title: A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica).
abstract: Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a haplotype map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China.
authors.forename: Guanqing
authors.initials: G
authors.lastname: Jia
authors.forename: Xuehui
authors.initials: X
authors.lastname: Huang
authors.forename: Hui
authors.initials: H
authors.lastname: Zhi
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Wenjun
authors.initials: W
authors.lastname: Li
authors.forename: Yang
authors.initials: Y
authors.lastname: Chai
authors.forename: Lifang
authors.initials: L
authors.lastname: Yang
authors.forename: Kunyan
authors.initials: K
authors.lastname: Liu
authors.forename: Hengyun
authors.initials: H
authors.lastname: Lu
authors.forename: Chuanrang
authors.initials: C
authors.lastname: Zhu
authors.forename: Yiqi
authors.initials: Y
authors.lastname: Lu
authors.forename: Congcong
authors.initials: C
authors.lastname: Zhou
authors.forename: Danlin
authors.initials: D
authors.lastname: Fan
authors.forename: Qijun
authors.initials: Q
authors.lastname: Weng
authors.forename: Yunli
authors.initials: Y
authors.lastname: Guo
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.forename: Tingting
authors.initials: T
authors.lastname: Lu
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Hangfei
authors.initials: H
authors.lastname: Hao
authors.forename: Hongkuan
authors.initials: H
authors.lastname: Liu
authors.forename: Ping
authors.initials: P
authors.lastname: Lu
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.forename: Yuhui
authors.initials: Y
authors.lastname: Li
authors.forename: Erhu
authors.initials: E
authors.lastname: Guo
authors.forename: Shujun
authors.initials: S
authors.lastname: Wang
authors.forename: Suying
authors.initials: S
authors.lastname: Wang
authors.forename: Jinrong
authors.initials: J
authors.lastname: Liu
authors.forename: Wenfei
authors.initials: W
authors.lastname: Zhang
authors.forename: Guoqiu
authors.initials: G
authors.lastname: Chen
authors.forename: Baojin
authors.initials: B
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Yongfang
authors.initials: Y
authors.lastname: Wang
authors.forename: Haiquan
authors.initials: H
authors.lastname: Li
authors.forename: Baohua
authors.initials: B
authors.lastname: Zhao
authors.forename: Jiayang
authors.initials: J
authors.lastname: Li
authors.forename: Xianmin
authors.initials: X
authors.lastname: Diao
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D002681:China; D019295:Computational Biology; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D006239:Haplotypes; D054643:INDEL Mutation; D015810:Linkage Disequilibrium; D058977:Molecular Sequence Annotation; D010641:Phenotype; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D032983:Setaria Plant / Q000235:genetics*