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.
Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy049.
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.
日本鹌鹑（Coturnix japonica）是一种新近驯化的家禽，不仅具有农业产品的重要性，还是遗传研究的模式鸟类。然而，关于基因组学、系统发育学以及一些重要经济性状的遗传学的大多数生物学问题尚未得到解答。因此，有必要完成高质量的基因组序列以及一系列比较基因组学、进化和功能研究。
在这里，我们呈现了一个跨度为 1.04Gb 的鹌鹑基因组组装，其中 86.63%的序列锚定在 30 条染色体上（28 条常染色体和 2 条性染色体 Z/W）。我们的基因组数据解决了日本鹌鹑、火鸡和鸡之间的长期系统发育争论。比较基因组学和功能基因组学数据发现，四个参与早期成熟的候选基因经历了正选择，其中一个基因编码滤泡刺激素β（FSHβ），它与鹌鹑和鸡之间不同的 FSHβ水平相关。我们重新测序了 31 只鹌鹑（10 只野生、11 只蛋鸡型和 10 只肉鸡型），并在蛋鸡型和肉鸡型中分别鉴定出 18 个和 26 个候选选择扫掠区域。它们之间只有一个是共享的，这表明它们受到了独立的选择。我们还在染色体 Z 上检测到一个单倍型，该单倍型与鹌鹑的栗色/黄色羽毛紧密相关，这是使用群体重测序和全基因组关联研究得出的。这个单倍型块将对鹌鹑的育种计划有用。
本研究提供了一个高质量的鹌鹑参考基因组，鉴定了鹌鹑特异性基因，并解决了鹌鹑的系统发育问题。我们已经确定了与鹌鹑早期成熟和羽毛颜色相关的基因，这对鹌鹑的育种具有重要意义。这些结果将促进鹌鹑的生物学发现，并帮助我们阐明雉科家族内的进化过程。
