畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (12): 5498-5510.doi: 10.11843/j.issn.0366-6964.2024.12.016
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,*(
)
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徐扩卫和李卓辉为同等贡献作者
基金资助:
XU Kuowei1(), LI Zhuohui2(
), LENG Tangjian1, XIONG Bao3, ZHOU Jielong1, GUO Panjiang1, WANG Yu2,*(
), CHEN Fenfen1,*(
)
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:
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(PN)、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(FROH)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。
中图分类号:
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.
表 1
群体遗传多样性指标"
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(PN) 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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