The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat

Prasad, Manoj; Varshney, Rajeev K.; Roy, Joy; Balyan, H. S.; Gupta, P. K.

doi:10.1007/s001220050077

Cited by 103 publications

(83 citation statements)

References 28 publications

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“…Therefore the number of alleles can be used for the evaluation of genetic diversity. Our results did not agree with those of Prasad et al (2000) who reported that the PIC value was not correlated with the number of alleles. A large sample size is necessary for the characterization of a reliable correlation coefficient.…”

Section: Discussioncontrasting

confidence: 57%

“…Ganal tifying QTLs (Parker et al 1998), marker-assisted selection in wheat (Korzun et al 1998;Huang et al 2000a) and verifying the integrity and genetic stability of gene bank accessions (Börner et al 2000a). Such markers also revealed a high level of polymorphism among diploid species , in the accessions of tetraploid wild wheat Triticum dicoccoides (Fahima et al 2002) and of Aegilops tauschii, the D-genome donor of bread wheat (Pestsova et al 2000), and as well as in hexaploid wheat varieties (Plaschke et al 1995;Donini et al 1998;Prasad et al 2000;Stachel et al 2000).…”

Section: Introductionmentioning

confidence: 99%

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Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers

et al. 2002

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A set of 24 wheat microsatellite markers, representing at least one marker from each chromosome, was used for the assessment of genetic diversity in 998 accessions of hexaploid bread wheat ( Triticum aestivum L.) which originated from 68 countries of five continents. A total of 470 alleles were detected with an average allele number of 18.1 per locus. The highest number of alleles per locus was detected in the B genome with 19.9, compared to 17.4 and 16.5 for genomes A and D, respectively. The lowest allele number per locus among the seven homoeologous groups was observed in group 4. Greater genetic variation exists in the non-centromeric regions than in the centromeric regions of chromosomes. Allele numbers increased with the repeat number of the microsatellites used and their relative distance from the centromere, and was not dependent on the motif of microsatellites. Gene diversity was correlated with the number of alleles. Gene diversity according to Nei for the 26 microsatellite loci varied from 0.43 to 0.94 with an average of 0.77, and was 0.78, 0.81 and 0.73 for three genomes A, B and D, respectively. Alleles for each locus were present in regular two or three base-pair steps, indicating that the genetic variation during the wheat evolution occurred step by step in a continuous manner. In most cases, allele frequencies showed a normal distribution. Comparative analysis of microsatellite diversity among the eight geographical regions revealed that the accessions from the Near East and the Middle East exhibited more genetic diversity than those from the other regions. Greater diversity was found in Southeast Europe than in North and Southwest Europe. The present study also indicates that microsatellite markers permit the fast and high throughput fingerprinting of large numbers of accessions from a germplasm collection in order to assess genetic diversity.

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Section: Discussioncontrasting

confidence: 57%

Section: Introductionmentioning

confidence: 99%

Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers

et al. 2002

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“…The genetic distance and dendrogram was constructed for rice (Oryza sativa L.) using ten microsatellites (Garland et al 1999) and 15 microsatellites in barley (Hordeum vulgare L.) (Struss and Plieske 1998). Twelve microsatellite loci were used for chromosomal inheritance studies of 59 wheat cultivars (Pestsova and Röder 2002), and a set of 12 primer pairs were able to distinguish 48 wheat genotypes (Prasad et al 2000).…”

Section: Microsatellite Analysis Of the Wi 3a And Cnn 3a Chromosomesmentioning

confidence: 99%

The use of microsatellite markers for the detection of genetic similarity among winter bread wheat lines for chromosome�3A

et al. 2004

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Previous studies with chromosome substitution and recombinant inbred chromosome lines identified that chromosome 3A of wheat cv. Wichita contains alleles that influence grain yield, yield components and agronomic performance traits relative to alleles on chromosome 3A of Cheyenne, a cultivar believed to be the founder parent of many Nebraska developed cultivars. This study was carried out to examine the genetic similarity among wheat cultivars based on the variation in chromosome 3A. Forty-eight cultivars, two promising lines and four substitution lines (in duplicate) were included in the study. Thirty-six chromosome 3A-specific and 12 group-3 barley simple sequence repeat (SSR) primer pairs were used. A total of 106 polymorphic bands were scored. Transferability of barley microsatellite markers to wheat was 73%. The coefficient of genetic distance (D) among the genotypes ranged from 0.40 to 0.91 and averaged D=0.66. Cluster analysis by the unweighted pair-group method with arithmetic averages showed one large and one small cluster with eight minor clusters in the large cluster. Several known pedigree relationships largely corresponded with the results of SSR clusters and principal coordinate analysis. Cluster analysis was also carried out by using 22 alleles that separate Wichita 3A from Cheyenne 3A, and three clusters were identified (a small cluster related to Cheyenne of mainly western Nebraska wheat cultivars; a larger, intermediate cluster with many modern Nebraska wheat cultivars; a large cluster related to Wichita with many modern high-yielding or Kansas wheat cultivars). Using three SSR markers that identify known agronomically important quantitative trait loci (QTL) regions, we again separated the cultivars into three main clusters that were related to Cheyenne or Wichita, or had a different 3A lineage. These results suggest that SSR markers linked to agronomically important QTLs are a valuable asset for estimating both genetic similarity for chromosome 3A and how the chromosome has been used in cultivar improvement.

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“…Because of their abundance, high polymorphism between individuals within populations or closely related genotypes and their multiallelic and codominant nature allowing the genotype establishment of individuals, microsatellite markers have been used for individual identification, diversity analysis (Powell et al 1996) and evolutionary and population structure studies of related species. In plants, they have been successfully used to map genomes of cereal species such as rice (Davierwala et al 2000) or soybean (Rongwen et al 1995), to fingerprint cultivars and breeding lines of barley (Pillen et al 2000), wheat (Prasad et al 2000), rapeseed, chickpea and sugar beet, to detect genetic diversity and carry out phylogenetic analysis on Cucumis (Danin-Poleg et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Structure and level of genetic diversity in various bean types evidenced with microsatellite markers isolated from a genomic enriched library

et al. 2002

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We have constructed a common bean genomic library enriched for microsatellite motifs (ATA), (CA), (CAC) and (GA). After screening, 60% of the clones selected from the library enriched for the (ATA) repeat contained microsatellites versus 21% of the clones from the library enriched for (GA) (CA) and (CAC) repeats. Fifteen primer pairs have been developed allowing for the amplification of SSR loci. We have evaluated the genetic diversity of these loci between 45 different bean lines belonging to nine various quality types. A total of 81 alleles were detected at the 15 microsatellite loci with an average of 5.3 alleles per locus. We have investigated the origin of allelic size polymorphism at the locus PvATA20 in which the number of repeats ranges from 24 to 85. We have related these large differences in repeat number to unequal crossing-over between repeated DNA regions. The diversity analysis revealed contrasted levels of variability according to the bean type. The lower level was evidenced for the very fine French bean, showing the effect of breeders intensive selection.

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The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat

Cited by 103 publications

References 28 publications

Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers

Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers

The use of microsatellite markers for the detection of genetic similarity among winter bread wheat lines for chromosome�3A

Structure and level of genetic diversity in various bean types evidenced with microsatellite markers isolated from a genomic enriched library

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