2015年1月
Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum)
MOLECULAR BREEDING
- 巻
- 35
- 号
- 1
- 開始ページ
- 55
- 終了ページ
- 65
- 記述言語
- 英語
- 掲載種別
- 研究論文(学術雑誌)
- DOI
- 10.1007/s11032-015-0265-x
- 出版者・発行元
- SPRINGER
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.
- リンク情報
- ID情報
-
- DOI : 10.1007/s11032-015-0265-x
- ISSN : 1380-3743
- eISSN : 1572-9788
- Web of Science ID : WOS:000348418700055