TY - JOUR
T1 - Population genomic data reveal genes related to important traits of quail
AU - Wu, Yan
AU - Zhang, Yaolei
AU - Hou, Zhuocheng
AU - Fan, Guangyi
AU - Pi, Jinsong
AU - Sun, Shuai
AU - Chen, Jiang
AU - Liu, Huaqiao
AU - Du, Xiao
AU - Shen, Jie
AU - Hu, Gang
AU - Chen, Wenbin
AU - Pan, Ailuan
AU - Yin, Pingping
AU - Chen, Xiaoli
AU - Pu, Yuejin
AU - Zhang, He
AU - Liang, Zhenhua
AU - Jian, Jianbo
AU - Zhang, Hao
AU - Wu, Bin
AU - Sun, Jing
AU - Chen, Jianwei
AU - Tao, Hu
AU - Yang, Ting
AU - Xiao, Hongwei
AU - Yang, Huan
AU - Zheng, Chuanwei
AU - Bai, Mingzhou
AU - Fang, Xiaodong
AU - Burt, David W.
AU - Wang, Wen
AU - Li, Qingyi
AU - Xu, Xun
AU - Li, Chengfeng
AU - Yang, Huanming
AU - Wang, Jian
AU - Yang, Ning
AU - Liu, Xin
AU - Du, Jinping
N1 - Publisher Copyright:
© The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
PY - 2018
Y1 - 2018
N2 - Background: 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. Results: 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. Conclusions: 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.
AB - Background: 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. Results: 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. Conclusions: 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.
KW - Early maturation
KW - Genome assembly
KW - Japanese quail
KW - Phylogeny
KW - Plumage color
KW - Quail breeding
KW - Resequencing
UR - http://www.scopus.com/inward/record.url?scp=85055182498&partnerID=8YFLogxK
U2 - 10.1093/gigascience/giy049
DO - 10.1093/gigascience/giy049
M3 - 文章
C2 - 29762663
AN - SCOPUS:85055182498
SN - 2047-217X
VL - 7
JO - GigaScience
JF - GigaScience
IS - 5
M1 - giy049
ER -