Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain.
Department Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
Genes (Basel). 2023 Oct 15;14(10):1941. doi: 10.3390/genes14101941.
Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.
近交衰退预计在与健康相关的特征中更为明显，例如猪的产仔数。最近的研究表明，近交衰退的遗传决定因素在整个基因组中可能存在异质性。因此，本研究的目的是对整个猪常染色体基因组进行基因组扫描，以检测控制伊比利亚猪（Entrepelado 和 Retinto）两个品种产仔数近交衰退的基因组区域。数据集包括 Entrepelado 和 Retinto 品种的 2069（338 头母猪）和 2028（327 头母猪）产仔数（总产仔数和活产仔数）记录。所有母猪均使用 Geneseek GGP PorcineHD 70 K 芯片进行基因分型。我们使用不利单倍型发现软件提取纯合区（ROH），并进行混合模型分析，以确定每个特定 ROH 中纯合和杂合母猪之间的高度显著差异。总共发现了 8 个位于 SSC2、SSC5、SSC7、SSC8 和 SSC13 上的与近交衰退显著相关的基因组区域，这些区域包含了一些相关基因，如 FSHR、LHCGR、CORIN、AQP6 和 CEP120。
