基于全基因组SNP标记分析中国地方鸡品种的遗传多样性和种群结构

doi:10.11843/j.issn.0366-6964.2023.02.013

摘要/Abstract

摘要： 旨在对中国地方鸡品种的遗传多样性与种群结构进行分析。本研究使用Affymetrix Axiom 600K高密度鸡基因分型芯片对来自8个品种的157只地方鸡及233只商品鸡进行基因分型，以品种作为分组来计算各分组的观测杂合度、期望杂合度、次等位基因频率、近交系数及核苷酸多样性分析地方鸡群体的遗传多样性，利用进化树、主成分分析、群体结构、MDS等方法分析鸡群体的群体结构，基于状态同源（IBS）和群体分化系数（Fst）分析种群内部与种群之间的亲缘关系，利用长纯合片段（runs of homozygosity，ROH）估算得到基于ROH的近交系数。结果表明，各群体的观测杂合度均高于期望杂合度，次等位基因频率在0.175~0.236之间，近交系数在0.018~0.205之间，核苷酸多样性在0~6×10^-4之间，进化树与主成分分析表明品种间出现了明显的群体分化，地方鸡群体与商品鸡群的MDS分析发现我国地方鸡与商业肉鸡品种的遗传距离较近；IBS遗传距离在0.092 9~0.319 9之间；各品种成对Fst分析表明，群体间呈现中高分化程度（0.09～0.22）；此次分析共得到了5 242个ROH，长度分布在1~41.51 Mb之间，基于ROH的近交系数在0.010~0.150之间。以上结果表明，地方鸡遗传多样性整体较为丰富，其中狼山鸡与皖南三黄鸡的遗传多样性最高。斗鸡、固始鸡及茶花鸡近交程度较高，可能经历过近交事件。不同品种间出现了较高遗传分化，该研究结果将有助于设计和实施遗传资源保护策略，促进遗传资源在保护中利用、利用中保护。

关键词: 中国地方鸡, 全基因组SNP标记, 遗传多样性, 群体结构, ROH分析

Abstract: The aim of this study was to analyze the genetic diversity and population structure of Chinese native chicken breeds. A total of 157 chickens from 8 Chinese native breeds and 233 commercial chickens were genotyped using Affymetrix Axiom 600K high-density chicken chip. Each breed's genetic diversity was calculated with observed heterozygosity, expected heterozygosity, minor allele frequency, inbreeding coefficient and nucleotide diversity. Population structure was analyzed with neighbor-joining phylogenetic analysis, principal component analysis, population structure analysis and multidimensional scaling (MDS). Identity by state (IBS) and pairwise differentiation coefficient (Fst) were used to study the genetic relationship between and within breeds. Runs of homozygosity (ROH) analysis was used to obtain more accurate inbreeding coefficients. The results showed that the observed heterozygosity of each population was higher than the corresponding expected heterozygosity. Minor allele frequencies ranged from 0.175 to 0.236. Inbreeding coefficients ranged from 0.018 to 0.205. Nucleotide diversity ranged from 0 to 6×10^-4. The obvious genetic differentiation was observed between breeds according to the phylogenetic tree and principal component analysis. MDS analysis revealed a relatively close genetic relationship between Chinese native chickens and purebred broiler lines. IBS genetic distance ranged from 0.092 9 to 0.319 9. The populations had a moderate genetic differentiation based on the pairwise Fst data (0.09-0.22). Furthermore, 5 242 ROHs with lengths ranging from 1 Mb to 41.51 Mb were discovered. The ROH-based inbreeding coefficient (F_ROH) ranged between 0.010 and 0.150. These results revealed that the overall genetic diversity of local chickens is richer. Langshan chicken and Wannan three-yellow chicken had the most genetic diversity. High-levels inbreeding occurred in Fighting chickens, Gushi chickens and Chahua chicken, which might had ever been suffered from inbreeding events. Different breeds existed high genetic differentiation. The results of this study will aid in designing and implementing conservation strategies, which will promote the utilization and conservation of genetic resources.

Key words: Chinese native chicken, genome-wide SNP, genetic diversity, population structure, ROH analysis

中图分类号:

S831.2

高超群, 曹然然, 杜文苹, 胡晓玉, 雷艳茹, 李文婷, 康相涛. 基于全基因组SNP标记分析中国地方鸡品种的遗传多样性和种群结构[J]. 畜牧兽医学报, 2023, 54(2): 554-562.

GAO Chaoqun, CAO Ranran, DU Wenping, HU Xiaoyu, LEI Yanru, LI Wenting, KANG Xiangtao. Genetic Diversity and Population Structure Analysis of Chinese Native Chicken Breeds using Genome-wide SNPs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 554-562.

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