College of Animal Science and Technology, Guangxi University, Nanning, 530004, China,
Guangxi Institute of Animal Science, Nanning, 530001, China, and.
G3 (Bethesda). 2020 Jan 7;10(1):379-386. doi: 10.1534/g3.119.400827.
Guangxi indigenous chicken breeds play a very important role in promoting the high-quality development of the broiler industry in China. However, studies on genomic information of Guangxi indigenous chicken to date remain poorly explored. To decipher the population genetic structure and differentially selected regions (DSRs) in Guangxi indigenous chickens, we dug into numerous SNPs from seven Guangxi native chickens (GX) by employing the restriction site associated with DNA sequencing (RAD-seq) technology. Another three breeds, Cobb, White Leghorn, and Chahua (CH) chicken, were used as a control. After quality control, a total of 185,117 autosomal SNPs were kept for further analysis. The results showed a significant difference in population structure, and the control breeds were distinctly separate from the Guangxi native breeds, which was also strongly supported by the phylogenetic tree. Distribution of F indicated that there were three SNPs with big genetic differentiation (F value all reach to 0. 9427) in GX CH group, which were located on chr1-96,859,720,chr4-86,139,601, and chr12-8,128,322, respectively. Besides, we identified 717 DSRs associated with 882 genes in GX Cobb group, 769 DSRs with 476 genes in GX Leghorn group, and 556 DSRs with 779 genes in GX CH group. GO enrichment showed that there were two significant terms, namely GPI-linked ephrin receptor activity and BMP receptor binding, which were enriched in GX Leghorn group. In conclusion, this study suggests that Guangxi native chickens have a great differentiation with Cobb and Leghorn. Our findings would be beneficial to fully evaluate the genomic information on Guangxi native chicken and facilitate the application of these resources in chicken breeding.
广西地方鸡种在中国肉鸡产业的高质量发展中发挥着非常重要的作用。然而，迄今为止，针对广西地方鸡种基因组信息的研究仍鲜有探索。为了解广西地方鸡种的群体遗传结构和差异选择区域（DSR），我们利用 RAD-seq 技术对 7 个广西本地鸡种（GX）进行了大量 SNP 的挖掘，并将另外 3 个品种（Cobb、White Leghorn 和 Chahua（CH）鸡）作为对照。经过质量控制，共保留了 185117 个常染色体 SNP 用于进一步分析。结果表明，群体结构存在显著差异，对照品种与广西本地品种明显分离，这也得到了系统发育树的有力支持。F 分布表明，在 GX-CH 组中存在 3 个具有较大遗传分化的 SNP（F 值均达到 0.9427），分别位于 chr1-96859720、chr4-86139601 和 chr12-8128322。此外，我们在 GX-Cobb 组中鉴定出与 882 个基因相关的 717 个 DSR，在 GX-Leghorn 组中鉴定出与 476 个基因相关的 769 个 DSR，在 GX-CH 组中鉴定出与 779 个基因相关的 556 个 DSR。GO 富集分析表明，在 GX-Leghorn 组中，有两个显著的术语，即 GPI 连接的 Eph 受体活性和 BMP 受体结合，被富集。总之，本研究表明，广西本地鸡种与 Cobb 和 Leghorn 存在很大的分化。我们的研究结果将有助于充分评估广西地方鸡种的基因组信息，并促进这些资源在鸡种培育中的应用。
