Reducing foreign genetic contributions to the YDH pig population by segment-based advanced optimum contribution selection

IF 4 2区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Animal Pub Date : 2024-08-08 DOI:10.1016/j.animal.2024.101292

L. Cao , T.H.E. Meuwissen , P. Berg , X. Yu , J. Yang , Z. Wu

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引用次数: 0

Abstract

Yuedonghei (YDH) is the only local pig breed with full black hair among the four well-known local pig breeds originated and distributed in Guangdong province, China, which caters to the consumers’ preference of the local market of 127 million residents and thus brings a significantly above-average price. However, considerable genetic introgression (GI) has been reported for the YDH population, i.e., gene flow into YDH from other pig breeds, which is mainly due to the recent crossbreeding with several mainstream breeds for upgrading reasons. Therefore, this study aimed to evaluate the GI as well as the conservation status in the current YDH population and test the feasibility of advanced optimum contribution selection (aOCS) in alleviating GI in YDH. We first analysed the genetic diversity, ancestral structure, population structure, and phylogeny of 360 YDH relative to 782 publicly downloaded pigs of 42 Eurasian or American breeds and wild boars, based on single nucleotide polymorphism chip data. Then, we selected 304 initial YDH and stochastically simulated a practical conservation programme that spanned 10 discrete generations and implemented haplotype segment-based aOCS in every generation. The expected and observed heterozygosity of 360 YDH were 0.344 and 0.336. The linkage disequilibrium-based recent effective population size (

N_{e}

) was 32.89. Considerable GI amounting to 32.9% foreign ancestry was found in 28 lowly related YDH individuals using admixture analysis. In the simulated YDH conservation programme, the average native genomic contribution was increased from 50.4 to 71.4% while maintaining a

N_{e}

of 100 by controlling classic kinship and native kinship. Our study showed that segment-based aOCS that required only genomic data can be used to alleviate GI in the current YDH population and meanwhile increase its

N_{e}

, which provided strategic insights into the sustainable conservation of local genetic resources of livestock.

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通过基于区段的高级最佳贡献选择，减少YDH猪群体中的外来遗传贡献

粤东黑（）是中国广东省原产和分布的四个著名地方猪种中唯一的全黑毛地方猪种，迎合了当地 1.27 亿居民的消费偏好，因此价格明显高于平均水平。然而，据报道，粤东黄猪种群存在相当大的基因导入（），即基因从其他猪种流入粤东黄猪，这主要是由于近年来粤东黄猪为升级换代与几个主流猪种杂交所致。因此，本研究旨在评估目前粤东黄猪群体的遗传变异和保育状况，并检验先进的最佳贡献选择（）在缓解粤东黄猪遗传变异方面的可行性。首先，我们基于单核苷酸多态性芯片数据分析了 360 头 YDH 相对于 782 头公开下载的 42 个欧亚或美洲猪种和野猪的遗传多样性、祖先结构、种群结构和系统发育。然后，我们选择了 304 个初始 YDH，随机模拟了一个跨越 10 个不连续世代的实际保护计划，并在每一代实施了基于单倍型片段的 aOCS。360 个 YDH 的预期杂合度为 0.344，观察到的杂合度为 0.336。基于连锁不平衡的近期有效种群规模（）为 32.89。通过掺杂分析，在 28 个低亲缘关系的 YDH 个体中发现了大量的 GI，即 32.9% 的外来祖先。在模拟的 YDH 保护方案中，通过控制经典亲缘关系和本地亲缘关系，本地基因组的平均贡献率从 50.4% 提高到 71.4%，同时保持 a 为 100。我们的研究表明，基于片段的 aOCS 只需要基因组数据，就能用于缓解当前 YDH 群体中的 GI，同时提高 YDH 群体的基因组贡献率，这为当地家畜遗传资源的可持续保护提供了战略性启示。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Animal 农林科学-奶制品与动物科学

CiteScore

7.50

自引率

2.80%

发文量

246

审稿时长

3 months

期刊介绍： Editorial board animal attracts the best research in animal biology and animal systems from across the spectrum of the agricultural, biomedical, and environmental sciences. It is the central element in an exciting collaboration between the British Society of Animal Science (BSAS), Institut National de la Recherche Agronomique (INRA) and the European Federation of Animal Science (EAAP) and represents a merging of three scientific journals: Animal Science; Animal Research; Reproduction, Nutrition, Development. animal publishes original cutting-edge research, ''hot'' topics and horizon-scanning reviews on animal-related aspects of the life sciences at the molecular, cellular, organ, whole animal and production system levels. The main subject areas include: breeding and genetics; nutrition; physiology and functional biology of systems; behaviour, health and welfare; farming systems, environmental impact and climate change; product quality, human health and well-being. Animal models and papers dealing with the integration of research between these topics and their impact on the environment and people are particularly welcome.