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  • 1
    Electronic Resource
    Electronic Resource
    Identification of minor DNA variations in rice somaclonal variants (1998)
    Springer
    Plant cell reports 18 (1998), S. 55-58 
    Details
    ISSN: 1432-203X
    Keywords: Key words Rice somaclonal variants ; Microsatellites ; Genetic polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Some somaclonal variants derived from a landrace rice variety, Indrayani, were shown to be high yielding and resistant to multiple diseases in previous analysis carried out in our laboratory. An attempt was made to assess the effect of culturing and regeneration of rice plants on DNA variation at microsatellite loci in R2 progeny of callus-derived rice plants. Different somaclones of the rice line Indrayani differing in yield and disease response (high, low and no change in yield, as compared to the original genotype) were used as genetic material for these analyses. Analysis of microsatellite loci was accomplished by digesting DNA from regenerated rice somaclones and assaying for polymorphisms at microsatellite loci by in-gel hybridization with synthetic oligonucleotide probes such as (GATA)4, (CAC)5 and (TG)10. Specific variation at a PCR-amplified locus containing three internal microsatellite repeats (1E6) using restriction site fingerprinting was also investigated. The locus-specific amplification of a sequence-tagged microsatellite marker followed by digestion with HinfI and Sau3AI restriction endonucleases showed differences in some somaclonal variants. The technique used in this study enables monitoring of DNA changes in successive generations of somaclonal variants as a measure of DNA variability and possibly to identify the regions which are responsible for specific traits.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002990050531
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  • 2
    Electronic Resource
    Electronic Resource
    DNA fingerprinting to detect genetic variation in rice using hypervariable DNA sequences (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 1000-1006 
    Details
    ISSN: 1432-2242
    Keywords: DNA fingerprinting ; Genetic variation ; Hypervariable DNA sequences ; Rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The suitability of miniand microsatellite related DNA sequences capable of detecting multiple loci was investigated for their ability to generate DNA fingerprints in rice. These included R18.1, a cattle-derived probe, the M13 repeat probe, pV47, a human minisatellite probe; and repeats in the Per gene, telomere, chi sequence and 3′ hypervariable region of apolipoprotein B. With the R18.1, pV47 and M13 repeat probes, the level of polymorphism was high enough to identify all of the cultivars and wild rice species used in this study. R18.1, which showed the highest level of polymorphism, was estimated to identify up to 2.5×1020 genotypes of rice. In a F2 population of a ‘Basmati-370’ and ‘Taichung-65’ cross, loci detected by R18.1 segregated in a Mendelian fashion. DNA fingerprints were somatically stable and the hybridization patterns were identical among different plants of the same cultivar. Application of the above molecular genetic markers for identification of rice genotypes is reported here for the first time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222913
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  • 3
    Electronic Resource
    Electronic Resource
    Evolutionary and polymorphic organization of the knotted1 homeobox in cereals (1998)
    Springer
    Theoretical and applied genetics 97 (1998), S. 135-140 
    Details
    ISSN: 1432-2242
    Keywords: Key words Homeobox ; Intron ; Cereals ; Phylogeny ; Ancestry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Homeobox genes are the master control genes harbouring the homeobox which is crucial for developmental associated functions. One homeobox gene, knotted1, which has a role in leaf development, is conserved in plants and might have arisen from a single ancestral gene. Using PCR, we identified multiple kn1 homeoboxes in diverse cereals and showed a cereal/ species-specific organization correlating them to evolutionary changes. We postulate the insertion of a large intron preceded by duplication of the kn1 homeobox in the lineage leading to rice.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050877
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  • 4
    Electronic Resource
    Electronic Resource
    Phylogenetic classification and molecular evolution of knotted1 homeobox genes (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 203-209 
    Details
    ISSN: 1432-2242
    Keywords: Key words Homeobox gene ; KNOTTED1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Homeobox genes encode a family of DNA-binding regulatory proteins which are crucial for development. The first plant homeobox gene identified was knotted1 which plays a major role in leaf development. The knotted1 gene has a homeobox which encodes a homeodomain (HD) and HD proteins have been shown to function as transcription factors. A phylogenetic classification of the KNOTTED1 HD is presented. Here, we report six kn1 HDs from the cereals oat, barley, wheat, rye and rice. The KN1 class-I and -II genes can be divided into two distinct clades. Further, we hypothesize that KN1 and BELL1/MEIS HDs, (the closest non-KN1 class HDs) evolved from a common ancestor after divergence from the common precursor of all the homeobox genes. Our analysis clearly shows the presence of an ancestral KN1 HD from which all the known plant kn1 class of genes evolved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051226
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  • 5
    Electronic Resource
    Electronic Resource
    DNA fingerprinting detects genetic variability in the pearl millet downy mildew pathogen (Sclerospora graminicola) (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 856-861 
    Details
    ISSN: 1432-2242
    Keywords: Downy mildew ; Microsatellites ; DNA fingerprinting ; Pearl millet
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genetic variability in six host genotype-specific pathotypes of pearl millet downy mildew pathogen S. graminicola was studied at the molecular level using mini- and micro-satellites. Our results indicated that microsatellites (GAA)6, (GACA)4, and especially (GATA)4 were quite informative and showed high levels of polymorphism among the pathotypes. The six pathotypes could be classified into five groups based on the cluster analysis of their genetic similarities, thereby confirming the existence of distinct host genotype-specific virulence in S. graminicola pathotypes. We demonstrate, for the first time, the use of DNA fingerprinting to detect genetic variation in downy mildew fungus of pearl millet.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223892
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  • 6
    Electronic Resource
    Electronic Resource
    Microsatellite (GATA)n reveals sex-specific differences in Papaya (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 1047-1052 
    Details
    ISSN: 1432-2242
    Keywords: Key words Dioecious plants ; Carica ; Papaya ; Seedling sex diagnosis ; Microsatellites ; An Indian patent pending
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Papaya, an economically important fruit plant, is polygamous in nature. The sex of dioecious papaya plants can be deduced only after they attain reproductive maturity (6–8 months). Normally, 50% of the population in a field is composed of unfruitful male plants and almost 45% of these have to be uprooted at the flowering stage. This unnecessary cultivation of unwanted males leads to wastage of resources, which can be avoided if the sex of the plant is determined at juvenile stage. Morphological and cytological studies conducted so far have failed to differentiate between the various sex forms of papaya. Its dioecious nature, occasional sex-reversal of male flowers and the absence of a heteromorphic pair of sex chromosomes make papaya an interesting system to study sex determination at the molecular level. In the present study, highly informative microsatellite and minisatellite probes were employed to identify sex-specific differences in papaya. Among these, only the microsatellite probe (GATA)4 demonstrated sex-specific differences in all the cultivars analysed. The diagnostic potential of this microsatellite marker was exploited to sex papaya plants at the seedling stage. This study also indicates that the genetic material of the X and Y chromosomes of papaya is diverging in a sex-specific manner and hence they are in the process of differentiation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051413
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  • 7
    Electronic Resource
    Electronic Resource
    Sequence variations at a complex microsatellite locus in rice and its conservation in cereals (2000)
    Springer
    Theoretical and applied genetics 101 (2000), S. 1291-1298 
    Details
    ISSN: 1432-2242
    Keywords: Key words Microsatellite ; Sequence variation ; Genetic diversity ; Cereals
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  In an attempt to study changes associated with microsatellites in rice, the DNAs of cultivated rice, including indica and japonica varieties, and wild rice genotypes were amplified by the polymerase chain reaction with primers flanking the (GATA) n and (AC) n repeats at a microsatellite-containing locus OS1E6 (Genebank accession number AFO16647) previously reported from a PstI rice (var. Malkolam) genomic library in pUC18. Eight alleles of varying sizes were obtained which were cloned and sequenced. Sequencing data indicated that the size variations of the different alleles were due to differences in the repeat number as well as to sequence variations in the region flanking the microsatellite motifs. In order to study the presence of this complex microsatellite-containing locus of rice in different cereals, their DNAs were amplified using primers flanking the OS1E6 locus. It was found that this locus was present in the various cereal genotypes analyzed, indicating its conservation across different cereal members.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051609
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  • 8
    Electronic Resource
    Electronic Resource
    Expansion of a (GA) Dinucleotide at a Microsatellite Locus Associated with Domestication in Rice (1998)
    Springer
    Biochemical genetics 36 (1998), S. 323-327 
    Details
    ISSN: 1573-4927
    Keywords: RICE ; MICROSATELLITE ; REPEAT EXPANSION ; DOMESTICATION EVOLUTION
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Microsatellites undergo rapid changes over shortevolutionary time periods which can be phylogeneticallyinformative in related species. Here we show the repeatunit expansion of a (GA)n-type microsatellite in the process of cultivation of rice from itswild ancestors. We amplified a microsatellite locusharboring (GA)n repeats from several wild andcultivated rices. Sequencing revealed an increase inrepeat number from 14 in distantly related wild ricespecies to 24 in the widely grown present-day indicarice cultivars.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1018793328896
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  • 9
    Electronic Resource
    Electronic Resource
    (CAC)5 detects DNA fingerprints and sequences homologous to gene transcripts in rice (1994)
    Springer
    Biochemical genetics 32 (1994), S. 1-8 
    Details
    ISSN: 1573-4927
    Keywords: rice ; simple repetitive sequence ; DNA fingerprinting ; (CAC)5 ; poly(A)+ transcripts
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract In the present report the potential of (CAC)5 is demonstrated for DNA fingerprinting in rice. Based on the fingerprint data, (CAC)5 was estimated to differentiate up to 6.3×108 genotypes of rice. In a search for homologous sequences in rice transcripts, four oligonucleotide probes, namely, (CAC)5, (GATA)4, (GACA)4, and (TG)10, were used. Among these probes, (CAC)5 showed hybridization to total rice RNA in a tissue-specific manner; while a band at 1.2 kb was common in both seed and leaf RNA, there were additional prominent bands at 1.9 and 2.3 kb in seed and leaf RNA, respectively. When (CAC)5 was hybridized to poly(A)+ RNA, in addition to a band at 1.2 kb in seed and leaf, hybridization was observed only in seed to heterogeneously sized RNAs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00557234
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  • 10
    Electronic Resource
    Electronic Resource
    DNA fingerprinting of Indian isolates of Xanthomonas oryzae pv. oryzae (1997)
    Springer
    Theoretical and applied genetics 95 (1997), S. 103-111 
    Details
    ISSN: 1432-2242
    Keywords: Key words DNA fingerprinting ; Xanthomonas ; Bacterial blight ; Rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A high level of genetic polymorphism was detected among Indian isolates of Xanthomonas oryzae pv. oryzae using hypervariable probes such as a microsatellite oligonucleotide, probe (TG)10, a human minisatellite probe, pV47, an avirulence gene probe, avrXa10 and a repeat clone, pBS101. These DNA probes detected multiple loci in the bacterial genome generating complex DNA fingerprints and differentiated all of the bacterial isolates. Analysis of fingerprints indicated that pV47, (TG)10 and pBS101 have a lower probability of identical match than avrXa10 and therefore are potential probes for DNA fingerprinting and variability analysis of Xanthomonas oryzae pv. oryzae pathogen populations. Cluster analysis based on hybridization patterns using all of the above probes showed five groups at 56% similarity. Studies on the methylation patterns of isolates representing the three important races of X. oryzae pv. oryzae indicated more methylation in the most virulent isolate, suggesting a possible role of methylation in pathogenicity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050537
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