Transcriptome-wide development and utilisation of novel intron-length polymorphic markers in common vetch (Vicia sativa subsp. sativa)

Abstract

Common vetch (Vicia sativa subsp. sativa) is one of the most economically important forage legumes, with high nutritional value and multiple uses. Although microsatellite markers have been developed and applied on a large scale for evaluation of common vetch germplasm, intron-length polymorphic (ILP) markers have not been systematically investigated and exploited. In this study, introns within the common vetch genome were located by aligning the RNA-Seq sequences of common vetch with barrel medic (Medicago truncatula), soybean (Glycine max) and Arabidopsis thaliana genome sequences, and then used for VsILP marker development. In total, 10400 markers were generated from 44582 common vetch unigenes. Of 300 randomly selected VsILP markers, 283 were successfully amplified in common vetch. Among these markers, 40 produced length variation in 30 accessions of common vetch, collectively yielding 166 alleles with an average of 4.0 alleles per locus. The polymorphic information content values extended from 0.06 to 0.81 with a mean of 0.49. Of the 283 VsILP markers, 84.8% exhibited transferability to other species, both leguminous (common vetch, lucerne (Medicago sativa), barrel medic, soybean, yellow sweet clover (Melilotus officinalis), Lotus corniculatus and Sophora alopecuroides) and non-leguminous (rice (Oryza sativa), Arabidopsis and tobacco (Nicotiana tabacum)). Here, we present the first large-scale development of ILP markers in common vetch and their utility in germplasm evaluation and transferability, which will be valuable for further comparative genomic studies, genetic relationship assessments, and marker-assisted breeding of leguminous and non-leguminous species.