基于全基因组重测序SNP分析宁蒗高原鸡保种群的群体遗传多样性和群体遗传结构

doi:10.11843/j.issn.0366-6964.2024.12.016

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (12): 5498-5510.doi: 10.11843/j.issn.0366-6964.2024.12.016

基于全基因组重测序SNP分析宁蒗高原鸡保种群的群体遗传多样性和群体遗传结构

徐扩卫¹(), 李卓辉²(), 冷堂健¹, 熊宝³, 周杰珑¹, 郭盘江¹, 王禹²^,*(), 陈粉粉¹^,*()

1. 西南林业大学生物与食品工程学院, 昆明 650224
2. 西北农林科技大学动物科技学院, 杨凌 712100
3. 宁蒗彝族自治县拉伯乡宁蒗高原鸡原种保种场, 宁蒗 674309

收稿日期:2024-05-22 出版日期:2024-12-23 发布日期:2024-12-27
通讯作者: 王禹,陈粉粉 E-mail:xukuowei@foxmail.com;lizhuohui2021@nwafu.edu.cn;wang_yu@nwsuaf.edu.cn;ffchen03@sina.com
作者简介:徐扩卫(1998-), 男, 云南曲靖人, 硕士生, 主要从事动物遗传资源保护及利用研究, E-mail: xukuowei@foxmail.com
李卓辉(1996-), 男, 甘肃天水人, 硕士生, 主要从事家畜遗传育种与繁殖研究, E-mail: lizhuohui2021@nwafu.edu.cn
第一联系人：
徐扩卫和李卓辉为同等贡献作者
基金资助:
云南省农业基础研究联合专项面上项目(202101BD070001-070)

Analysis of Population Genetic Diversity and Population Genetic Structure of Conservation Population in Ninglang Plateau Chickens Based on Whole-genome Resequencing SNP

XU Kuowei¹(), LI Zhuohui²(), LENG Tangjian¹, XIONG Bao³, ZHOU Jielong¹, GUO Panjiang¹, WANG Yu²^,*(), CHEN Fenfen¹^,*()

1. College of Biological Science and Food Engineering, Southwest Forestry University, Kunming 650224, China
2. College of Animal Sciences and Technology, Northwest A & F University, Yangling 712100, China
3. Ninglang Plateau Chickens Original Breed Conservation Farm, Labai Township, Ninglang Yi Autonomous County, Ninglang 674309, China

Received:2024-05-22 Online:2024-12-23 Published:2024-12-27
Contact: WANG Yu, CHEN Fenfen E-mail:xukuowei@foxmail.com;lizhuohui2021@nwafu.edu.cn;wang_yu@nwsuaf.edu.cn;ffchen03@sina.com

摘要/Abstract

摘要：

旨在分析宁蒗高原鸡保种群的群体遗传多样性和群体遗传结构，以期更好的保护和利用宁蒗高原鸡这一种质资源。本研究利用全基因组重测序技术检测宁蒗高原鸡(n=57)、大围山微型鸡(n=20)、尼西鸡(n=11)和独龙鸡(n=10)群体的单核苷酸多态性(single-nucleotide polymorphism, SNP)，以群体观测杂合度(Ho)、期望杂合度(He)、多态性标记比例(P_N)、核苷酸多态性(Pi)、次等位基因频率(Maf)以及连锁不平衡(linkage disequilibrium, LD)衰减情况分析群体遗传多样性；使用主成分分析、系统发育树、群体结构分析探究不同品种的群体遗传结构；以群体分化指数(Fst)评估品种间的分化程度，以状态同源(identity by state, IBS)、G矩阵和群体近交系数(F_ROH)分析宁蒗高原鸡保种群体的亲缘关系。结果显示，宁蒗高原鸡群体的观测杂合度(Ho)为0.212，小于其0.221的期望杂合度(He)，而大围山微型鸡、独龙鸡和尼西鸡的Ho均高于He，表明宁蒗高原鸡群体遗传多样性较为丰富；LD衰减分析表明，4个品种的衰减速度由快到慢依次为宁蒗高原鸡、大围山微型鸡、尼西鸡、独龙鸡，说明宁蒗高原鸡群体遗传多样性最高，基因组受选择程度最低；主成分分析和系统发育树结果表明，宁蒗高原鸡分为3个支系，大围山微型鸡与宁蒗高原鸡、独龙鸡和尼西鸡之间的遗传背景差异较大；群体结构分析显示，当K=2时为最优分群数，宁蒗高原鸡血统较为复杂，独龙鸡和尼西鸡血统较为相似；群体遗传分化结果发现，宁蒗高原鸡与大围山微型鸡、尼西鸡、独龙鸡之间均出现中等程度的分化，而独龙鸡和尼西鸡之间的遗传分化指数较小；IBS矩阵和G矩阵分析发现，宁蒗高原鸡保种群体间大部分个体亲缘关系较远，少数个体亲缘关系较近。以上结果表明，宁蒗高原鸡与大围山微型鸡、尼西鸡、独龙鸡之间均存在中等程度的分化，宁蒗高原鸡保种群体的遗传多样性较为丰富，但保种群体间存在一定的近交趋势，应建立有效的育种方案，加强保种，避免近交衰退。

关键词: 全基因组, 宁蒗高原鸡, 群体遗传多样性, 群体遗传结构

Abstract:

In order to better protect and utilize the Ninglang Plateau chickens, the population genetic diversity and population genetic structure of Ninglang Plateau chickens conserved population were explored in this study. Whole-genome resequencing technology was used to detect single-nucleotide polymorphism (SNP) in Ninglang Plateau chickens(n=57), Daweishan Mini chickens(n=20), Dulong chickens(n=10) and Nixi chickens(n=11) populations, and population genetic diversity was analyzed by observing heterozygosity (Ho), expected heterozygosity (He), polymorphic nucleotide ratio (P_N), nucleotide diversity (Pi), and minor allele frequency (Maf), and linkage disequilibrium (LD) decay. Principal component analysis, phylogenetic tree, and population structure analysis were employed to examine the population genetic structure of different breeds. The degree of differentiation between breeds was evaluated using the fixation index (Fst). Additionally, the genetic relatedness within the conservation population of Ninglang Plateau chickens were analyzed using identity by state (IBS), G matrix, and the coefficient of inbreeding (F_ROH). The results showed that the observed heterozygosity (Ho) of the Ninglang Plateau chickens population was 0.212, which was lower than its expected heterozygosity (He) of 0.221, while the Ho values of Daweishan Mini chickens, Dulong chickens, and Nixi chickens were higher than their respective He values, indicating that the genetic diversity of the Ninglang Plateau chickens population was relatively high; LD decay analysis showed that the decay rates of the 4 breeds from fastest to slowest was Ninglang Plateau chickens, Daweishan Mini chickens, Nixi chickens, and Dulong chickens, indicating that Ninglang Plateau chickens population had the highest genetic diversity and the lowest degree of genome selection. The results of principal component analysis and phylogenetic tree showed that Ninglang Plateau chickens were divided into 3 branches. Daweishan Mini chickens exhibited significant genetic divergence from Ninglang Plateau chickens, Dulong chickens, and Nixi chickens. Population structure analysis revealed that the optimal number of clusters was K=2, with Ninglang Plateau chickens exhibiting a complex genetic background, while Dulong chickens and Nixi chickens had relatively similar genetic backgrounds. Population genetic differentiation analysis found moderate levels of differentiation between Ninglang Plateau chickens and Daweishan Mini chickens, Nixi chickens, and Dulong chickens, whereas the genetic differentiation index between Dulong chickens and Nixi chickens was lower; IBS matrix and G matrix analysis revealed that most individuals within the conservation population of Ninglang Plateau chickens were distantly related, with a few individuals showing closer relationships. The results showed that there was a moderate differentiation between Ninglang Plateau chickens and Daweishan Mini chickens, Nixi chickens, and Dulong chickens. The genetic diversity of the Ninglang Plateau chickens breeding population was relatively rich, but there was a trend of inbreeding within the conservation population. Therefore, effective breeding programs should be established, and conservation efforts should be strengthened to avoid inbreeding depression.

Key words: whole genome, Ninglang Plateau chickens, population genetic diversity, population genetic structure

中图分类号:

S831.2

徐扩卫, 李卓辉, 冷堂健, 熊宝, 周杰珑, 郭盘江, 王禹, 陈粉粉. 基于全基因组重测序SNP分析宁蒗高原鸡保种群的群体遗传多样性和群体遗传结构[J]. 畜牧兽医学报, 2024, 55(12): 5498-5510.

XU Kuowei, LI Zhuohui, LENG Tangjian, XIONG Bao, ZHOU Jielong, GUO Panjiang, WANG Yu, CHEN Fenfen. Analysis of Population Genetic Diversity and Population Genetic Structure of Conservation Population in Ninglang Plateau Chickens Based on Whole-genome Resequencing SNP[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5498-5510.

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品种 Breed	观测杂合度(Ho) Observed heterozygosity	期望杂合度(He) Expected heterozygosity	多态标记比例(P_N) Polymorphic marker ratio	核苷酸多态性(Pi) Nucleotide diversity	次等位基因频率(Maf) Minor allele frequency
大围山微型鸡Daweishan	0.232	0.229	0.819 0	4.04×10^-3	0.164
独龙鸡Dulong	0.239	0.225	0.736 7	4.06×10^-3	0.162
尼西鸡Nixi	0.231	0.219	0.730 6	3.83×10^-3	0.158
宁蒗高原鸡Ninglang	0.212	0.221	0.868 3	3.94×10^-3	0.159

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基于全基因组重测序SNP分析宁蒗高原鸡保种群的群体遗传多样性和群体遗传结构

Analysis of Population Genetic Diversity and Population Genetic Structure of Conservation Population in Ninglang Plateau Chickens Based on Whole-genome Resequencing SNP

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