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Gigascience. 2017 Feb 1;6(2):1-8. doi: 10.1093/gigascience/giw005.

Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population.

Ni X1,2, Xia Q1,2, Zhang H1,2, Cheng S1,2, Li H1,2, Fan G3, Guo T1,2, Huang P1,2, Xiang H1,2, Chen Q1,2, Li N1,2, Zou H1,2,4, Cai X1,2, Lei X1,2, Wang X3, Zhou C1,2,5,6,7, Zhao Z3, Zhang G1,2,5,6,7, Du G4, Cai W4, Quan Z1,2,5,6,7.

Author information

BGI-Shenzhen, Shenzhen 518083, China.
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou 075000, China.
BGI Millet Co., Ltd, 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.


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.

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