外来品种的引进和育种公司新品系的培育,对华南地区的土鸡提出了挑战,包括品种特征的丧失,降低遗传多样性,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于进一步推进育种工作至关重要。在这项研究中,我们分析了来自中国南方10个不同品种的321个个体的群体遗传结构和遗传多样性。通过比较商业鸡和本地鸡,我们确定了在本地鸡和商业品种之间发生的选择特征。对种群遗传结构的分析表明,华南本地鸡种群表现出相当高的遗传多样性。此外,小白鸡和黄马鸡的商业路线表现出更高的遗传多样性水平,在聚类级别将它们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与本地种群表现出明显的遗传关系。值得注意的是,这两个商业品种也保留了显著程度的遗传相似性,他们各自的本地同行。为了研究本地鸡商业化过程中发生的基因组变化,我们采用了4种方法(FST,杆,XPCLR,和XPEHH)以确定在中国南方土鸡种群中显示选择性特征的潜在候选区域。共发现168个(由Fst和ROD鉴定)和86个(由XPCLR和XPEHH鉴定)重叠基因。功能注释分析显示这些基因可能与繁殖和生长有关(SAMSN1,HYLS1,ROBO3,FGF14,PRSS23),肌肉骨骼发育(DNER,MYBPC1,DGKB,ORC1,KLF10),抗病性和环境适应性(PUS3,CRB2,CALD1,USP15,SGCD,LTBP1),以及鸡蛋生产(ADGRB3,ACSF3)。总的来说,与商品鸡相比,华南地区的土鸡拥有许多选择性扫掠区域,为今后的遗传研究和育种保护丰富宝贵的基因组资源。
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.