Comparative Transcriptomics Uncovers Alternative Splicing Events and Marker Discovery in Radish (Raphanus sativus L.)

Single nucleotide polymorphisms (SNPs), insertion/deletion (InDel) are abundant polymorphisms and co-dominant inheritance markers, they have been widely used in plant genetics and breeding. So far, however, little information is available on development and utilization of SNP and InDel markers from transcriptome in radish. In this study, a total of 177,540 alternative splicing (AS) events were identified from three radish transcriptome datasets. They were distributed in 64 % of the total expressed genes, and the most predominant and least type of AS events was alternative 5’ first exon and exon skipping, respectively. In all, 22,412 SNPs and 9,366 InDels were identified with an average frequency of one SNP per 18.8 kb and one InDel per 4.5 kb, respectively. The major types of SNPs were transition with nucleotide transitions A/G and C/T in the radish. The ratio of SNPs with nonsynonymous/synonymous mutations was 1.05:1. The length of InDels ranged from 1 to 12 bp, and the 1–2 bp in length were the most abundant types. Moreover, the reliability of thirty SNPs and eighty InDels were validated using Sanger sequencing and PCR-base marker. In total, 27 (92.5 %) SNPs and 60 (75.0 %) InDels exhibited polymorphism. Furthermore, 40 informative InDels markers were tested on 32 radish genotypes for genetic diversity analysis, in which the polymorphism information content values ranged from 0.09 to 0.69. These results would not only provided new insights into transcriptome complexity and AS regulation, but also furnish large molecular markers resource for germplasm identification, genetic mapping and marker assisted selection in radish.