Development of EST Markers in Jananese Bunching Onion (Allium fistulosum)

Japanese bunching onion (JBO; Allium fistulosum L.) is one of the most important vegetables in Japan. Although bulb onion (A. cepa L.) EST-derived markers have been developed from middle-scale sequencing of ESTs, there are no applicable EST sequences in JBO. In this study, we obtained a JBO EST set of 54,862 unigenes by utilizing two NGS technologies, GS-FLX and HiSeq2000. Between the JBO and bulb onion unigenes, 10,688 were estimated as reciprocal best-hit relationships. From the JBO unigenes, we found 2,396 di- pentanucleotide SSR motifs and 5,505 exon-intron boundary sites. Moreover, we also detected 9,002 SNPs and 4,335 InDels by comparing reads obtained from two inbred lines, ‘F’ and ‘A’. We designed EST-derived SSR, CAPS, InDels and intron-spanning markers and constructed a linkage map. The genetic map (FA map) consisted of 17 linkage groups with 364 markers (190 JBO ESTs, 96 gSSRs, 1 STS, 39 bulb onion ESTs and 3 gSSRs) covering 1,150 cM. Thus the JBO EST markers developed in this study will provide for understanding Allium comparative genomics.