基于全基因组SNP评估中国地方鸡不同保种群体的保种效果

doi:10.1016/j.jia.2023.10.009

摘要/Abstract

摘要：

为了保护各保种群体的遗传多样性和环境适应力，保种计划需要进行严格的评估。本研究利用全基因组SNP对中国两个地方鸡品种，固始鸡 (GS) 和淅川乌骨鸡 (XB) 的不同保种群进行了比较分析，以探究它们的遗传多样性和群体结构随时间的动态变化。根据保护方法和世代的不同，本研究GS与XB分为五个保种群：GS1 (2010年采样，异地保种)、GS2 (2019年采样，异地保种)、GS3 (2019年采样，原产地保种)、XB1 (2010年采样，原产地保种) 和 XB2 (2019年采样，原产地保种)。研究采用该分组计算观测杂合度、期望杂合度、多态性位点、等位基因丰度、核苷酸多样性、近交系数、连续性纯合片段、遗传多样性贡献度、连锁不平衡衰减及历史有效群体大小变化分析保种群遗传多样性动态变化。利用进化树、主成分分析和祖先成分分析等方法分析保种群的群体结构。结果表明，GS保种群 (GS1,G2及GS3)的遗传多样性指标变化趋势相一致，原产地保护策略下的GS3种群具有最高的多样性，异地保种策略下的GS2种群遗传多样性最低，且GS2的近交程度高于GS1和GS3。采用原产地保种策略的XB保种群 (XB1和XB2) 的遗传多样性没有明显变化。根据遗传多样性贡献度分析，GS3在GS品种中对总基因和等位基因多样性的贡献最高，而XB1和XB2的遗传贡献相似。此外，尽管GS2和GS3属于相同的世代，但在不同的保护计划（原产地和异地保种）下，GS2的遗传多样性较低，而XB1和XB2的遗传多样性水平相似。在群体结构方面，GS保种群与XB保种群呈现群体分层，GS3与GS1及GS2呈现群体分层，XB1与XB2无明显群体分层。总体而言，我们的研究结果表明，异地保种策略可以减缓近交事件的发生，但在保种群规模较小的情况下，无法完全防止遗传多样性的丧失；而原产地保护种群由于种群规模较大，可以维持较低的近交增量，维持相对较高的遗传多样性水平。

Abstract: Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations (GS1, 2010, ex-situ; GS2, 2019, ex-situ; GS3, 2019, in-situ; XB1, 2010, in-situ; and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs (in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

Key words: Genome-wide SNPs , Conservation , Genetic diversity , Ex-situ , in-situ

. 基于全基因组SNP评估中国地方鸡不同保种群体的保种效果[J]. Journal of Integrative Agriculture, 2024, 23(3): 975-987.

Wenting Li, Chaoqun Gao, Zhao Cai, Sensen Yan, Yanru Lei, Mengya Wei, Guirong Sun, Yadong Tian, Kejun Wang, Xiangtao Kang.

Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs [J]. Journal of Integrative Agriculture, 2024, 23(3): 975-987.

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