Exploring the genetic diversity of Ethiopian grass pea (Lathyrus sativus L.) using EST-SSR markers

Abstract

Expressed sequence tags (ESTs) in public databases and cross-species transferable markers are considered to be a cost-effective means for developing sequence-based markers for less-studied species. In this study, EST-simple sequence repeat (SSR) markers developed from Lathyrus sativus L. EST sequences and cross-transferable EST-SSRs derived from Medicago truncatula L. were utilized to investigate the genetic diversity among grass pea populations from Ethiopia. A total of 45 alleles were detected using eleven EST-SSRs with an average of four alleles per locus. The average polymorphism information content for all primers was 0.416. The average gene diversity was 0.477, ranging from 0.205 for marker Ls942 to 0.804 for MtBA32F05. FST values estimated by analysis of molecular variance were 0.01, 0.15, and 0.84 for among regions, among accessions and within accessions respectively, indicating that most of the variation (84%) resides within accessions. Model-based cluster analysis grouped the accessions into three clusters, grouping accessions irrespective of their collection regions. Among the regions, high levels of diversity were observed in Gojam, Gonder, Shewa and Welo regions, with Gonder region showing a higher number of different alleles. From breeding and conservation aspects, conducting a close study on a specific population would be advisable for genetic improvement in the crop, and it would be appropriate if future collection and conservation plans give due attention to under-represented regions.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-011-9662-y) contains supplementary material, which is available to authorized users.

Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes

“…The 373 soybean genotypes evaluated in the present study were classified into eight subpopulations with significant divergence among subpopulations. Similar results have been found in other crops using SSR markers (Aranzana et al 2010;Belamkar et al 2011;Cao et al 2012;Shiferaw et al 2012;Wang et al 2011). The low genetic differentiation among genotypes could be a result of gene flow due to movement of seeds.…”

EST‐SSR analysis provides insights about genetic relatedness, population structure and gene flow in grass pea (Lathyrus sativus)

“…As described by Shiferaw et al. (), the model‐based program structure version 2.3.1 (Stanford University, Stanford, California) was used to analyse the population structure that takes into account both admixture model and correlated allele frequency between population (Pritchard et al. , Falush et al.…”

“…Genetic structure: As described by Shiferaw et al (2012), the modelbased program STRUCTURE version 2.3.1 (Stanford University, Stanford, California) was used to analyse the population structure that takes into account both admixture model and correlated allele frequency between population (Pritchard et al 2000, Falush et al 2003, with K values set from 1 to 10 with 10 replications and without incorporating population information. The approximate value of K was determined using a burn-in length of 20 000 and a total of 200 000 Monte Carlo Markov Chain runs.…”

Grain Legumes

“…Analysis of the diversity of 20 Ethiopian Lathyrus sativus accessions (12 plants per accession) with expressed sequence tag-derived simple sequence repeats (EST-SSR) showed an increase of the distribution of the alleles among populations that also could indicate outcrossing (Shiferaw et al 2012). The observed heterozygosity between 2 and 10 % in Italian grass pea landraces, detected with six polymorphic loci, revealed with the application of SSR markers, may be attributed to reproductive biology of grass pea and confirmed natural outcrossing ).…”