title: Dissection of genetic architecture of rice plant height and heading date by multiple-strategy-based association studies.
abstract: Xieyou9308 is a certified super hybrid rice cultivar with a high grain yield. To investigate its underlying genetic basis of high yield potential, a recombinant inbred line (RIL) population derived from the cross between the maintainer line XieqingzaoB (XQZB) and the restorer line Zhonghui9308 (ZH9308) was constructed for identification of quantitative trait SNPs (QTSs) associated with two important agronomic traits, plant height (PH) and heading date (HD). By re-sequencing of 138 recombinant inbred lines (RILs), a total of ~0.7 million SNPs were identified for the association studies on the PH and HD. Three association mapping strategies (including hypothesis-free genome-wide association and its two complementary hypothesis-engaged ones, QTL-based association and gene-based association) were adopted for data analysis. Using a saturated mixed linear model including epistasis and environmental interaction, we identified a total of 31 QTSs associated with either the PH or the HD. The total estimated heritability across three analyses ranged from 37.22% to 45.63% and from 37.53% to 55.96% for the PH and HD, respectively. In this study we examined the feasibility of association studies in an experimental population (RIL) and identified several common loci through multiple strategies which could be preferred candidates for further research.
authors.affiliation: Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Liyuan
authors.initials: L
authors.lastname: Zhou
authors.affiliation: Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Shouye
authors.initials: S
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou 311401, China.
authors.forename: Weixun
authors.initials: W
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou 311401, China.
authors.forename: Daibo
authors.initials: D
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou 311401, China.
authors.forename: Xiaodeng
authors.initials: X
authors.lastname: Zhan
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou 311401, China.
authors.forename: Aike
authors.initials: A
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou 311401, China.
authors.forename: Yingxin
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou 311401, China.
authors.forename: Shihua
authors.initials: S
authors.lastname: Cheng
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou 311401, China.
authors.forename: Liyong
authors.initials: L
authors.lastname: Cao
authors.affiliation: Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, Louisiana, 1440 Canal St., Suite 2001, New Orleans, LA 70112-2632, USA.
authors.forename: Xiangyang
authors.initials: X
authors.lastname: Lou
authors.affiliation: Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Haiming
authors.initials: H
authors.lastname: Xu
mesh_terms: D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable