Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice

Varshney, Rajeev K.; Sigmund, Ralf; Börner, Andreas; Korzun, Viktor; Stein, Nils; Sorrells, Mark E.; Langridge, Peter; Graner, Andreas

doi:10.1016/j.plantsci.2004.08.001

Cited by 266 publications

(198 citation statements)

References 31 publications

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“…Since ESTs or genes represent the transcribed regions of the genome (transcriptome), which are considered more conserved portions of the genome, transcriptome-derived markers generally have a lower polymorphism content (Varshney et al 2005a). Nevertheless such markers are supposed to be more transferable between related species (Varshney et al 2005b). Thus, depending on the objective, genomic DNA-derived SSR markers with higher PIC value (for breeding purpose) or EST/gene-derived SSR markers with a lower PIC value (for using across the cereal species) may be selected from the present consensus map.…”

Section: Features Of the Barley Ssr Consensus Mapmentioning

confidence: 99%

A high density barley microsatellite consensus map with 775 SSR loci

Varshney

Marcel

Ramsay³

et al. 2007

Theor Appl Genet

301

230

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Section: Features Of the Barley Ssr Consensus Mapmentioning

confidence: 99%

A high density barley microsatellite consensus map with 775 SSR loci

Varshney

Marcel

Ramsay³

et al. 2007

Theor Appl Genet

301

230

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“…This is particularly true in plants, where transferability among economically important crop taxa has been demonstrated on a number of occasions (Decroocq et al, 2003;Thiel et al, 2003;Bandopadhyay et al, 2004;Saha et al, 2004;Varshney et al, 2005b). Until recently, however, little attention had been paid to the potential for transferring EST-SSRs from well-characterized taxa to lesser studied relatives as a means for facilitating evolutionary analyses (but see Arnold et al, 2002;Ellis et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

EST-SSRs as a resource for population genetic analyses

2007

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Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.

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“…SSR markers tend to be among the most polymorphic genetic marker types and have been introduced into the process of cultivar and variety identification as well as in pedigree reconstruction and genetic mapping (Holton et al, 2002;Yu et al, 2004a;Celucia et al, 2009), to analyze functional diversity (Senior et al, 1998;Leigh et al, 2003;Dreisigacker et al, 2004), and for comparative mapping (Yu et al, 2004b;Varshney et al, 2005a). Although the identification of SSRs in gene sequences of plants started as early as 1993 (Varshney et al, 2005b), full exploitation of this marker during this period was limited by the amount of sequence data available for SSR analysis, and therefore, only a few genomic SSRs were reported. The increase in the amount of sequence data generated from expressed sequence tag (EST) projects in tomato and several other plant species has facilitated the identification of genomic SSRs in large numbers .…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

Korir¹,

Diao²,

Tao³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

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Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice

Cited by 266 publications

References 31 publications

A high density barley microsatellite consensus map with 775 SSR loci

A high density barley microsatellite consensus map with 775 SSR loci

EST-SSRs as a resource for population genetic analyses

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

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