title: Haplotype variation at Badh2, the gene determining fragrance in rice.
abstract: Fragrance is an important component of end-use quality in rice. A set of 516 fragrant rice accessions were genotyped and over 80% of them carried the badh2.7 allele. A subset of 144 mostly fragrant accessions, including nine of Oryza rufipogon, was then subjected to a detailed diversity and haplotype analysis. The level of linkage disequilibrium in the Badh2 region was higher among the fragrant accessions. Re-sequencing in the Badh2 region showed that badh2.7, badh2.2 and badh2.4-5 all arose in the japonica genepool, and spread later into the indica genepool as a result of deliberate crossing. However, loss-of-function alleles of Badh2 are also found in the indica genepools, and then transferred into japonica. Evidence for three new possible FNPs was obtained from the Badh2 sequence of 62 fragrant accessions. Based on these data, we have elaborated a model for the evolution of Badh2 and its participation in the rice domestication process.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Gaoneng
authors.initials: G
authors.lastname: Shao
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Shaoqing
authors.initials: S
authors.lastname: Tang
authors.affiliation: Jiangxi academy of agricultural sciences, Nanchang 330200, China.
authors.forename: Mingliang
authors.initials: M
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Xiangjin
authors.initials: X
authors.lastname: Wei
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Jiwai
authors.initials: J
authors.lastname: He
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Ju
authors.initials: J
authors.lastname: Luo
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Guiai
authors.initials: G
authors.lastname: Jiao
authors.affiliation: Hunan agricultural university, Changsha 410128, China.
authors.forename: Yichao
authors.initials: Y
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Lihong
authors.initials: L
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China. Electronic address: hupeisong@yahoo.com.cn.
authors.forename: Peisong
authors.initials: P
authors.lastname: Hu
mesh_terms: D000483:Alleles; D019143:Evolution, Molecular; D005091:Exons; D005788:Gene Pool; D017343:Genes, Plant; D014644:Genetic Variation; D006239:Haplotypes; D015810:Linkage Disequilibrium; D009812:Odorants; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA