indicates that changes in mitochondrial genomic organization and the relative representation of certain genomic regions occur during in vitro somatic embryogenic cell culture ofLarix species. We observed differences in the mitochondrial (mt)DNA hybridization patterns between somatic embryogenic cell cultures and trees grown from seed forLarix leptolepis,L. decidua, and the reciprocal hybrids of these twoLarix species. This is the first study to describe the correlation of molecular changes in a gymnosperm mitochondrial genome with in vitro somatic embryogenic cell culture. Quantitative differences in mtDNA hybridization signals were also observed among a 4-year-old somatic embryogenic cell culture ofLarix ×eurolepis trees regenerated from this culture, and the seed source tree from which the somatic embryogenic cell cultures were initiated.
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    Theoretical and applied genetics 89 (1994), S. 1014-1018 
    ISSN: 1432-2242
    Keywords: CMS-Secale ; RFLP ; Differential transcription ; cob ; atpA ; atp9
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The mitochondrial (mt) genomes of rye (Secale cereale L.) lines with “normal” and cytoplasmic male sterility (CMS) inducing “Pampa” cytoplasm were compared by detailed restriction fragment length polymorphism (RFLP) and Northern analyses. RFLP analyses using several heterologous mt genes as probes revealed considerable differences in the overall structure of the two mt genomes. With cob and atpA, the data indicate intragenic recombination and/or different copy numbers of these genes in the two cytoplasms. In spite of this heterogeneity at DNA level, the transcriptional patterns of nine out of ten mitochondrial genes analysed are unaffected. The exception is in the “Pampa” cytoplasm which contains an additional cob-homologous transcript. Since this transcript is strongly reduced in the presence of restorer genes, it might causally be correlated to the CMS phenotype.
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    Theoretical and applied genetics 89 (1994), S. 297-304 
    ISSN: 1432-2242
    Keywords: Storage protein ; Genome ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The predominant storage protein of soybean [Glycine max (L.) Merr.] seed is a globulin called glycinin. Thus far five genes encoding glycinin subunits have been described, and these are denoted by the gene symbols Gy1 to Gy5. The objectives of this study were to map two of these genes, Gy4 and Gy5, and to conduct a genetic analysis of a subunit size-variant from an allele of Gy4. For this purpose a population was formed with an interspecific cross between PI 468916 (G. soja) and A81-356022 (G. max). The two size forms of G4, the subunit from Gy4, segregated codominantly in the mapping population, and were due to a short insertion in the hypervariable region of the mutant protein. The biochemical and molecular characteristics of the two subunits indicate that they are produced from alternate alleles of the same gene. The gene symbols Gy a and Gy b have been assigned to the normal and variant genes, respectively. When genomic DNA from the two parents was probed with a Gy4 cDNA, RFLPs were identified for both Gy4 and Gy5. Using these genetic markers, the Gy4 and Gy5 glycinin genes were mapped in linkage group “O” and “F” on the public soybean genomic map.
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  • 82
    ISSN: 1432-2242
    Keywords: Avena byzantina ; A. sativa ; RFLP ; Homoeology ; C-banding ; Aneuploids ; RFLP mapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The use of RFLP markers, together with a partial set of monosomics available in Avena byzantina cv Kanota, has enabled us to identify putative homoeologous chromosome sets in hexaploid Avena species (2n = 6x = 42, AACCDD). We first identified probes producing distinct three-band patterns on Southern blots that possibly reflect orthologous loci of the three genomes present in the hexaploid. Using monosomic analysis, 51 different restriction fragments that hybridized to 26 probes were localized to 12 different chromosomes for which monosomic stocks were available. These DNA restriction fragments were localized to specific monosomics using image analysis to quantify band intensity relative to other bands in the same lane. From these data, we have tentatively identified two complete homoeologous sets of three chromosomes each and two partial sets of two of the three chromosomes. The results indicate that RFLP dosage analysis is useful in the characterization of homoeologous chromosomes in hexaploid oat where nullisomics for many of the chromosomes are not available. Mention of a trademark or proprietary product does not constitute a guarantee or warranty by the USDA-ARS or the University of Minnesota and does not imply approval over other products that also may be suitable
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  • 83
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    Theoretical and applied genetics 89 (1994), S. 397-402 
    ISSN: 1432-2242
    Keywords: RFLP ; Eucalypts ; Inheritance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The level of polymorphism using genomic and cDNA probes with a number of restriction enzymes and the inheritance of the RFLP loci was investigated in E. nitens. The polymorphism detected with 366 genomic and cDNA probes and three to six restriction enzymes was analysed in three-generation outbred pedigrees. No difference in the level of polymorphism detected with genomic versus cDNA probes was observed. There was a difference in the efficiency of detection of polymorphism with six different restriction enzymes, with three of the enzymes (BglII, DraI and EcoRI) showing substantially more polymorphism than the others. There was no significant correlation between the size of the DNA fragments generated by the enzymes and the detection of polymorphism. Several cases of restriction-site mutations resulting in a polymorphism were observed. The inheritance of 69 loci was analysed in two pedigrees resulting from interpopulational crosses. The majority of the loci segregated according to expected ratios with distortion observed in only 3% of loci. Probes from the cDNA library detected a greater proportion of loci with more than two alleles than did probes from the genomic library. The high polymorphism, large number of alleles, and ease of interpretation of RFLPs in E. nitens means that they will be useful in a range of applications such as genetic linkage maps and paternity analysis.
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  • 84
    ISSN: 1432-2242
    Keywords: Sunflower ; RFLP ; Genetic diversity ; Cytoplasmic male sterility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract One-hundred-and-eighty-one nuclear DNA probes were used to examine restriction-fragment length polymorphism in inbred lines of the cultivated sunflower (Helianthus annuus L.). The probes were from six libraries: two genomic libraries — one made with PstI and the other with HindIII, and four cDNA libraries — from etiolated plantlets, green leaves, ovaries, petals and anthers. Total DNA from 17 inbred lines representing an overview of the genetic stocks of sunflower, including restorer and maintainer lines of the classical cytoplasmic male sterility, was digested with four different restriction enzymes and probed in 331 probe-enzyme combinations. Of 181 clones analysed, 73 probes were found to be polymorphic. Genetic distances between inbreds were calculated from the resultant proportion of shared bands and submitted to principal component analysis and the UPGMA ‘tree-making’ method. The RFLP analysis allowed a clear differentiation between restorer and maintainer lines of the cytoplasmic male sterility, together with a grouping of some of the genotypes from the same origin. The analysis of the accuracy of distance estimation as a function of the number of probe-enzyme combinations used, indicates that 40–50 combinations ensure a confidence level of near 95%. Considering the inbreds as representatives of the range of cultivated inbreds, estimates of gene diversity, as well as estimates of average gene diversity between and within the sets of restorer and maintainer lines, were calculated. Estimation of gene diversity showed that the available genetic variability in cultivated sunflower, based on allelic frequencies, is lower than that of other plants (H=0.20). Moreover, we show that the proportion of genetic variability due to the difference between maintainer and restorer lines (Dm) is about 2%.
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  • 85
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    Theoretical and applied genetics 89 (1994), S. 481-487 
    ISSN: 1432-2242
    Keywords: Pearl millet ; RFLP ; Translocation Genetic maps
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Analysis of a sample of diverse pearl millet genotypes with 200 genomic DNA probes revealed this crop species to be extremely polymorphic. Among these genotypes, 85% of probes detected polymorphism using only two restriction enzymes, with an average pair-wise polymorphism between all of the probe-enzyme combinations of 56%. Two crosses were employed to construct an RFLP-based genetic map. In an intervarietal F2 population, derived from a single F1 plant, 181 loci were placed on a linkage map. The total length of this map, which comprised seven linkage groups, was 303 cM and the average map distance between loci was about 2 cM, although a few intervals in excess of 10 cM were present at the ends of a few linkage groups. Very few clones, including those which hybridized to more than one copy, detected more than one locus in the pearl millet genome. The analysis was complicated initially because 83 of the 181 loci mapped to a single linkage group. Analysis of a second cross identified a probable translocation breakpoint in the middle of this large linkage group.
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  • 86
    ISSN: 1432-0762
    Keywords: Honey bee ; Subfamily ; RFLP ; Task specialization ; Dwarf honey bee ; Thailand ; Multiple mating
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Workers in a wild in situ colony of the dwarf honey bee, Apis florea, were observed undertaking the following behavior: liquid foraging, pollen foraging, guarding, stinging, fanning and wagging abdomen. Bees of each behavioral class were separately collected and frozen. Collections were made over a period of 10 days. Random samples of brood and workers were also collected. DNA was extracted from each bee and “fingerprinted” using a probe of unknown sequence obtained from an A. mellifera genomic library. Patterns of fingerprints (Fig. 1) were dissimilar among behavioral classes (Tables 1 and 2), strongly suggesting a genetic component to division of labor in this species. This result supports similar findings in A. mellifera in a species that is not troubled by many of the experimental difficulties inherent in A. mellifera.
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  • 87
    ISSN: 1615-6110
    Keywords: Homosporous ferns ; Parkeriaceae ; Ceratopteris ; C. thalictroides ; C. richardii ; RFLP ; cDNA ; polyploidy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have used cDNA clones as probes on Southern blots to detect restriction fragment length polymorphisms among sevenCeratopteris thalictroides accessions, threeC. richardii accessions, and one putative interspecific hybrid. We found that the stringency of post-hybridization washes was a critical parameter affecting the quality of our blots; even with homologous cDNA sequences low stringency conditions resulted in a smear of signal, but high stringency washes gave blots with distinct bands. Most probes showed hybridization with four or more genomic fragments. Similarities in the number and size of fragments between and within species indicated that (i)C. richardii shows limited polymorphism among accessions tested, (ii)C. thalictroides is highly polymorphic, and (iii) Hawaiian accessions ofC. thalictroides are divergent relative to their continental cohorts and among themselves. The putative interspecific hybrid did not group closely with either of these species.
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  • 88
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    Plant systematics and evolution 191 (1994), S. 131-146 
    ISSN: 1615-6110
    Keywords: Leguminosae ; Phaseolus ; Vigna ; Lectin genes ; phylogeny ; diversity ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction fragment length polymorphisms at the phytohemagglutinin (PHA) locus were determined among 21 genotypes ofPhaseolus vulgaris, P. coccineus, P. acutifolius, P. lunatus, and threeVigna species, using five restriction enzymes and one double digestion, in order to provide molecular evidence for their genetic relatedness. The dissimilarity between genotypes was estimated from binary RFLP data. The dissimilarity was high among species (from 0.75 to 0.95), and of variable extent among genotypes of the same species (0.33–0.89). InP. vulgaris, two different DNA hybridization patterns were found, giving further evidence for two major gene pools in that species. The restriction patterns ofP. vulgaris var.aborigineus, the putative ancestral form ofP. vulgaris, exhibit clear homology toP. vulgaris genotypes. An undefined landrace from Taiwan could be identified as aP. vulgaris genotype. RFLP-based trees for the phytohemagglutinin genes of the species studied were computed with several distance matrix and parsimony methods.
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  • 89
    ISSN: 1617-4623
    Keywords: Potato ; Solanum tuberosum ; Phytophthora infestans ; RFLP ; R genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phytophthora infestans (Mont.) de Bary is the most important fungal pathogen of the potato (Solanum tuberosum). The introduction of major genes for resistance from the wild species S. demissum into potato cultivars is the earliest example of breeding for resistance using wild germplasm in this crop. Eleven resistance alleles (R genes) are known, differing in the recognition of corresponding avirulence alleles of the fungus. The number of R loci, their positions on the genetic map and the allelic relationships between different R variants are not known, except that the R1 locus has been mapped to potato chromosome V The objective of this work was the further genetic analysis of different R alleles in potato. Tetraploid potato cultivars carrying R alleles were reduced to the diploid level by inducing haploid parthenogenetic development of 2n female gametes. Of the 157 isolated primary dihaploids, 7 set seeds and carried the resistance alleles R1, R3 and R10 either individually or in combinations. Independent segregation of the dominant R1 and R3 alleles was demonstrated in two F1 populations of crosses among a dihaploid clone carrying R1 plus R3 and susceptible pollinators. Distorted segregation in favour of susceptibility was found for the R3 allele in 15 of 18 F1 populations analysed, whereas the RI allele segregated with a 1:1 ratio as expected in five F1 populations. The mode of inheritance of the R10 allele could not be deduced as only very few F1 hybrids bearing R10 were obtained. Linkage analysis in two F1 populations between R1, R3 and RFLP markers of known position on the potato RFLP maps confirmed the position of the R1 locus on chromosome V and localized the second locus, R3, to a distal position on chromdsome XI.
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  • 90
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    Molecular genetics and genomics 245 (1994), S. 424-430 
    ISSN: 1617-4623
    Keywords: Pollen thermotolerance ; Maize ; Quantitative trait loci (QTLs) ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Pollen thermotolerance is an important component of the adaptability of crops to high temperature stress. The tolerance level of the different genotypes in a population of 45 maize recombinant inbred lines was determined as the degree of injury caused by high temperature to pollen germinability (IPGG) and pollen tube growth (IPTG) in an in vitro assay. Both traits revealed quantitative variability and high heritability. The traits were genetically dissected by the analysis of molecular markers using 184 mapped restriction fragment length polymorphisms (RFLPs). Significant genetic correlation between the markers and the trait allowed us to identify a minimum number of five quatitative trait loci (QTLs) for IPGG and six QTLs for IPTG. Their chromosomal localization indicated that the two characters are controlled by different sets of genes. In addition, IPGG and IPTG were shown to be basically independent of the pollen germination ability and pollen tube growth rate under non-stress conditions. These results are discussed in relation to their possible utilization in a breeding strategy for the improvement of thermotolerance in maize.
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  • 91
    ISSN: 1617-4623
    Keywords: Lycopersicon esculentum ; Ac/Ds ; Transposon tagging ; Inverse PCR ; RFLP ; linkage analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have introduced a genetically marked Dissociation transposable element (Ds HPT ) into tomato (Lycopersicon esculentum) by Agrobacterium tumefaciens-mediated transformation. Probes for the flanking regions of the T-DNA and transposed Ds HPT elements were obtained with the inverse polymerase chain reaction (IPCR) technique and used in RFLP linkage analyses. The RFLP map location of 11 T-DNAs carrying Ds HPT was determined. The T-DNAs are distributed on 7 of the 12 tomato chromosomes. To explore the feasibility of gene tagging strategies in tomato using Ds HPT , we examined the genomic distribution of Ds HPT receptor sites relative to the location of two different, but very closely linked, T-DNA insertion sites. After crosses with plants expressing Ac transposase, the hygromycin phosphotransferase (HPT) marker on the Ds element and the excision markers β-glucuronidase (GUS) and Basta resistance (BAR) facilitated the identification of plants bearing germinally transposed Ds HPT elements. RFLP mapping of 21 transposed Ds HPT elements originating from the two different T-DNA insertions revealed distinct patterns of reintegration sites.
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  • 92
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    Journal of plant research 107 (1994), S. 339-348 
    ISSN: 1618-0860
    Keywords: Chloroplast DNA ; Lardizabalaceae ; Molecular phylogeny ; rbcL ; RFLP ; Sequencing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Eleven species belonging to seven genera in the Lardizabalaceae were analyzed in terms of restriction fragment length polymorphism (RFLP) of chloroplast DNA and the sequence of the chloroplast gene,rbcL, of Lardizabalaceae and its related families. Phylogenetic trees inferred from parsimony, neighbor joining and maximum likelihood methods based on RFLP data showed that two South American genera,Boquila andLardizabala, and three East Asian genera,Akebia, Holboellia andStauntonia are closely related to each other, respectively. On the other hand, the parsimony, neighbor joining and maximum likelihood trees constructed using sequence data of therbcL gene showed thatAkebia, Stauntonia, Boquila andLardizabala clustered as(((Akebia, Stauntonia), Boquila), Lardizabala). This difference may be attributable to fewer informative sites inrbcL genes than in RFLP in this family.Decaisnea diverges at the very base of the Lardizabalaceae.
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  • 93
    ISSN: 1573-5060
    Keywords: introgression ; phylogeny ; polyploidy ; RFLP ; Saccharum ; sugarcane
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary DNA restriction fragment length polymorphism (RFLP) analysis was performed on 50 wild and old cultivated sugarcane accessions. Ninety-four maize low copy nuclear DNA sequences of known chromosomal position were screened for hybridization to digested sugarcane genomic DNA blots. Seventy-five (80%) gave very strong hybridization signals and usually yielded many bands and detected profuse polymorphism. Twenty-nine probes and 36 probe/enzyme combinations were selected on the basis of the scorability of the banding profiles. A total of 1110 fragments were separately identified among the 50 genotypes. Multivariate analyses of the data allowed the separation of the three basic species, Saccharum spontaneum, S. robustum and S. officinarum, showed that S. spontaneum had structure which could be related to the geographic origin of the clones and supported current hypotheses on the origin of secondary species S. barberi and S. sinense. The use of more probes did not improve the resolution between the various species examined but identified a few key polymorphisms which were not accounted for by current phylogenetic hypotheses and can guide future analyses. RFLPs in sugarcane will be useful essentially for depicting the genomic constitution of modern varieties of interspecific origin.
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  • 94
    ISSN: 1573-5060
    Keywords: aneuploidy ; linkage disequilibrium ; polyploidy ; RFLP ; sugarcane varieties ; Saccharum officinarum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary RFLP analysis was performed on 40 sugarcane cultivated varieties. Twenty-two maize low copy DNA clones located on different regions of the 10 maize chromosomes were used as probes to survey variability among the sugarcane varieties. A total of 425 fragments, 411 of which were polymorphic, were identified for 22 probe/enzyme combinations. Each variety displayed an average of 7.28 fragments per combination, revealing the complex polyploid origin of modern sugarcane varieties. The average genetic similarity between sugarcane varieties was 0.61. Although cultivated varieties appear closely related to S. officinarum clones, the genes of S. spontaneum seem to constitute the principal component of varietal diversity. A very weak global structuring among the 40 varieties is observed, in agreement with the profuse exchanges of parental materials between sugarcane breeding stations. Traces of linkage disequilibrium can be attributed to the distribution of S. spontaneum chromosomes among sugarcane varieties. The possibility of using modern varieties as a population for detecting associations between molecular markers and agronomic traits is suggested.
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  • 95
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    Antonie van Leeuwenhoek 65 (1994), S. 21-28 
    ISSN: 1572-9699
    Keywords: black yeasts ; Hortaea werneckii ; mtDNA ; RFLP ; tinea nigra
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Fifteen isolates ofHortaea werneckii, causative agent of tinea nigra in man, were examined with respect to restriction fragment length polymorphisms of mitochondrial DNA. Seven types of mtDNA, interpreted as populations, could be distinguished, with similarities between the restriction patterns ranging from 32 to 79%. Much of the variance originated from length mutations. Of the seven populations four represented isolates from man, two of which also comprised isolates from other sources. This makes adaptation ofH. werneckii towards association with man in its evolution unlikely; similarity in the chemical and/or physical characteristics of the different isolation sources, viz. salinity, seems more probable. mtDNA types were not correlated with geographic origin. Isolates with the same mtDNA type are widely geographically distributed.
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  • 96
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    Euphytica 79 (1994), S. 175-179 
    ISSN: 1573-5060
    Keywords: Gene mapping ; genomic library ; Lycopersicon ; RFLP ; wild germplasm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The cultivated tomato contains only a small fraction of the genetic variation present in its wild relatives. In order to use the wild germplasm in tomato breeding and genetic studies we developed a new kind of genetic resource which is composed of 50 L. esculentum lines each containing a single introgression from the green fruited species L. pennellii (LA 716). Each of the introgression lines is nearly isogenic to the cultivated tomato; these lines provide complete coverage of the wild species genome. The lines contain on the average an introgression of 33 cM from a total genome size of 1200 cM. The size and identity of the introgressed segments was determined based on RFLP analysis of 350 markers. This resource can be viewed as a genomic library of the wild species in the cultivated background. It covers the entire genome with single independent ‘inserts’ per line and therefore every phenotypic difference between the introgression lines can be associated with the unique introgressed segment. The development and potential application of this resource are discussed.
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  • 97
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    Euphytica 80 (1994), S. 95-103 
    ISSN: 1573-5060
    Keywords: RFLP ; cpDNA ; clonal identification ; germplasm classification ; banana ; plantain ; Musa species
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Nineteen single-copy clones isolated from a PstI genomic library (cv. Maiden Plantain), and eight Vigna chloroplast DNA clones were used to probe total genomic DNA digests of 57 genotypes of Musa from India. The 19 genomic clones detected a total of 107 polymorphisms among the 57 genotypes. Principal coordinates and phenetic analyses of these data placed cultivars and species into distinct groups that were in general agreement with a previously published RAPD-based classification of these same plant materials. The 107 polymorphisms were sufficient to differentiate each clone from every other clone. Heterologous Vigna chloroplast DNA probes were used to characterize the cytoplasm of Musa cultivars and species. PCO analysis of these RFLPs were detected both within and between the generally recognized genome groups, indicating multiple hybridization pathways in the origin of hybrid clones. Data presented demonstrate that RFLPs are sufficiently abundant to classify Musa germplasm and that genetic relationships among Musa cultivars, based upon RFLP data, are in general agreement with relationships determined by analysis of morphology and RAPDs.
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  • 98
    ISSN: 1573-5060
    Keywords: cyst nematode ; Heterodera glycines ; diversity ; resistance ; RFLP ; RAPD ; soybean ; Glycine max
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Cultivar Peking has been extensively used as a source of resistance to Race 3 and Race 5 of soybean cyst nematode, Heterodera glycines I., and Peking genes for resistance are present in a wide range of resistant soybean cultivars. Peking is also used as a host differential in the soybean cyst nematode race classification system. Thirteen Peking lines maintained in the USDA Soybean Germplasm Collection and in several breeding programs were surveyed using RFLP and RAPD markers for genetic characterization. Based on the molecular diversity combined with reaction to soybean cyst nematode, Peking genotypes from a common original source were identified. Peking lines PI 297543 (introduction from Hungary), and PI 438496A, PI 438496B and PI 438496C (introductions from Russia) represented unrelated germplasms. Identified molecular polymorphism can be used to validate the genetic purity of Peking lines used as host differentials for soybean cyst nematode classification system as well as utilization of an individual germplasm line in genetic-breeding programs.
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  • 99
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    Euphytica 76 (1994), S. 177-183 
    ISSN: 1573-5060
    Keywords: M13 ; minisatellite ; common bean ; Phaseolus vulgaris ; genetic diversity ; RFLP ; DNA fingerprinting
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Analyses of genetic diversity within populations could be of great benefit to plant genetic resources conservation. In order to identify genetic markers that are variable within populations, the genome of Phaseolus vulgaris was screened with several DNA sequences in order to identify hypervariable sequences. Polymorphisms were observed between Middle American and Andean cultivars using the protein III tandem repeat of the M13 phase and the 33.15 human minisatellite. Extensive differences were observed when the DNA of two divergent lines—BAT93 and Jalo EEP558, of Middle American and Andean origin, respectively—were digested with HinfI, TaqI, HaeIII and hybridized with the 33.15 human minisatellite. Similarly, numerous polymorphisms were observed when the M13 protein III tandem repeat region was hybridized with TaqI digests of these cultivars. Polymorphism was also detected among sister lines of two F6 backcross materials involving Middle American and Andean lines when genomic DNA was digested with TaqI and hybridized with M13 tandem repeat region. In addition, polymorphism was observed among Porrillo cultivars that resulted from selection within a single landrace population. Whereas only one isozyme difference had been observed previously among the Porrillo cultivars, eleven restriction fragments detected by the M13 protein III tandem repeat sequence differentiated these cultivars. Ribosomal DNA also hybridized to several polymorphic bands on TaqI and EcoRI genomic Southern blots of the F6 backcross material. Only one polymorphism was observed with EcoRI-digested genomic DNA of BAT93 and Jalo EEP558 was hybridized with microsatellite (GACA)4. This probe might be useful in ascertaining relationships at the species and subspecies level, and as a marker in mapping studies. Our results show that both the human 33.15 minisatellite and M13 should be useful probes to detect within-population variability in common bean.
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  • 100
    ISSN: 1573-5060
    Keywords: cassava ; Manihot ; RFLP ; phylogenetic relationships ; multilocus probes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Two cloned cassava genes (pCAS6, pHNL) and a barley gene (pBLT63) which is highly conserved in higher plants, were evaluated as potential multilocus probes for RFLP analysis of phylogenetic relationships of species within the genus Manihot. For M. rubricaulis, M. chlorosticta and M. esculenta subsp. flabellifolia dendrograms based on 13 probe-restriction enzyme combinations show very little variation between accessions of the same species. A close relationship is demonstrated between the Mexican species M. chlorosticta and the M. esculenta subsp. flabellifolia accessions, which does not support the classification of flabellifolia as a true South American wild species.
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