Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
Present Address: The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
BMC Biol. 2020 Feb 12;18(1):13. doi: 10.1186/s12915-020-0738-1.
Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes.
In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system.
Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.
杂交和基因渗入在动物物种的进化历史中起着关键作用。它们在野生鸟类的几个目内都很常见。家鸡 Gallus gallus domesticus 是最常见的家畜物种。每年有超过 650 亿只鸡被饲养，以生产肉类和 8000 万吨鸡蛋供全球商业部门消费。揭示其遗传多样性的起源对可持续的育种改良计划具有重要的应用价值。
在这项研究中，我们报告了对本土家鸡和四种野生 Gallus 物种之间基因渗入的全基因组分析。我们首先评估了 Gallus 属的全基因组系统发育和分化时间。全基因组序列分化分析支持灰原鸡 G. sonneratii 和锡兰原鸡 G. lafayettii 之间的姐妹关系。这两个物种形成了一个与红原鸡 G. gallus 姐妹的分支，绿原鸡 G. varius 是属内最古老的谱系。我们揭示了灰原鸡与家鸡之间以及与锡兰原鸡之间广泛的双向基因渗入，而与绿原鸡的基因渗入则要少得多。我们发现了一个绿原鸡基因渗入的单一案例。这些渗入的区域包括与发育和免疫系统相关的生物学功能的基因。
我们的研究表明，虽然红原鸡是主要的祖先物种，但基因渗入的杂交事件已经影响了基因组，并为家鸡的多样性做出了贡献，尽管在其地理分布范围内的不同水平上可能有所不同。
