Microsatellite markers in rice: abundance, diversity, and applications

McCouch, Susan R.; Temnykh, Svetlana V.; Lukashova, Angelika; Coburn, J.; DeClerck, Genevieve; Cartinhour, Samuel; Harrington, Sandra E.; Thomson, Michael J.; Septiningsih, Endang M.; Semon, Mandé; Moncada, P.; Li, Jiming

doi:10.1142/9789812814296_0008

Cited by 46 publications

(34 citation statements)

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“…This feature, in combination with the ease of PCR amplification, the co-dominant profiles and the potential for automation, has contributed to the widespread use of these markers in a range of genetic studies. SSR has been widely used in various plants and in rice alone it has been used to fingerprint accessions, analyze diversity, identify introgressions in interspecific crosses, trace pedigrees, locate genes and quantitative trait loci on rice chromosomes and in marker assisted selection [3] . The primary objective of this study was to differentiate 8 Bario rice cultivars in Sarawak and to determine their genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Sarawak Bario Rice Diversity Using Microsatellite Markers

Wong¹,

Hung²,

Bong³

et al. 2009

American J. of Agricultural and Biological Sciences

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Problem statement: There are numerous claims on varieties of Bario rice cultivars in Sarawak. Many of them might be synonyms or homonyms. This preliminary study was to differentiate Bario Rice cultivars using microsatellite molecular markers. Approach: Microsatellite marker panels distributed on all 12 chromosomes on rice genome were employed to study 8 Bario rice cultivars in Sarawak. Results: Current study indicated that the microsatellite panel were able to differentiate the 8 Bario rice cultivars. A total of 31 alleles were generated at 12 polymorphic microsatellite loci among the cultivars using the selected polymorphic SSR primer pairs with an average of 2.6 alleles per locus. Average PIC value obtained was 0.5204. An UPGMA dendrogram based on SSR polymorphism indicated high variation among the rice varieties with the coefficient ranging from 0.16 and 0.92. Genetic diversity determination using cluster analysis showed differentiation of rice cultivars into 2 major groups and several sub-groups. Conclusion: The SSR markers were useful for differentiating the genotypes and assessment of genetic relationships due to its reproducibility and to multiallelic, codominant and informative properties.

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Section: Introductionmentioning

confidence: 99%

Analysis of Sarawak Bario Rice Diversity Using Microsatellite Markers

Wong¹,

Hung²,

Bong³

et al. 2009

American J. of Agricultural and Biological Sciences

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“…This revealed significant differences in allelic diversity among various microsatellite loci. Many studies have also reported remarkable differences in allelic diversity among various microsatellite loci (Akagi et al, 1997;McCouch et al, 2001;Ravi et al, 2003;Ram et al, 2007). The alleles revealed by markers showed a higher degree of polymorphism.…”

Section: Discussionmentioning

confidence: 95%

Molecular characterization of wheat germplasm using microsatellite markers

Ijaz¹,

Khan²

2009

Genet. Mol. Res.

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ABSTRACT. We investigated the genetic diversity of 63 wheat genotypes, composed of 48 accessions and 15 varieties, using 56 polymorphic simple sequence repeat primers. One hundred and eighty-six loci were found, with a mean of 131.26 alleles per locus. Cluster analysis based on microsatellite allelic diversity discriminated the accessions and varieties into different clusters; genetic diversity was the highest between variety Kohistan-97 and accession number 011512, giving a genetic similarity value of 0.4198. Accession numbers 011484 and 011356 gave a genetic similarity value of 0.9589, indicating that these accessions were 95.89% similar. We found that microsatellite markers could characterize and discriminate all of the genotypes; more primers could be used for saturation of different regions in further studies.

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“…In recent years, high accuracy molecular markers like the single nucleotide polymorphism (SNP), which can detect variation at the DNA level are increasingly used for efficient characterization and evaluation of germplasm. Among the various classes of molecular markers available in rice, microsatellite markers (SSR markers) are the most popular markers due to their abundance, high discriminatory power, co-dominance, and economic use in both manual and automated systems (McCouch et al 2001). Thousands SSR markers for rice are already available (McCouch et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Upland Rice Landraces From Java Island as Revealed by SSR Markers

Sutoro

Lestari

Kurniawan

2015

Indones. J. Agric. Sci.

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Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic information content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.

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Microsatellite markers in rice: abundance, diversity, and applications

Cited by 46 publications

References 0 publications

Analysis of Sarawak Bario Rice Diversity Using Microsatellite Markers

Analysis of Sarawak Bario Rice Diversity Using Microsatellite Markers

Molecular characterization of wheat germplasm using microsatellite markers

Genetic Diversity of Upland Rice Landraces From Java Island as Revealed by SSR Markers

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