title: Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice.
abstract: Awn is one of the most important domesticated traits in rice (Oryza sativa). Understanding the genetic basis of awn length is important for grain harvest and production, because long awn length is disadvantageous for both grain harvest and milling. We investigated the awn length of 529 rice cultivars and performed a Genomewide association studies (GWAS) in the indica and japonica subpopulations, and the whole population. In total, we found 17 loci associated with awn length. Of these loci, seven were linked to previously reported quantitative trait loci, and one was linked to the awn gene An-1. Nine novel loci were repeatedly identified in different environments. One of the nine associations was identified in both the whole and japonica populations. Special interest was the detection of the most significant association SNP, sf0136352825, which was less than 95 kb from the seed shattering gene qSH1. These results may provide potentially favourable haplotypes for molecular breeding in rice.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, People's Republic of China.a020809@webmail.hzau.edu.cn.
authors.forename: Risper Auma
authors.initials: RA
authors.lastname: Magwa
authors.forename: Hu
authors.initials: H
authors.lastname: Zhao
authors.forename: Wen
authors.initials: W
authors.lastname: Yao
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.forename: Lin
authors.initials: L
authors.lastname: Yang
authors.forename: Yongzhong
authors.initials: Y
authors.lastname: Xing
authors.forename: Xufeng
authors.initials: X
authors.lastname: Bai
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D008040:Genetic Linkage; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D006239:Haplotypes; D012275:Oryza / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D012639:Seeds / Q000235:genetics*; D012641:Selection, Genetic