New cDNA-SSR markers in the narrow-leaved vetch (Vicia sativa subsp nigra) using 454 pyrosequencing

摘要

Transcriptomes from high-throughput sequencing technology provide a good resource for molecular markers. Here, we report the development of polymorphic simple sequence repeat (SSR) markers from transcript sequences via 454 pyrosequencing for Vicia sativa subsp. nigra (narrow-leaved vetch). In contrast to V. sativa subsp. sativa, the most commonly grown vetch species, the narrow-leaved vetch survives in diverse soil and climate conditions, serving as a valuable breeding resource of environmental tolerance. We found 2,429 SSR loci from 17,971 individual sequence reads, and 100 primer pairs were designed and synthesized. In total, 49 primer pairs were polymorphic when screened in 32 accessions. The number of alleles was 2-19, the frequency of major alleles per locus varied from 0.19 to 0.87, the genotype numbers ranged from 2 to 19, and observed and expected heterozygosity values ranged from 0.00 to 0.78 and from 0.23 to 0.92, respectively. Polymorphism index content values ranged from 0.20 to 0.86. Considering the relatively high polymorphism in the selected cDNA-SSR marker sets, these markers can be applied to assess genetic diversity, population structure, and positional cloning for the narrow-leaved vetch to facilitate vetch breeding programs.