Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Abstract

Abstract:The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

Molecular characterization of edible pea through EST-SSR markers

“…The results of 20 EST-SST primer pairs showed clear bands and were applied to investigate the genetic diversity among selected pea lines. It was observed that five markers showed a different PCR product size range compared to the already reported size, which is in accordance with a previous observation (Gong et al, 2010). The PIC value is a measure of polymorphism for a marker locus used in linkage analysis (Shete et al, 2000) and determines the level of allelic variation.…”

“…The PIC value is a measure of polymorphism for a marker locus used in linkage analysis (Shete et al, 2000) and determines the level of allelic variation. In our study, the PIC value ranged from 0.32 to 0.63 with a mean of 0.50, compared to 0.18-0.58 with mean of 0.41 as previously reported (Gong et al, 2010). This value varied from 0.055 to 0.660 with a mean of 0.460 in the work of Ahmad et al (2012).…”

“…Another approach is to produce a dendrogram (or tree diagram), a grouping of samples together in clusters that are more genetically similar to each other than to samples in other clusters (Govindaraj et al, 2015). Our study divided all 23 pea lines into two main linkages that were further subdivided into seven subclusters, comparable to previous studies where cluster analysis grouped 35 pea accessions into two major clusters and eight subclusters (Gong et al, 2010;Xu et al, 2012;Zhang et al, 2013). Similarly, the study of Gixhari et al (2014) delineated 28 pea lines into 27 groups.…”

“…Loridon et al (2005) used EST-SSR markers for molecular mapping in pea. Gong et al (2010) also used EST-SSR markers in pea to determine its polymorphism and transferability.…”

Genetic Diversity Among Varieties and Hybrid Lines of Pea (pisum sativuml.) as Revealed by Morphological Traits and SSR Markers

“…The simple sequence repeats (SSR), also known as microsatellites, have been used on various collections of peas as a sole source of variation (Burstin et al, 2001;Choudhury et al, 2006;Nasiri et al, 2009 andSarıkamı et al, 2010) and in combination with morphological variation (Tar'an et al, 2005;Smykal et al, 2008;Tihomir et al, 2009;Sarikamis et al, 2010 andSmýkal et al, 2012). Although several hundreds of simple sequence repeats (SSR) markers have been identified (Burstin et al, 2001;Loridon et al, 2005;Zong et al, 2008 andGong et al, 2010). Additional SSR markers with polymorphism are needed, for the development of linkage maps for use in breeding new varieties with resistant to white mold disease and for mapping studies (Zhuang et al, 2013).…”