Genomic consequences of intensive inbreeding in miniature inbred pigs

	Genomic consequences of intensive inbreeding in miniature inbred pigs
	Chen, HM; Zhao, H; Zhu, QY; Yan, C; Liu, YQ; Si, S; Jamal, MA; Xu, KX; Jiao, DL; Lv, MJ; Wang, W; Zhao, HY; Chen, L; Wang, MS; Wei, HJ
	2025
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	26 期号:1
摘要	Background Inbreeding, a central theme in evolutionary and conservation biology, is a crucial practice in breeding to stabilize and enhance the specific traits or to establish inbred lines. It also carries the risk of inbreeding depression, reduced fitness, and increased potential for extinction. Nevertheless, inbreeding has been extensively studied in small and endangered populations but its effects in large domesticated animals are poorly understood. Here, we aim to investigate the genomic consequences of inbreeding in the Banna miniature inbred pig (BN), a breed that has been inbred for over 40 years. Results We have sequenced 41 genomes of BN and Diannan miniature pig (DN) at high-coverage (> 31x) and combined them with published whole-genomes of swine to comprehensively investigate the genetic consequences of inbreeding. We find that BN is genetically closely related to DN, which is consistent with breeding records. All families of BN have undergone an extreme bottleneck due to intensive inbreeding, resulting in higher genomic inbreeding coefficients, reduced genetic diversity, and a lower effective population size (Ne) compare to non-inbred pigs. Furthermore, BN and DN exhibit an increased genetic load relative to Asian wild boars. Prolonged inbreeding and bottlenecks have led to some purging of deleterious mutations in BN compared to DN, and a conversion from masked load to realized load. Conclusions We present a comprehensive analysis to understand and assess the consequences of inbreeding in miniature inbred pigs from a perspective of population genomics. Utilizing genomic measurements proves effective in estimating the consequences of inbreeding, especially when a detailed and accurate historical record of pedigree are lacking. Our results provide valuable resources and a detailed perspective on the genomic impacts of inbreeding, potentially guiding efforts in breeding, breed improvement, and conservation.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14462
专题	科研部门_进化与生物多样性基因组学（王明山）
推荐引用方式 GB/T 7714	Chen, HM,Zhao, H,Zhu, QY,et al. Genomic consequences of intensive inbreeding in miniature inbred pigs[J]. BMC GENOMICS,2025,26(1).
APA	Chen, HM.,Zhao, H.,Zhu, QY.,Yan, C.,Liu, YQ.,...&Wei, HJ.(2025).Genomic consequences of intensive inbreeding in miniature inbred pigs.BMC GENOMICS,26(1).
MLA	Chen, HM,et al."Genomic consequences of intensive inbreeding in miniature inbred pigs".BMC GENOMICS 26.1(2025).

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