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  • 1
    Electronic Resource
    Electronic Resource
    Genetic diversity of Striga hermonthica and Striga asiatica populations in Kenya (2005)
    Oxford, UK : Blackwell Science Ltd
    Weed research 45 (2005), S. 0 
    Details
    ISSN: 1365-3180
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: The parasitic angiosperms, Striga hermonthica and Striga asiatica, severely constrain cereal production in sub-Saharan Africa by causing huge losses in grain yield. Understanding the diversity of Striga populations is important because it allows identification of races or biotypes thus improving chances of breeding success. Amplified fragment length polymorphism (AFLP) analysis was used to study genetic diversity among 17 populations of S. asiatica and 24 populations of S. hermonthica from Kenya. A total of 349 DNA fragments ranging from 51 to 500 bp were obtained from four EcoRI and MseI primer combinations. Genetic distances for S. asiatica populations ranged from 0.009 to 0.116 with a mean of 0.032. S. hermonthica populations had a genetic distance that ranged from 0.007 to 0.025 with a mean of 0.015. Only two clusters were found in S. asiatica populations whereas no apparent structure was evident in S. hermonthica populations. There was no evidence of isolation by distance for the two species. Although the low genetic diversity suggests Striga is relatively uniform across the populations studied, it is possible that pathogenicity and virulence genes may be located in genomic regions that were not sampled. The data, however, does not provide evidence to support diversification of both Striga species in the region where the study was conducted.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-3180.2004.00432.x
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular characterization can quantify and partition variation among genebank holdings: a case study with phenotypically similar accessions of Brassica oleracea var. capitata L. (cabbage) `Golden Acre' (1997)
    Springer
    Theoretical and applied genetics 94 (1997), S. 227-234 
    Details
    ISSN: 1432-2242
    Keywords: Key words AMOVA ; Conservation ; Curation ; Genetic markers ; Molecular genetic screening ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To better characterize and conserve crop genetic resources, the assessment of genetic identity, relatedness, and structure among entries and collections becomes a priority. In the present study, a random amplified polymorphic DNA (RAPD) assay was applied as a quick, cost-effective, and preliminary screen to quantify and partition the molecular variation among accessions. Fourteen phenotypically uniform accessions of Brassica oleracea var. capitata L. (cabbage) similarly designated as `Golden Acre' were tested with nine decamer oligonucleotide primers. These amplifications generated 110 fragments, of which 80 were polymorphic ranging in size from 370 to 1720 bp. The 80 polymorphic fragments were sufficient to distinguish between all 14 accessions. Data based on the partitioning of variation among accessions indicated that `Golden Acre' entries could be reduced to as few as four groups, with the potential loss of variation being only 4.6% of the absolute current genetic variation in those holdings as estimated from RAPD analysis. This proposed grouping would concurrently save approximately 70% [$750–1000 (US) per accession] for each cycle of regeneration (approximately 20–25 years at most) which alternatively could then be used for other priorities in B. oleracea conservation and use. This case represents but one example where targeted use of a molecular-marker assay linked with rigorous statistical analysis will be useful for plant genebank management, particularly for questions at the intraspecific level. Molecular markers will provide genebank curators with additional sources of information to better plan and organize collection holdings and use finite financial support in a more effective manner.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050404
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  • 3
    Electronic Resource
    Electronic Resource
    Characterization and analysis of simple sequence repeat (SSR) loci in seashore paspalum (Paspalum vaginatum Swartz) (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 47-52 
    Details
    ISSN: 1432-2242
    Keywords: Simple sequence repeats ; Microsatellite ; Molecular marker ; Seashore paspalum ; Germ plasm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A size-fractionated TaqI genomic library of seashore paspalum (Paspalum vaginatum Swartz) was screened for the presence of (GA) n and (CA) n simple sequence repeats (SSRs). A total of 54 clones with a positive signal were detected among 13,000 clones screened. Forty-seven clones having repeats of n⩾ 3 were identified, of which 85% were perfect, 13% were imperfect and 2% were compound repeat sequences. Five of ten primer pairs synthesized to amplify selected loci resulted in a product in the expected size range and were subsequently used to examine SSR polymorphisms among 46 ecotypes of P. vaginatum. The number of alleles resolved on agarose or polyacrylamide gels were similar and ranged from 6 to 16 with an average of 14 per locus. Phenetic analysis of SSR polymorphisms revealed genetic relationships among the P. vaginatum ecotypes that were in general agreement with relationships determined previously by RAPD analysis of the same plant materials. Further screening of the genomic library did not identify (AT) n , trimeric or tetrameric repeats. Hybridization of an (ATT)8 oligonucleotide probe to genomic DNA isolated from I. batatas, E. coli, Citrullis lanatus and P. vaginatum suggested that the P. vaginatum genome contained significantly fewer ATT repeats than either the I. batatas or C. lanatus genome.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220857
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  • 4
    Electronic Resource
    Electronic Resource
    Abundance and characterization of simple-sequence repeats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed) (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 206-211 
    Details
    ISSN: 1432-2242
    Keywords: Genetic analysis ; Fluorescence-based detection ; STR ; Microsatellite DNA ; Multiplex PCR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A size-fractionated library of Brassica napus L. (rapeseed), composed of 15000 clones, was screened for the presence of GA-, CA-, and GATA-simple-sequence repeats (SSRs). GA-SSRs were four- and five-fold more abundant than CA- and GATA-SSRs, respectively, and present at a frequency of approximately one SSR for every 100 kb of DNA. Following the sequencing of 124 positive clones, primer pairs were designed and evaluated for seven selected SSRs. Products were amplified in an array of individuals of B. napus, B. oleracea and B. rapa, demonstrating that the seven SSRs were conserved among species. Two SSRs were polymorphic. Among 11 accessions, the dinucleotide (GA)-repeat, B.n.9A, yielded 12 fragments, while the tetranucleotide-repeat (GATA), B.n.6A2, revealed two fragments. Automated, fluorescence-based detection of polyacrylamide gels has been employed to simultaneously increase throughput, reduce unit cost, improve analytical resolution, and expedite data acquisition of SSR analysis. Though initial financial investment and technical capabilities may prevent some from directly employing our documented approach, SSR analysis warrants further investigation as a tool in genetic studies for enhancing both the conservation and utilization of genetic resources.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220879
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  • 5
    Electronic Resource
    Electronic Resource
    Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 534-538 
    Details
    ISSN: 1432-2242
    Keywords: Key words DNA marker ; Genetic analysis ; Genetic diversity ; Genotyping ; Microsatellite
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The application of simple sequence repeat (SSR) genotyping for the characterization of genetic variation in crop plants has been hindered by ready access to useful primer pairs and potentially limited conservation of the repeat sequences among related species. In this phase of work, we report on the identification and characterization of SSRs that are conserved in Brassica napus L. (rapeseed) and its putative progenitors, B. oleracea L. (cabbage, and related vegetable types) and B. rapa (vegetable and oil types). Approximately 140 clones from a size-fractionated genomic library of B. napus were sequenced, and primer pairs were designed for 21 dinucleotide SSRs. Seventeen primer pairs amplified products in the three species and, among these, 13 detected variation between and within species. Unlike findings on SSR information content in human, no relationship could be established between the number of tandem repeats within the target sequence and heterozygosity. All primer pairs have been designed to work under identical amplification conditions; therefore, single-reaction, multiplex polymerase chain reaction (PCR) with these SSRs is possible. Once moderate numbers of primer pairs are accessible to the user community, SSR genotyping may provide a useful method for the characterization, conservation, and utilization of agricultural crop diversity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050311
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  • 6
    Electronic Resource
    Electronic Resource
    Differentiation of bermudagrass (Cynodon spp.) genotypes by AFLP analyses (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 895-902 
    Details
    ISSN: 1432-2242
    Keywords: Key words AFLP (amplified fragment length polymorphism) ; Bermudagrass (Cynodon spp.) ; DNA fingerprinting ; Semi-automated fluorescence-based genotyping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Bermudagrasses (Cynodon spp.) are major turfgrasses for home lawns, public parks, golf courses and sport fields, and are widely adapted to tropical and warmer temperate climates. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subject to environmental influence. In this study, a DNA-typing technique, amplified fragment length polymorphism (AFLP), was used to differentiate bermudagrass genotypes and to explore their genetic relationships. Twenty seven bermudagrass cultivars and introductions, mostly from the Coastal Plain Experiment Station in Tifton, Ga., were assayed by the radioactive (32P) and the fluorescence-labeled AFLP methods. The AFLP technique produced enough polymorphism to differentiate all 27 bermudagrass genotypes, even the closely related ones. An average of 48–74 bands in the 30–600-bp size range was detected by the 32P-labeled AFLP method. The results indicated that most of the 14 primer combinations tested in this study could be used to distinguish bermudagrass genotypes, and that some single primer-pairs could differentiate all 27 of them. To test the reliability and reproducibility of the AFLP procedure, three DNA isolations (replications) of the 27 bermudagrass genotypes were assayed using five primer pairs. Only 0.6% of the bands were evaluated differently among the three replications. One replication of one genotype (which was most likely a planting contaminant) was grouped in an unexpected cluster using the Unweighted Pair Group Mean Average (UPGMA) method. A one- or two-band difference in scoring did not change the clustering of genotypes or the replications within genotypes. The 27 genotypes were grouped into three major clusters, many of which were in agreement with known pedigrees. Trees constructed with different primer combinations using 32P- and fluorescence-labelling formed similar major groupings. The semi-automated fluorescence-based AFLP technique offered significant improvements on fragment sizing and data handling. It was also more accurate for detection and more efficient than the radioactive labelling method. This study shows that the AFLP technique is a reliable tool for differentiating bermudagrass genotypes and for determining genetic relationships among them.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051148
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  • 7
    Electronic Resource
    Electronic Resource
    Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench] (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 190-198 
    Details
    ISSN: 1432-2242
    Keywords: Microsatellite ; Germplasm ; Genetic resources ; Genetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Simple sequence repeats (SSRs), also known as microsatellites, are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. Three approaches were followed for the development of PCR primers for the amplification of DNA fragments containing SSRs from sorghum [Sorghum bicolor (L.) Moench]: a search for sorghum SSRs in public DNA databases; the use of SSR-specific primers developed in the Poaceae species maize (Zea mays L.) and seashore paspalum grass (Paspalum vaginatum Swartz); and the screening of sorghum genomic libraries by hybridization with SSR oligonucleotides. A total of 49 sorghum SSR-specific PCR primer pairs (two designed from GenBank SSR-containing sequences and 47 from the sequences of genomic clones) were screened on a panel of 17 sorghum and one maize accession. Ten primer pairs from paspalum and 90 from maize were also screened for polymorphism in sorghum. Length polymorphisms among amplification products were detected with 15 of these primer pairs, yielding diversity values ranging from 0.2 to 0.8 with an average diversity of 0.56. These primer pairs are now available for use as markers in crop improvement and conservation efforts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00225745
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  • 8
    Electronic Resource
    Electronic Resource
    Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench] (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 190-198 
    Details
    ISSN: 1432-2242
    Keywords: Key words Microsatellite ; Germplasm ; Genetic resources ; Genetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Simple sequence repeats (SSRs), also known as microsatellites, are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. Three approaches were followed for the development of PCR primers for the amplification of DNA fragments containing SSRs from sorghum [Sorghum bicolor (L.) Moench]: a search for sorghum SSRs in public DNA databases; the use of SSR-specific primers developed in the Poaceae species maize (Zea mays L.) and seashore paspalum grass (Paspalum vaginatum Swartz); and the screening of sorghum genomic libraries by hybridization with SSR oligonucleotides. A total of 49 sorghum SSR-specific PCR primer pairs (two designed from GenBank SSR-containing sequences and 47 from the sequences of genomic clones) were screened on a panel of 17 sorghum and one maize accession. Ten primer pairs from paspalum and 90 from maize were also screened for polymorphism in sorghum. Length polymorphisms among amplification products were detected with 15 of these primer pairs, yielding diversity values ranging from 0.2 to 0.8 with an average diversity of 0.56. These primer pairs are now available for use as markers in crop improvement and conservation efforts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050265
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  • 9
    Electronic Resource
    Electronic Resource
    Characterization of genetic identities and relationships of Brassica oleracea L. via a random amplified polymorphic DNA assay (1992)
    Springer
    Theoretical and applied genetics 85 (1992), S. 190-196 
    Details
    ISSN: 1432-2242
    Keywords: DNA typing ; Genetic similarity ; Genetic structure ; Genetic resource conservation ; Vegetable and forage cole crops
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Effective conservation and the use of plant genetic resources are essential for future agricultural progress. Critical to this conservation effort is the development of genetic markers which not only distinguish individuals and accessions but also reflect the inherent variation and genetic relationships among collection holdings. We have examined the applicability of the random amplified polymorphic DNA (RAPD) assay for quick, cost-effective, and reliable use in addressing these needs in relation to collection organization and management. Twenty-five decamer oligonucleotide primers were screened individually with a test array composed of individuals representing a range of genetic relationships in Brassica oleracea L. (vegetable and forage cole crops). Over 140 reproducible, polymorphic fragments were generated for study. Each individual of the test array exhibited a unique molecular genotype and composites specific for accessions and botanical varieties could be established. An analysis of similarity based on amplified DNA fragments reflected the known genetic relationships among the selected entries. These results demonstrated that RAPD markers can be of great value in gene bank management for purposes of identification, measurement of variation, and establishment of genetic similarity at the intraspecific level.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222859
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  • 10
    Electronic Resource
    Electronic Resource
    Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 534-538 
    Details
    ISSN: 1432-2242
    Keywords: DNA marker ; Genetic analysis ; Genetic diversity ; Genotyping ; Microsatellite
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The application of simple sequence repeat (SSR) genotyping for the characterization of genetic variation in crop plants has been hindered by ready access to useful primer pairs and potentially limited conservation of the repeat sequences among related species. In this phase of work, we report on the identification and characterization of SSRs that are conserved in Brassica napus L. (rapeseed) and its putative progenitors, B. oleracea L. (cabbage, and related vegetable types) and B. rapa (vegetable and oil types). Approximately 140 clones from a size-fractionated genomic library of B. napus were sequenced, and primer pairs were designed for 21 dinucleotide SSRs. Seventeen primer pairs amplified products in the three species and, among these, 13 detected variation between and within species. Unlike findings on SSR information content in human, no relationship could be established between the number of tandem repeats within the target sequence and heterozygosity. All primer pairs have been designed to work under identical amplification conditions; therefore, single-reaction, multiplex polymerase chain reaction (PCR) with these SSRs is possible. Once moderate numbers of primer pairs are accessible to the user community, SSR genotyping may provide a useful method for the characterization, conservation, and utilization of agricultural crop diversity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00417944
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