Transferability of cereal EST-SSR markers to ryegrass

Abstract

A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of cereal EST-SSRs in ryegrass (Lolium spp.). A total of 165 cereal EST-SSRs were tested; a high rate of transferability (57%) and polymorphism (67% of functional EST-SSRs) was demonstrated between cereals and ryegrass. A total of 46 segregating loci derived from 37 EST-SSRs were mapped on an existing ryegrass genetic map. The mapped loci were uniformly distributed across all seven linkage groups without significant clustering at the distal regions of linkage groups. Sequences of ryegrass amplicons generated by randomly selected 16 EST-SSRs were aligned with reference sequences of cereal EST-SSRs. The SSR motifs and repeat lengths of the cereal EST-SSR markers were different from the majority of ryegrass amplicons. Furthermore, a majority of EST-SSRs amplified different flanking sequences of SSRs in ryegrass than the original cereal sequences. Our results suggest that the high degree of cereal EST-SSR transferability to ryegrass can be a useful enhancement to the molecular database of PCR-based markers but sequence analysis is essential before transferring genetic information using comparative mapping.

Characterization of novel genic SSR markers in Linum usitatissimum (L.) and their transferability across eleven Linum species

“…The remarkable level of transferability supports previous findings in other plant species (Saha et al 2004;Varshney et al 2005;Pashley et al 2006;Fu and Peterson, 2010). These results confirm the usefulness of EST-SSRs since they are derived from transcribed and conserved regions of the DNA, allowing cross-species transferability Sim et al 2009). In addition, the four botanical sections belong to the genus Linum; for which higher rates of transferability of EST-SSR loci is expected within genus Pashley et al 2006) as confirmed by ≈ 65% of average cross amplification in our study.…”

“…In fact, sequencing PCR amplicons of EST-SSRs have shown high similarities, especially within genus (Zhang et al 2005;Pashley et al 2006). Our results suggest that EST-SSRs might help to elucidate the evolutionary relationships of Linum species, providing genetic information from cultivated flax to its wild relatives and vise versa (Sim et al 2009). Among polymorphic loci in L. usitatissimum, 69.6% showed polymorphism across Linum species.…”

“…On the other hand, 34.1% of them disclosed multi allele/loci compared to L. usitatisimum amplicons which might entail intra-species variation as a consequence of bulked samples. By the contrary, other possible reason could be the high rate of conservation of EST sequences, suggesting amplifications from either orthologous or paralogous copies (Saha et al 2004;Sim et al 2009), particularly in polyploidy species such as L. narbonense (Muravenko et al 2010). Similarly, Yu et al (2004) reported that 39% of EST-SSRs detected multiple loci in wheat (hexaploide).…”

Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions

“…Between species within a genus, EST-SSR marker transferability reported varies from 26 to 100% (Ma et al 2009;Moccia et al 2009;Sharma et al 2009;Tang et al 2009). Transferability reported between species from different genera varies between 11 and 86% (Saha et al 2004;Varshney et al 2005;Heesacker et al 2008;Chapman et al 2009;Choudhary et al 2009;Raji et al 2009;Sim et al 2009). The subgenome transferability of EST-SSR markers in switchgrass estimated in this study is comparable to transferability between distantly related species within a genus or species from closely related genera in other plants.…”

Rapid identification of red-flesh loquat cultivars using EST-SSR markers based on manual cultivar identification diagram strategy

“…Since the EST-SSR markers are derived from transcribed regions of DNA, they are expected to be more conserved and have a higher rate of transferability and polymorphism than genomic SSR markers (Decroocq et al, 2003). Therefore, in view of the utilization of the transferability of EST microsatellite markers across taxa or from related species (Saha et al, 2004;Sim et al, 2009), EST-SSR markers could be an alternative approach for species with few EST sequences distributed in the NCBI (National Center for Biotechnology Information) database.…”