Table_1_Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data.DOCX

Following chicken domestication, diversified chicken breeds were developed by both natural and artificial selection, which led to the accumulation of abundant genetic and phenotypic variations, making chickens an ideal genetic research model. To better understand the genetic structure of chicken breeds under different selection pressures, we genotyped various chicken populations with specific selection targets, including indigenous, commercial, gamecock, and wild ancestral chickens, using the 600K SNP array. We analyzed the population structure, genetic relationships, run of homozygosity (ROH), effective population number (Ne), and other genetic parameters. The wild ancestral population, red junglefowl (RJF), possessed the highest diversity, in comparison with all other domesticated populations, which was supported by linkage disequilibrium decay (LD), effective population number, and ROH analyses. The gamecock breeds, which were subjected to stronger male-biased selection for fighting-related traits, also presented higher variation than the commercial and indigenous breeds. Admixture analysis also indicated that game breed is a relatively independent branch of Chinese local breeds. Following intense selection for reproductive and productive traits, the commercial lines showed the least diversity. We also observed that the European local chickens had lower genetic variation than the Chinese local breeds, which could be attributed to the shorter history of the European breed. ROH were present in a breed specific manner and 191 ROH island were detected on four groups (commercial, local, game and wild chickens). These ROH islands were involved in egg production, growth and silky feathers and other traits. Moreover, we estimated the effective sex ratio of these breeds to demonstrate the change in the ratio of the two sexes. We found that commercial chickens had a greater sex imbalance between females and males. The commercial lines showed the highest female-to-male ratios. Interestingly, RJF comprised a greater proportion of males than females. Our results show the population genetics of chickens under selection pressures, and can aid in the development of better conservation strategies for different chicken breeds.

家鸡驯化后，经自然与人工选择培育出多样的家鸡品种，积累了丰富的遗传与表型变异，使家鸡成为理想的遗传学研究模型。为深入解析不同选择压力下家鸡品种的遗传结构，本研究采用600K单核苷酸多态性（SNP）芯片，对具有特定选择目标的多类家鸡群体进行基因分型，包括地方品种、商业品系、斗鸡及野生祖先群体红原鸡（RJF）。本研究分析了群体结构、遗传亲缘关系、纯合子片段（ROH）、有效群体大小（Ne）及其他遗传参数。野生祖先群体红原鸡（RJF）的遗传多样性在所有驯化群体中最高，这一结果得到连锁不平衡衰减（LD）、有效群体大小及ROH分析的支持。斗鸡品种因针对打斗相关性状受到更强的雄性偏向性选择，其遗传变异水平也高于商业品系与地方品种。群体混合分析（Admixture分析）同样表明，斗鸡是中国地方家鸡品种的一个相对独立的分支。经针对繁殖与生产性状的高强度选择后，商业品系的遗传多样性最低。本研究还发现，欧洲地方家鸡的遗传变异水平低于中国地方家鸡，这一现象可归因于欧洲家鸡的驯化历史更短。ROH呈现品种特异性分布模式，在四类群体（商业品系、地方品种、斗鸡及野生原鸡）中共检测到191个ROH岛。这些ROH岛涉及产蛋性能、生长发育及丝羽等性状。此外，本研究估算了各品种的有效性别比例，以解析雌雄两性的比例变化情况。研究发现商业品系家鸡的雌雄性别比例失衡程度更高，其雌雄性比为所有群体中最高。值得注意的是，红原鸡群体的雄性占比高于雌性。本研究结果阐明了选择压力下家鸡的群体遗传特征，可为不同家鸡品种的优化保护策略制定提供参考。