基于RAD-seq简化基因组测序的19个地方鸡种遗传进化研究

旨在基因组水平上揭示地方鸡种的遗传进化，发掘重要种质特性基因。本研究利用简化基因组RAD-seq测序鉴定19个地方鸡种（每个品种按照家系选取30个个体，10公、20母）基因组SNP标记，计算观察杂合度（Ho）、核苷酸多样度（Pi）、近交系数（Fis）、遗传分化系数（Fst）和基因流（Nm）等遗传统计量指标，分析地方鸡种的遗传多样性和遗传结构，并通过选择信号检测鉴定基因组受选择基因。结果表明，在19个地方鸡种中鉴定出400 562个SNPs标记。瓢鸡（PJ）和文昌鸡（WC）的遗传多样性最为丰富，观察杂合度（Ho）分别为0.246 8、0.243 0，核苷酸多样度（Pi）分别为0.278 1、0.265 5；河南斗鸡（DJ）的遗传多样性相对匮乏，Ho为0.156 0，Pi为0.175 2；东乡绿壳蛋鸡（DX）和边鸡（BJ）的近交系数最高（Fis>0.160 0）。瓢鸡与文昌鸡、惠阳胡须鸡（HX）、藏鸡（ZZ）、大围山微型鸡（WX），惠阳胡须鸡与文昌鸡，藏鸡与茶花鸡（CH）间的遗传分化最低（Fst<0.100 0），对应的基因流最高（Nm>0.240 0）。河南斗鸡与其它品种间的遗传分化均处于较高水平，与其中15个品种间的Fst>0.200 0、Nm<1.000 0。遗传聚类分析（2个引入品种做外群）将地方鸡种总体上分为5类，与品种形成历史和地理分布基本吻合。通过选择信号分析，在19个地方鸡种合并群体中检测出9个常染色体上的26个区域受到选择作用，包含31个受选择基因。这些受选择基因广泛参与免疫系统调节、生殖机能调控、应激响应、代谢等生物学过程。利用基因组SNP标记能更全面准确地揭示地方鸡种的遗传多样性和遗传结构，选择作用主要体现在对地方鸡种抗逆抗病特性、配子活力及行为等方面的塑造。

Study on Genetic Evolution of 19 Indigenous Chicken Breeds Based on RAD-seq

The purposes of this study were to reveal the genetic evolution of local chicken breeds at the genomic level and to discover genes with important germplasm characteristics. Restriction site-associated DNA sequencing (RAD-seq) technology was employed to identify single nucleotide polymorphism (SNP) markers in 19 indigenous chicken breeds. For each breed, thirty individuals(10 males and 20 females) were selected as experimental materials according to their family records. The genetic diversity and structure were analyzed by calculating the indicators of genetic statistics, which contained observed heterozygosity (Ho), nucleotide diversity (Pi), inbreeding coefficients (Fis), genetic differentiation coefficients (Fst) and gene flows (Nm). The selected genes were also identified through genome selective signals testing. The results showed that 400 562 SNP markers were identified in 19 indigenous chicken populations after data quality control. The PJ and WC populations had the highest genetic diversity, with Ho 0.246 8, 0.243 0, and Pi 0.278 1, 0.265 5, respectively. The DJ population had the lowest Ho and Pi, which were 0.156 0 and 0.157 2,respectively. The Fis in DX and BJ populations were higher than 0.160 0. The Fst among PJ and WC, HX, ZZ, WX, HX and WC, ZZ and CH were all lower than 0.100 0, correspondingly the Nm were all higher than 0.240 0. In terms of single population, the DJ population had higher Fst and lower Nm when compared to other chicken breeds. The phylogenetic tree, constructed using two foreign chicken breeds AK and RW as outgroups, divided the 19 indigenous chicken breeds into 5 clusters, which was consistent with their breeding history and geography distribution. In total, 26 selected areas and 31 candidate genes were identified through the Z transformation of heterozygosity (ZHp) signal testing. These selected genes were widely involved in the biological processes of immune system regulation, reproduction regulation, response to stress and metabolism. In conclusion, the genomic SNP markers have more advantage in revealing genetic diversity and structure of indigenous chicken breeds. The selection effects are mainly reflected in the shaping of local chicken breeds' resistance and disease resistance characteristics, gamete vitality and behavior.