“优信-1”在地方鸡种遗传多样性与结构分析中的应用效果。

Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China.

Poultry Institute of Jiangsu Province, Yangzhou 225125, China.

Yi Chuan. 2024 Aug;46(8):640-648. doi: 10.16288/j.yczz.24-068.

China's local chicken breeds are rich in resources, and have formed different germplasm characteristics in the process of long-term selection and evolution. Scientific assessment of population genetic diversity and identification of inter-breed genetic structure are of great value to the protection and innovative utilization of local chicken breed resource. In order to evaluate the application effectiveness of 23K SNP chip "Youxin-1" in the analysis of genetic diversity and genetic structure of local chickens, we used RADseq to identify genomic genetic variation of 21 local chicken breeds and developed 23K chip "Youxin-1". The genetic statistics of each variety were calculated based on two sets of SNP data, and correlation, fitting and phylogenetic analysis were carried out to evaluate the application effectiveness of the chip. The results showed that the observed heterozygosity (), polymorphism information content (PIC), inbred coefficient () and genetic differentiation coefficient () calculated based on the two SNP data sets were basically consistent in the 21 local chicken breeds. The genetic diversity of Langya chicken (LA), Piao chicken (PJ) and Wenchang chicken (WC) was relatively rich. The genetic diversity of Bian chickens (BJ), Langshan chickens (LS), Gushi chickens (GS), Dongxiang blue-eggshell chickens (DX) and Beijing fatty chickens (BY) was relatively poor, and the correlation coefficients of , PIC, and average in the two groups were 0.794, 0.901, 0.926 and 0.984, respectively, all reaching extremely significant levels (<0.01) with a high degree of fit (<0.001) and were 0.644, 0.827, 0.916 and 0.927. For the two sets of SNP data, the evolutionary tree constructed by neighbor-joining (NJ) method and maximum likelihood (ML) method was reasonable, and the 21 local chicken breeds were generally divided into six categories, which was consistent with the formation history and geographical distribution of the varieties. The 23K chip also realized reasonable clustering of the five new varieties without individual deviation. There are some differences in the estimation of genetic statistics using SNP with different densities, and data standardization is needed. 23K chip has good efficacy in the analysis of genetic diversity and structure of local chickens.

中国地方鸡种资源丰富，在长期的选育和进化过程中形成了不同的种质特性。科学评估群体遗传多样性，鉴定品种间的遗传结构，对于保护和创新利用地方鸡种资源具有重要意义。为评估 23K SNP 芯片“优信 1 号”在分析地方鸡种遗传多样性和遗传结构中的应用效果，本研究利用 RADseq 技术对 21 个地方鸡种进行基因组遗传变异分析，并开发了 23K 芯片“优信 1 号”。基于两套 SNP 数据计算各品种的遗传统计量，进行相关性、拟合度和系统进化分析，评估芯片的应用效果。结果表明，在 21 个地方鸡种中，基于两套 SNP 数据计算的观测杂合度（）、多态信息含量（PIC）、近交系数（）和遗传分化系数（）基本一致。狼牙鸡（LA）、瓢鸡（PJ）和文昌鸡（WC）的遗传多样性较丰富，边鸡（BJ）、狼山鸡（LS）、固始鸡（GS）、东乡绿壳蛋鸡（DX）和北京油鸡（BY）的遗传多样性较贫乏，两组间的相关系数为 0.794、0.901、0.926 和 0.984，均达到极显著水平（<0.01），拟合度均<0.001，为 0.644、0.827、0.916 和 0.927。两套 SNP 数据构建的基于邻接法（NJ）和最大似然法（ML）的系统进化树合理，21 个地方鸡种基本分为六大类，与品种的形成历史和地理分布一致。23K 芯片对 5 个新培育品种也能实现合理聚类，无个体偏离。不同密度 SNP 数据对遗传统计量的估计存在一定差异，需要数据标准化。23K 芯片在地方鸡种遗传多样性和遗传结构分析中具有较好的功效。