title: Genome wide association mapping for grain shape traits in indica rice.
abstract: Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Feng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Lu
authors.affiliation: Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China.
authors.forename: Rongrong
authors.initials: R
authors.lastname: Zhai
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Mengchen
authors.initials: M
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Yaolong
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Hanyong
authors.initials: H
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
authors.forename: Yiping
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China. weixinghua@caas.cn.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D002523:Edible Grain / Q000033:anatomy & histology / Q000235:genetics*; D005787:Gene Frequency; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D015810:Linkage Disequilibrium; D012275:Oryza / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D000069600:Plant Breeding / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D013045:Species Specificity
keywords: Genome-wide association mapping; Grain shape; Rice; Single nucleotide polymorphism