Transcriptome-wide Development and Utilization of Novel Intron-length Polymorphic (ILP) 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 rich nutritional value and multiple uses. Though the large-scale development and application of microsatellite markers have been conducted in common vetch germplasm evaluation, the investigation and exploitation of intron-length polymorphic (ILP) markers have not been systematically analyzed. In this study, the intron positions of common vetch genome were located by aligning the RNA-Seq sequences of common vetch with Medicago truncatula, soybean (Glycine max), and Arabidopsis thaliana genomic sequences, and used for VsILP marker development. A total of 10,400 markers were generated from 44,582 common vetch unigenes. Out of 300 randomly selected VsILP markers, 283 resulted in successful amplification in common vetch. Among these markers, 40 produced length variation in 30 common vetch accessions, collectively yielding 166 alleles with an average of 4.0 alleles per locus. The polymorphic information content (PIC) values extended from 0.06 to 0.81 with a mean of 0.49. Of the 283 VsILP markers, 84.8% exhibited transferability to leguminous and non-leguminous species. We presented here 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.