文献类型： 外文期刊
作者： Tao, Lin 1 ; Liu, Hang 1 ; Adeola, Adeniyi C. 1 ; Xie, Hai-Bing 1 ; Feng, Shu-Tang 3 ; Zhang, Ya-Ping 1 ;
作者机构： 1.Chinese Acad Sci, Kunming Inst Zool, Key Lab Genet Evolut & Anim Models, Kunming 650223, Peoples R China
2.Chinese Acad Sci, Kunming Inst Zool, Yunnan Key Lab Mol Biol Domest Anim, Kunming 650223, Peoples R China
3.Beijing Grand Life Sci & Technol Co, Beijing 102206, Peoples R China
4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
5.Yunnan Univ, State Key Lab Conservat & Utilizat Bioresource Yun, Sch Life Sci, Kunming 650091, Peoples R China
6.Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China
关键词： Inbreeding depression; Deleterious mutations; Inbred pigs; RNA-seq
期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）
ISSN： 1471-2164
年卷期： 2025 年 26 卷 1 期
页码：
收录情况： SCI
摘要： BackgroundSince their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations and the increase of runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand the genetic underpinnings of inbreeding depression.ResultsHere we integrated a comprehensive dataset comprising 7239 domesticated pigs and wild boars genotyped by single nucleotide polymorphism (SNP) chips, along with phenotypic data encompassing growth, reproduction and disease-associated traits. Our study revealed differential ROH landscapes during domestication and artificial selection of Eurasian pigs. We observed associations between ROH burden and phenotypic traits such as body conformation and susceptibility to diseases like scrotal hernia. By examining associations of whole-genome and regional ROH burden with gene expression, we identified specific genes and pathways affected by inbreeding depression. Associations of regional ROH burden with gene expression also enabled the discovery of novel regulatory elements. Lastly, we inferred recessive lethal mutations by examining depletion of ROH in an inbred population with relatively small sample size, following by fine mapping with sequencing data.ConclusionsThese findings suggested that both phenotypic and genetic variations have been reshaped by inbreeding, and provided insights to the genetic mechanisms underlying inbreeding depression.
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