Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning

IF 3.8 1区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Poultry Science Pub Date : 2024-11-22 DOI:10.1016/j.psj.2024.104585

Fu Wei , Zhang Ran , Ding Hong , Wang Wenjun , Liu Huage , Zang Sumin , Zhou Rongyan

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Abstract

Taihang is an indigenous breed in Hebei Province and has a long history of evolution. To uncover the genetic basis and protect the genetic resources, it is important to develop accurate markers to identify Taihang at the molecular level. In this study, a total of 137 individuals from Taihang and other 4 breeds were selected to construct a genome-wide SNP map. The population genetic structure analysis revealed clear differentiation among the five breeds. A total of 47 SNPs were identified for differentiating Taihang from other breeds based on the fixation index (FST), linkage disequilibrium (LD) pruning, and machine learning, further validated using principal component analysis (PCA) and genetic relationship matrix (GRM). The 47 SNPs were annotated to genes associated with production, growth and development, immunity, adaptation, and appearance. Overall, the combination of 47 SNPs enables precise identification of Taihang, which significantly contributes to the preservation of native genetic resources.

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利用全基因组 SNP 和机器学习鉴定太行鸡特异性遗传标记

太行是河北省的本土品种，有着悠久的进化历史。为了揭示其遗传基础并保护遗传资源，开发准确的标记物在分子水平上识别太行非常重要。本研究选取了太行和其他 4 个品种共 137 个个体，构建了全基因组 SNP 图谱。种群遗传结构分析表明，5个品种之间存在明显分化。基于固定指数（FST）、连锁不平衡（LD）剪枝和机器学习，共鉴定出47个SNPs，并利用主成分分析（PCA）和遗传关系矩阵（GRM）进一步验证了这些SNPs，以区分太行和其他品种。47 个 SNP 被注释为与生产、生长发育、免疫、适应和外观相关的基因。总之，47 个 SNPs 的组合实现了对太行的精确鉴定，极大地促进了本土遗传资源的保护。

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来源期刊

Poultry Science 农林科学-奶制品与动物科学

CiteScore

7.60

自引率

15.90%

发文量

审稿时长

94 days

期刊介绍： First self-published in 1921, Poultry Science is an internationally renowned monthly journal, known as the authoritative source for a broad range of poultry information and high-caliber research. The journal plays a pivotal role in the dissemination of preeminent poultry-related knowledge across all disciplines. As of January 2020, Poultry Science will become an Open Access journal with no subscription charges, meaning authors who publish here can make their research immediately, permanently, and freely accessible worldwide while retaining copyright to their work. Papers submitted for publication after October 1, 2019 will be published as Open Access papers. An international journal, Poultry Science publishes original papers, research notes, symposium papers, and reviews of basic science as applied to poultry. This authoritative source of poultry information is consistently ranked by ISI Impact Factor as one of the top 10 agriculture, dairy and animal science journals to deliver high-caliber research. Currently it is the highest-ranked (by Impact Factor and Eigenfactor) journal dedicated to publishing poultry research. Subject areas include breeding, genetics, education, production, management, environment, health, behavior, welfare, immunology, molecular biology, metabolism, nutrition, physiology, reproduction, processing, and products.