Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum)

Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. Although expressed sequence tag (EST)-derived markers for bulb onion (A. cepa L.) have been developed from medium-scale sequencing, comparable EST sequences in bunching onion are lacking. In this study, we obtained 54,903 bunching onion unigenes using transcriptome shotgun assembly (TSA) and two next-generation sequencing technologies, GS-FLX and HiSeq 2000. When bunching onion and bulb onion unigenes were compared, 10,688 were estimated as reciprocal best-hit relationships. In the bunching onion TSA sequences, we discovered 2,396 di- to pentanucleotide simple sequence repeat (SSR) motifs and 5,505 exon–intron boundary sites. Moreover, we detected 9,002 single nucleotide polymorphisms and 4,335 insertion–deletion (InDel) by comparing sequence reads obtained from two inbred lines, “F” and “A.” TSA-derived SSR, cleaved amplified polymorphic sequences, InDels and intron-spanning markers were used to develop a linkage map. The genetic map, designated the FA map, contained 17 linkage groups with 364 markers (190 bunching onion TSAs, 96 bunching onion genomic SSRs, 39 bulb onion ESTs and 4 other markers) and covered a distance of 1,150 cM.