中国南方地方鸡与商业鸡之间的遗传特征和选择信号。

Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens.

机构信息

State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou Guangzhou 510642, China.

出版信息

Poult Sci. 2024 Jul;103(7):103863. doi: 10.1016/j.psj.2024.103863. Epub 2024 May 16.

DOI:10.1016/j.psj.2024.103863

PMID:38810566

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11166977/

Abstract

The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation.

摘要

中国南方引进外来品种和养殖公司培育新品系给土鸡带来了挑战，包括品种特征丧失、遗传多样性降低和纯度下降。了解中国南方土鸡的种群遗传结构和遗传多样性对进一步开展选育工作至关重要。本研究分析了来自中国南方 10 个不同品种的 321 只个体的种群遗传结构和遗传多样性。通过比较商品鸡和土鸡，我们确定了本地鸡与商品品种之间发生的选择特征。种群遗传结构分析表明，中国南方的土鸡群体表现出相当水平的遗传多样性。此外，小白鸡和黄麻鸡的商业品系显示出更高的遗传多样性，在聚类水平上与其他本地品种区分开来。然而，这些商业品种中的某些个体在遗传上与本地群体有明显的关系。值得注意的是，这两个商业品种也与其各自的本地品种保持着显著的遗传相似性。为了研究中国南方本地鸡商业化过程中的基因组变化，我们使用了 4 种方法（Fst、ROD、XPCLR 和 XPEHH）来鉴定中国南方本地鸡群体中存在选择特征的潜在候选区域。总共发现了 168 个（由 Fst 和 ROD 鉴定）和 86 个（由 XPCLR 和 XPEHH 鉴定）重叠基因。功能注释分析表明，这些基因可能与繁殖和生长（SAMSN1、HYLS1、ROBO3、FGF14、PRSS23）、肌肉骨骼发育（DNER、MYBPC1、DGKB、ORC1、KLF10）、疾病抗性和环境适应性（PUS3、CRB2、CALD1、USP15、SGCD、LTBP1）以及产蛋量（ADGRB3、ACSF3）有关。总的来说，与商品鸡相比，中国南方的本地鸡拥有更多的选择清扫区域，为未来的遗传研究和选育保护提供了宝贵的基因组资源。