Genome-wide candidate signatures of divergent selection between broody Silkie and White Leghorn chickens revealed by high-density SNP genotyping.

IF 1.7 3区农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE

British Poultry Science Pub Date : 2026-09-02 DOI:10.1080/00071668.2026.2721458

A Basheer, I Zahoor

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Abstract

1. In this study, genome-wide population structure, genetic differentiation and homozygosity patterns were investigated between Silkie (SLK) and White Leghorn (WLH) chickens, using high-density autosomal SNP genotypes. These breeds were selected as they have markedly different breed histories and productive performances.2. Principal component analysis revealed complete genetic separation between the two breeds, explaining 75.82% of total genomic variance and indicating strong divergence. Genome-wide differentiation showed heterogeneous patterns across autosomes. The top 1% of windows (FST ≥ 0.7467) were used as an empirical threshold for prioritising regions showing elevated differentiation.3. The study identified 20 protein-coding positional candidate genes, including TRHDE, GABBR2, SEMA3A, SEMA5A, IGF1, SOCS2, AR and NLGN4, which have roles in neuroendocrine, behavioural, growth and reproduction.4. Breed-specific runs of homozygosity (ROH) revealed marked differences in autozygosity, with Silkie chickens showing substantially higher genomic inbreeding coefficients (F) of ROH (mean FROH = 0.396) than White Leghorns (mean FROH = 0.175). Island analysis identified 30 islands in Silkie and 19 in White Leghorn chickens, predominantly located on macrochromosomes. There were breed-specific and partially overlapping differentiated genomic intervals, highlighting concurrent differentiation and homozygosity in the two breeds.5. The results showed substantial genome-wide differentiation between Silkie and White Leghorn chickens. This provided a population-genomic framework for prioritising candidate regions for maternal behaviour, reproductive physiology and egg production.

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高密度SNP基因分型揭示了育雏利来客鸡和白来客鸡不同选择的全基因组候选特征。

1. 本研究采用高密度常染色体SNP基因型技术，研究了白来角鸡（WLH）和Silkie鸡的全基因组群体结构、遗传分化和纯合子模式。选择这些品种是因为它们有明显不同的品种历史和生产性能。主成分分析显示，两个品种之间存在完全的遗传分离，解释了总基因组方差的75.82%，表明存在强烈的差异。全基因组分化在常染色体中表现出异质模式。前1%的窗口（FST≥0.7467）作为经验阈值，优先考虑表现出高度分化的区域。本研究确定了20个蛋白编码位置候选基因，包括TRHDE、GABBR2、SEMA3A、SEMA5A、IGF1、SOCS2、AR和NLGN4，这些基因在神经内分泌、行为、生长和生殖等方面发挥作用。纯合子（ROH）的品种特异性运行显示出显著的自合子性差异，乌鸡的ROH基因组近交系数(F)（平均FROH = 0.396）显著高于白来角鸡（平均FROH = 0.175）。海岛分析发现，Silkie鸡30个，White Leghorn鸡19个，主要位于大染色体上。存在品种特异性和部分重叠的分化基因组间隔，突出了两个品种的同步分化和纯合性。结果显示，利来霍恩白鸡和利来霍恩白鸡之间存在显著的全基因组差异。这为母性行为、生殖生理和卵子生产的优先候选区域提供了一个种群基因组框架。

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

British Poultry Science 农林科学-奶制品与动物科学

CiteScore

3.90

自引率

5.00%

发文量

审稿时长

4.5 months

期刊介绍： From its first volume in 1960, British Poultry Science has been a leading international journal for poultry scientists and advisers to the poultry industry throughout the world. Over 60% of the independently refereed papers published originate outside the UK. Most typically they report the results of biological studies with an experimental approach which either make an original contribution to fundamental science or are of obvious application to the industry. Subjects which are covered include: anatomy, embryology, biochemistry, biophysics, physiology, reproduction and genetics, behaviour, microbiology, endocrinology, nutrition, environmental science, food science, feeding stuffs and feeding, management and housing welfare, breeding, hatching, poultry meat and egg yields and quality.Papers that adopt a modelling approach or describe the scientific background to new equipment or apparatus directly relevant to the industry are also published. The journal also features rapid publication of Short Communications. Summaries of papers presented at the Spring Meeting of the UK Branch of the WPSA are published in British Poultry Abstracts .