EST versus Genomic Derived Microsatellite Markers for Genotyping Wild and Cultivated Barley

Abstract

Genetic variation present in wild and cultivated barley populations was investigated using two sources of microsatellite also known as simple sequence repeat (SSR) markers. EST-SSRs are derived from expressed sequences and genomic SSRs are isolated from genomic DNA. Genomic SSR markers detected a higher level of polymorphism than those derived from ESTs. Polymorphism information content was higher in genomic SSRs than EST-derived SSRs. This study showed that the EST-SSR markers developed in cultivated barley are polymorphic in wild and cultivated varieties and produced high quality markers. Ten of these functional markers were polymorphic across the accessions studied. EST markers indicated clearer separation between wild and cultivated barley than genomic SSRs. The EST-SSRs are a valuable source of new polymorphic markers and should be highly applicable to barley genetic resources, providing a direct estimate of functional biodiversity.

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

“…The difference in genome coverage is thought to reflect the processes used to develop each type of marker. Anonymous SSRs are usually developed from random genomic libraries, in which microsatellites located in the heterochromatic regions are over-represented (Roder et al, 1998) and the development of EST-SSRs from genic regions reduces the representation of regions that are rich in repetitive DNA (Parida et al, 2006;Chabane et al 2005). It appeared that DArT markers may have a stronger tendency than genomic SSR and AFLP markers in particular, to map to gene-rich regions (Vuylsteke et al 1999) provided that the right combinations of endonucleases are used in complexity reduction.…”

EST-SSRs as a resource for population genetic analyses

“…Another obvious concern is that since EST-SSRs are located within genes, and thus more conserved across species, they may be less polymorphic than anonymous SSRs. This concern has been borne out in a number of taxa, including rice (Cho et al, 2000), bread wheat (Gupta et al, 2003), pines (Liewlaksaneeyanawin et al, 2004), barley (Chabane et al, 2005) and sunflower . However, the levels of genetic diversity revealed by these markers are still considerably higher than those revealed by most alternative marker types, such as allozymes (Hamrick and Godt, 1996).…”

Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

“…In plants, genomic SSRs revealed much-higher genetic diversity than that revealed by EST-SSRs (for example, Chabane et al, 2005;Peleg et al, 2008). In this study, relatively lower polymorphism was detected using 26 pairs of EST-SSR primers (H E ¼ 0.284, ranged 0.240-0.336) in R. oldhamii populations compared with that utilizing genomic-derived SSR markers in R. brachycarpum (H E ¼ 0.815, ranged 0.676-0.913; Hirao, 2010) and R. ripense (H E ¼ 0.800, ranged 0.794-0.809; Kondo et al, 2009) of Japan, and R. simsii of China (H E ¼ 0.754, ranged 0.278-0.944; Tan et al, 2009).…”