Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat

Abstract

Genetic variation present in 64 durum wheat accessions was investigated by using three sources of microsatellite (SSR) markers: EST-derived SSRs (EST-SSRs) and two sources of SSRs isolated from total genomic DNA. Out of 245 SSR primer pairs screened, 22 EST-SSRs and 20 genomic-derived SSRs were polymorphic and used for genotyping. The EST-SSR primers produced high quality markers, but had the lowest level of polymorphism (25%) compared to the other two sources of genomic SSR markers (53%). The 42 SSR markers detected 189 polymorphic alleles with an average number of 4.5 alleles per locus. The coefficient of similarity ranged from 0.28 to 0.70 and the estimates of similarity varied when different sources of SSR markers were used to genotype the accessions. This study showed that EST-derived SSR markers developed in bread wheat are polymorphic in durum wheat when assaying loci of the A and B genomes. A minumum of ten EST-SSRs generated a very low probability of identity (0.36x10(-12)) indicating that these SSRs have a very high discriminatory power. EST-SSR markers directly sample variation in transcribed regions of the genome, which may enhance their value in marker-assisted selection, comparative genetic analysis and for exploiting wheat genetic resources by providing a more-direct estimate of functional diversity.

A new integrated genetic linkage map of the soybean

“…Markers derived from genomic libraries also contained more repeat units as well as a greater range of allele sizes and genetic diversity than markers isolated from EST libraries. The striking difference of polymorphism between the soybean SSRs derived from the two sources is consistent with differences reported in rice (Temnykh et al 1999;Cho et al 2000), sugarcane (Cordeiro et al 2001), tomato (Arshchenkova and Ganal 2002), wheat (Eujayl et al 2002), and barley (Thiel et al 2003). For example, Arshchenkova and Ganal (2002) reported that only 20 of 27,000 tomato ESTs contained microsatellites of more than ten repeat units.…”

“…Some ESTs contain di-and trinucleotide-repeat motifs, making EST collections a potential source of microsatellite markers. The use of ESTs as a source of SSRs has been reported in a number of crop species including rice (Cho et al 2000), grape (Scott et al 2000), barley (Kota et al 2001), sugarcane (Cordeiro et al 2001), and wheat (Eujayl et al 2002).…”

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

“…(Peng and Lapitan 2005). In the present study, higher PIC value for gSSRs versus EST-SSRs suggesting that transcribed portions of the genome are conserved in the genomes (La Rota et al 2005;Eujayl et al 2002). In multiple reports, inconsistency in PIC values data have been reported (Kebede et al 2007;Liu et al 2000;Kalivas et al 2011) which is attributed to the kind of germplasm explored, bottleneck in domestication (Thuillet et al 2004;Vigouroux et al 2005) and the kind of DNA markers (Liu et al 2000;Gutierrez et al 2002).…”

Development and Application of Est-Ssr Markers in Quails

“…SSRs developed from ESTs has been reported in many plants, such as grapes (Pen et al, 2005), wheat (Eujayi et al, 2002), and barley (Thie et al, 2003), also in animals, such as zebra fish (Serapion et al, 2004), prawns (Perez et al, 2005,Zhang et al, 2010, catfish (Ju et al, 2005), sheep (Yan et al, 2007,Wang et al, 2010,Wang et al, 2011a,Wang et al, 2011b,Zhang et al, 2014, goat (Feng et al, 2008,Zhao et al, 2009, and silkworms (Bombyx mori; Mi et al, 2011). EST, as a new developed molecular marker, reflects the gene encoding part.…”