Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China.
BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China.
PLoS One. 2022 Mar 15;17(3):e0250392. doi: 10.1371/journal.pone.0250392. eCollection 2022.
Guangxi chickens play a crucial role in promoting the high-quality development of the broiler industry in China, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Guangxi indigenous chicken, we analyzed the whole genomes of 185 chickens from 8 phenotypically and geographically representative Guangxi chicken breeds, together with 12 RJFt, 12 BRA and 12 WL genomes available from previous studies. Calculation of heterozygosity (Hp), nucleotide diversity (π), and LD level indicated that Guangxi populations were characterized by higher genetic diversity and lower differentiation than RJFt and commercial breeds except for HGFC. Population structure analysis also confirmed the introgression from commercial broiler breeds. Each population clustered together while the overall differentiation was slight. MA has the richest genetic diversity among all varieties. Selective sweep analysis revealed BCO2, EDN3 and other candidate genes had received strong selection in local breeds. These also provided novel breeding visual and data basis for future breeding.
广西鸡在中国肉鸡产业高质量发展中扮演着重要的角色，但它们的价值和潜力尚未被发掘。为了确定广西地方鸡种的遗传多样性和群体结构，我们对来自 8 个表型和地理上具有代表性的广西鸡种的 185 只鸡的全基因组进行了分析，同时还分析了 12 个 RJFt、12 个 BRA 和 12 个 WL 基因组，这些基因组数据来自之前的研究。杂合度（Hp）、核苷酸多样性（π）和 LD 水平的计算表明，与 RJFt 和商业品种相比，广西鸡种的遗传多样性更高，分化程度更低，除了 HGFC 之外。群体结构分析也证实了商业肉鸡品种的渗入。每个群体都聚集在一起，而整体分化程度较小。MA 在所有品种中具有最丰富的遗传多样性。选择扫描分析表明，BCO2、EDN3 和其他候选基因在地方品种中受到了强烈的选择。这些也为未来的育种提供了新的视角和数据基础。
