title: Genetic variation and association mapping for 12 agronomic traits in indica rice.
abstract: BACKGROUND
  Increasing rice (Oryza sativa L.) yield is a crucial challenge for modern agriculture. The ideal plant architecture is considered to be critical to enhance rice yield. Elite plant morphological traits should include compact plant type, short stature, few unproductive tillers, thick and sturdy stems and erect leaves. To reveal the genetic variations of important morphological traits, 523 germplasm accessions were genotyped using the Illumina custom-designed array containing 5,291 single nucleotide polymorphisms (SNPs) and phenotyped in two independent environments. Genome-wide association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model.
  
  
  RESULTS
  In total, 126 and 172 significant loci were identified and these loci explained an average of 34.45% and 39.09% of the phenotypic variance in two environments, respectively, and 16 of 298 (~5.37%) loci were detected across the two environments. For the 16 loci, 423 candidate genes were predicted in a 200-kb region (±100 kb of the peak SNP). Expression-level analyses identified four candidate genes as the most promising regulators of tiller angle. Known (NAL1 and Rc) and new significant loci showed pleiotropy and gene linkage. In addition, a long genome region covering ~1.6 Mb on chromosome 11 was identified, which may be critical for rice leaf architecture because of a high association with flag leaf length and the ratio of flag leaf length and width. The pyramid effect of the elite alleles indicated that these significant loci could be beneficial for rice plant architecture improvements in the future. Finally, 37 elite varieties were chosen as breeding donors for further rice plant architectural modifications.
  
  
  CONCLUSIONS
  This study detected multiple novel loci and candidate genes related to rice morphological traits, and the work demonstrated that genome-wide association studies are powerful strategies for uncovering the genetic variations of complex traits and identifying candidate genes in rice, even though the linkage disequilibrium decayed slowly in self-pollinating species. Future research will focus on the biological validation of the candidate genes, and elite varieties will also be of interest in genome selection and breeding by design.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. luqing2016@126.com.
authors.forename: Qing
authors.initials: Q
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. theJust@126.com.
authors.forename: Mengchen
authors.initials: M
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. xiaojunwords@126.com.|College of Agricultural Sciences, Shanxi Agricultural University, Taigu, 030801, China. xiaojunwords@126.com.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Niu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. wangshan7628@163.com.
authors.forename: Shan
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. xuqun37@hotmail.com.
authors.forename: Qun
authors.initials: Q
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. fy_555500@163.com.
authors.forename: Yue
authors.initials: Y
authors.lastname: Feng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. wangcaihong@caas.com.
authors.forename: Caihong
authors.initials: C
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. hongzhongdeng@163.com.
authors.forename: Hongzhong
authors.initials: H
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. yxp641110@163.com.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. yuhy540@163.com.
authors.forename: Hanyong
authors.initials: H
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. cnwangyp@126.com.
authors.forename: Yiping
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. weixinghua@caas.cn.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
mesh_terms: D000483:Alleles; D001947:Breeding; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D056726:Genetic Association Studies; D008040:Genetic Linkage; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable