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Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy049.

Population genomic data reveal genes related to important traits of quail.

Wu Y1,2,3, Zhang Y4,5,6, Hou Z7, Fan G4,5,8,6, Pi J1, Sun S5, Chen J4,6, Liu H9, Du X5, Shen J1, Hu G5, Chen W4, Pan A1, Yin P5, Chen X4, Pu Y1, Zhang H4, Liang Z1, Jian J4, Zhang H1, Wu B4, Sun J1, Chen J4, Tao H1, Yang T4, Xiao H1, Yang H4, Zheng C1, Bai M4, Fang X4, Burt DW10, Wang W11, Li Q5, Xu X4,6, Li C5, Yang H4,12, Wang J4,12, Yang N7, Liu X4,6, Du J1.

Author information

Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China.
Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province,Wuhan 430064, China.
Hubei Innovation Center of Agricultural Science and Technology, Wuhan, Hubei, 430064, China.
BGI-Shenzhen, Shenzhen 518083, China.
BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China; Agricultural University, Beijing 100193, China.
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.
Hubei Shendan Healthy Food Co., Ltd., Wuhan 430206, China.
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China.
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.



Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies.


Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs.


This study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.

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