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

文献类型： 外文期刊

作者： Qi, Lin 1 ; Xiao, Liangchao 1 ; Fu, Rong 1 ; Nie, Qinghua 1 ; Zhang, Xiquan 1 ; Luo, Wen 1 ;

作者机构： 1.South China Agr Univ, State Key Lab Livestock & Poultry Breeding, Guangzhou 510642, Peoples R China

2.South China Agr Univ, Lingnan Guangdong Lab Agr, Guangzhou 510642, Peoples R China

3.South China Agr Univ, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Guangzhou 510642, Peoples R China

4.South China Agr Univ, Key Lab Chicken Genet Breeding & Reprod, Minist Agr & Rural Affair, Guangzhou 510642, Peoples R China

5.South China Agr Univ, Coll Anim Sci, Dept Anim Genet Breeding & Reprod, Guangzhou 510642, Peoples R China

关键词： population structure; genetic diversity; selection signature; South China native chicken; commercialization

期刊名称：POULTRY SCIENCE （ 影响因子：3.8； 五年影响因子：4.1 ）

ISSN： 0032-5791

年卷期： 2024 年 103 卷 7 期

页码：

收录情况： SCI

摘要： 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 identi fied 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 signi ficant 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 (identi fied by Fst and ROD) and 86 (identi fied 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.

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