title: Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'.
abstract: Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Jun-Ichi
authors.initials: J
authors.lastname: Yonemaru
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Sun Hee
authors.initials: SH
authors.lastname: Choi
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Tsuyu
authors.initials: T
authors.lastname: Ando
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Ayahiko
authors.initials: A
authors.lastname: Shomura
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan ; NARO Institute of Crop Science , 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518 , Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Yano
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.
authors.forename: Shuichi
authors.initials: S
authors.lastname: Fukuoka
keywords: DNA marker; Oryza sativa L.; diverse cultivars; insertion-deletion (indel); next-generation sequencing; validation