TY - DATA
T1 - Supporting data for “Population genomic data reveal genes related to important traits of quail”
AU - Ailuan, Pan
AU - Bin, Wu
AU - Chengfeng, Li
AU - Chuanwei, Zheng
AU - David, Burt W.
AU - Gang, Hu
AU - Guangyi, Fan
AU - Hao, Zhang
AU - He, Zhang
AU - Hongwei, Xiao
AU - Hu, Tao
AU - Huan, Yang
AU - Huanming, Yang
AU - Huaqiao, Liu
AU - Jian, Wang
AU - Jianbo, Jian
AU - Jiang, Chen
AU - Jianwei, Chen
AU - Jie, Shen
AU - Jing, Sun
AU - Jinping, Du
AU - Jinsong, Pi
AU - Mingzhou, Bai
AU - Ning, Yang
AU - Pingping, Yin
AU - Qingyi, Li
AU - Shuai, Sun
AU - Ting, Yang
AU - Wen, Wang
AU - Wenbin, Chen
AU - Xiao, Du
AU - Xiaodong, Fang
AU - Xiaoli, Chen
AU - Xin, Liu
AU - Xun, Xu
AU - Yan, Wu
AU - Yaolei, Zhang
AU - Yuejin, Pu
AU - Zhenhua, Liang
AU - Zhuocheng, Hou
DO - 10.5524/100441
UR - http://gigadb.org/dataset/100441
AB - 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 1.04Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and two sex chromosomes Z/W). Our genomic data has 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 process within the Phasianidae family.
KW - Genomic
KW - Transcriptomic
KW - japanese quail
KW - genome assembly
KW - early maturation
KW - phylogeny
KW - resequencing
KW - plumage color
KW - quail breeding
PY - 2018
PB - GigaScience Database
LA - en
ER -