title: Genetic dissection of yield traits in super hybrid rice Xieyou9308 using both unconditional and conditional genome-wide association mapping.
abstract: With the development and application of super rice breeding, elite rice hybrids with super high-yielding potential have been widely developed in last decades in China. Xieyou9308 is one of the most famous super hybrid rice varieties. To uncover the genetic mechanism of Xieyou9308's high yield potential, a recombinant inbred line (RIL) population derived from cross of XieqingzaoB and Zhonghui9308 was re-sequenced and investigated on the grain yield (GYD) and its three component traits, number of panicles per plant (NP), number of filled grains per panicle (NFGP), and grain weight (GW). Unconditional and conditional genome-wide association analysis, based on a linear mixed model with epistasis and gene-environment interaction effects, were conducted, using ~0.7 million identified SNPs. There were six, four, seven, and seven QTSs identified for GYD, NP, NFGP, and GW, respectively, with accumulated explanatory heritability varying from 43.06% to 48.36%; additive by environment interactions were detected for GYD, some minor epistases were detected for NP and NFGP. Further, conditional genetic mapping analysis for GYD given its three components revealed several novel QTSs associated with yield than that were suppressed in our unconditional mapping analysis.
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: Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.|Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Liyuan
authors.initials: L
authors.lastname: Zhou
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: Xihong
authors.initials: X
authors.lastname: Shen
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: 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: 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: Qunen
authors.initials: Q
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: Aike
authors.initials: A
authors.lastname: Zhu
authors.affiliation: Department of Pediatrics, Biostatistics Section, Arkansas Children's Hospital Research Institute School of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, 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
authors.affiliation: State Key Laboratory of Rice Biology and Zhejiang Key Laboratory of Super Rice Research, China National Rice Research Institute, Hangzhou, 311401, China. shcheng@mail.hz.zj.cn.
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. caolycgf@mail.hz.zj.cn.
authors.forename: Liyong
authors.initials: L
authors.lastname: Cao
mesh_terms: D002874:Chromosome Mapping; D002523:Edible Grain / Q000235:genetics / Q000254:growth & development; D059647:Gene-Environment Interaction; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D006824:Hybridization, Genetic; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable