老挝本地山羊气候适应和生产性状相关候选基因的选择分析。

IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Sang Van Le, Panoraia Alexandri, Julius H J van der Werf, Luisa Olmo, Stephen W Walkden-Brown, Sara de Las Heras-Saldana
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引用次数: 0

摘要

检测选择足迹提供了有价值的见解进化过程和机制的表型多样性的选择性状。驯化、自然和人工选择以及繁殖产生了适应当地环境的本地山羊,使它们成为重要的遗传资源。了解这些适应性的遗传基础可以指导制定有效的育种策略,以保护和改善当地山羊品种。本研究利用Illumina的山羊SNP50 BeadChip对老挝本地山羊的选择特征进行了研究,分析了420只老挝本地山羊、87只来自3个中国品种的山羊和51只来自巴基斯坦的Teddi山羊作为测试群体。我们采用了去相关复合多重信号(DCMS)方法,结合了9个统计检验的p值,包括老挝山羊群体的纯合子序列,老挝山羊与测试群体之间的固定指数和跨群体扩展单倍型纯合子。采用0.05的阈值对多重检验进行调整,确定了显著的基因组区域。我们的研究结果发现了24个基因组区域,其中包含68个独特的编码基因。分析显示,已注释的和新的候选基因与多种特征相关,包括对热带季风气候的适应(如ABHD6、GATA4和MSRA)和经济性状,如生长和状态(如CNTNAP5、FAM135B和GATA4)、繁殖(如NPHP3、ARSJ和GATA4)、产奶量(如MRPL32、PRSS51和EPHA7)和胴体特征(如GNAI1、SOX7和FAM135B)。这些结果为老挝本地山羊经济性状和热带气候适应的遗传机制提供了有见地的信息。将来自各种统计检验的p值组合到一个单一的DCMS框架中,有效地帮助选择和优先考虑候选基因以进行进一步分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Signature of Selection Analysis Reveals Candidate Genes Related to Climate Adaptation and Production Traits in Lao Native Goats.

Detecting selection footprints offers valuable insight into evolutionary processes and the mechanisms underlying phenotypic diversity in selected traits. Domestication, natural and artificial selection, and breeding have produced indigenous goats well-adapted to their local environments, making them crucial genetic resources. Understanding the genetic foundation of these adaptations can guide the development of effective breeding strategies to preserve and improve local goat breeds. This study investigated selection signatures in Lao native goats using Illumina's Goat SNP50 BeadChip, analysing 420 Lao native goats, 87 goats from three Chinese breeds, and 51 Teddi goats from Pakistan as test populations. We applied the de-correlation composite multiple signals (DCMS) method, incorporating p values from nine statistical tests, including runs of homozygosity in the Lao goat population, and fixation index and cross-population extended haplotype homozygosity between Lao goats and test populations. Significant genomic regions were identified using a 0.05 threshold adjusted for multiple testing. Our results uncovered 24 genomic regions harbouring 68 unique-coding genes. Analysis revealed both annotated and novel candidate genes linked to a variety of characteristics, including adaptation to the tropical monsoon climate (e.g., ABHD6, GATA4 and MSRA) and economic traits like growth and status (e.g., CNTNAP5, FAM135B and GATA4), reproduction (e.g., NPHP3, ARSJ and GATA4), milk production (e.g., MRPL32, PRSS51 and EPHA7), and carcass characteristics (e.g., GNAI1, SOX7 and FAM135B). These results offered insightful information about genetic mechanisms driving economic traits and tropical climate adaptation of Lao native goats. Combining p values from various statistical tests into a single DCMS framework effectively assists in selecting and prioritising candidate genes for further analysis.

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来源期刊
Journal of Animal Breeding and Genetics
Journal of Animal Breeding and Genetics 农林科学-奶制品与动物科学
CiteScore
5.20
自引率
3.80%
发文量
58
审稿时长
12-24 weeks
期刊介绍: The Journal of Animal Breeding and Genetics publishes original articles by international scientists on genomic selection, and any other topic related to breeding programmes, selection, quantitative genetic, genomics, diversity and evolution of domestic animals. Researchers, teachers, and the animal breeding industry will find the reports of interest. Book reviews appear in many issues.
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