A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica).

Nature Genetics, doi:10.1038/ng.2673

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica).

Guanqing Jia, Xuehui Huang, Hui Zhi, Yan Zhao, Qiang Zhao, Wenjun Li, Yang Chai, Lifang Yang, Kunyan Liu, Hengyun Lu, Chuanrang Zhu, Yiqi Lu, Congcong Zhou, Danlin Fan, Qijun Weng, Yunli Guo, Tao Huang, Lei Zhang, Tingting Lu, Qi Feng, Hangfei Hao, Hongkuan Liu, Ping Lu, Ning Zhang, Yuhui Li, Erhu Guo, Shujun Wang, Suying Wang, Jinrong Liu, Wenfei Zhang, Guoqiu Chen, Baojin Zhang, Wei Li, Yongfang Wang, Haiquan Li, Baohua Zhao, Jiayang Li, Xianmin Diao & Bin Han

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.