Development of SNP and InDel markers via de novo transcriptome assembly in Sesamum indicum L

Cultivated sesame (Sesamum indicum L.) is an important oil crop because of its high oil content and quality. In order to discover the single nucleotide polymorphisms (SNPs) and insertion/deletions (InDels) in RNA-Seq, we collected a total of 33.47 Gbp of data from three sesame transcriptome datasets. A reference transcriptome covering 267,508 unigenes was constructed. Among the 37,646 transcripts with complete open reading frames, a total of 7,450 SNPs and 362 InDels were found with frequencies of one SNP per 6.66 kb and one InDel per 137 kb, respectively. Most of the SNPs were transition-type with the nucleotide transitions C–T or A–G. A total of 21 InDel types with lengths ranging from 1 to 38 bp were identified, and the short InDels (1–2 bp) were most abundant at a ratio of over 80 %. Furthermore, 4,959 (66.56 %) SNPs were detected in protein-coding regions: 2,899 (58.46 %) were synonymous and 2,060 (41.54 %) were nonsynonymous. All SNPs and InDels detected in this study were bi-allelic. Of the randomly selected 40 SNPs and 40 InDels, 92.5 % of the SNPs and 95.0 % of the InDels exhibited polymorphism according to the PCR-based and Sanger-sequenced results. Furthermore, the efficiencies of the newly developed polymorphic SNP and InDel markers were evaluated among 36 commercial sesame cultivars. More than 90.0 % of the markers displayed the expected polymorphic amplifications. The polymorphism information content values ranged from 0.05 to 0.58 with an average of 0.38. Moreover, all genotypes of the 36 commercial cultivars tested were definitively distinguished by 21 SNPs and 16 InDels. These newly identified molecular markers may provide a foundation for cultivar identification, genetic diversity analysis, qualitative and quantitative trait mapping and marker-assisted selection breeding in sesame.