Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

• DOI: 10.1270/jsbbs.65.249
• Publication Date: 2015-07-14T22:04:47Z
• Authors: Jun-ichi Yonemaru; Sun Hee Choi; Hiroaki Sakai; Tsuyu Ando; Ayahiko Shomura; Masahiro Yano; Jianzhong Wu; Shuichi Fukuoka
• Keywords: Indel

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used DNA markers to identify QTLs and genes facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing 5 indica, 2 aus, 3 tropical japonica cultivars Japanese elite cultivar 'Koshihikari' was performed extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel for the discrimination genomic between other cultivars, we subtracted detected in from those Two sets markers, KNJ8-indel (shared eight or more including 'Khao Nam Jen' a representative cultivar) C5-indel five cultivars), were established, with 915 9,899 regions, respectively. Validation two marker using 23 showed high PCR success rate (≥95%) 83.3% 73.9% The will therefore useful effective breeding