title: Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population.
abstract: Foxtail millet (Setaria italica) provides food and fodder in semi-arid regions and infertile land. Resequencing of 184 foxtail millet recombinant inbred lines (RILs) was carried out to aid essential research on foxtail millet improvement. A total 483 414 single nucleotide polymorphisms were determined. Bin maps were constructed based on the RILs' recombination data. Based on the high-density bin map, we updated Zhanggu reference with 416 Mb after adding 16 Mb unanchored scaffolds and Yugu reference with some assembly error correction and 3158 gaps filled. Quantitative trait loci (QTL) mapping of nine agronomic traits was done based on this RIL population, five of which were controlled by a single gene. Meanwhile, two QTLs were found for plant height, and a candidate gene showed 89% identity to the known rice gibberellin-synthesis gene sd1. Three QTLs were found for the trait of heading date. The whole genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding. Resequencing of the RILs could also provide an effective way for high-quality genome assembly and gene identification.
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Ni
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Qiuju
authors.initials: Q
authors.lastname: Xia
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Houbao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Shu
authors.initials: S
authors.lastname: Cheng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.affiliation: Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou 075000, China.
authors.forename: Guangyu
authors.initials: G
authors.lastname: Fan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Guo
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Haitao
authors.initials: H
authors.lastname: Xiang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Qingchun
authors.initials: Q
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.|BGI Millet Co., Ltd, BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Hongfeng
authors.initials: H
authors.lastname: Zou
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Cai
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xuejing
authors.initials: X
authors.lastname: Lei
authors.affiliation: Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou 075000, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.|Key Lab of Genomics,Chinese Ministry of Agriculture, BGI-Shenzhen, Shenzhen 518083, China.|Guangdong Province Key Laboratory of Crop Germplasm Research and Application, BGI-Shenzhen, Shenzhen 518083, China.|Shenzhen Engineering Laboratory of Molecular Design Breeding, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chengshu
authors.initials: C
authors.lastname: Zhou
authors.affiliation: Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou 075000, China.
authors.forename: Zhihai
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.|Key Lab of Genomics,Chinese Ministry of Agriculture, BGI-Shenzhen, Shenzhen 518083, China.|Guangdong Province Key Laboratory of Crop Germplasm Research and Application, BGI-Shenzhen, Shenzhen 518083, China.|Shenzhen Engineering Laboratory of Molecular Design Breeding, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Gengyun
authors.initials: G
authors.lastname: Zhang
authors.affiliation: BGI Millet Co., Ltd, BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Guohua
authors.initials: G
authors.lastname: Du
authors.affiliation: BGI Millet Co., Ltd, BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Cai
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.|Key Lab of Genomics,Chinese Ministry of Agriculture, BGI-Shenzhen, Shenzhen 518083, China.|Guangdong Province Key Laboratory of Crop Germplasm Research and Application, BGI-Shenzhen, Shenzhen 518083, China.|Shenzhen Engineering Laboratory of Molecular Design Breeding, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhiwu
authors.initials: Z
authors.lastname: Quan
mesh_terms: D056905:Chromosome Breakpoints; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D007178:Inbreeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D011995:Recombination, Genetic; D032983:Setaria Plant / Q000235:genetics*
chemical_list: D005819:Genetic Markers