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 -