Abstract：
Inbreeding can lead to the accumulation of homozygous single nucleotide polymorphisms (SNPs) in the genome, which can significantly affect gene expression and phenotype. In this study, we examined the impact of homozygous SNPs resulting from inbreeding on alternative polyadenylation (APA) site selection and the underlying genetic mechanisms using inbred Luchuan pigs. Genome resequencing revealed that inbreeding results in a high accumulation of homozygous SNPs within the pig genome. 3\' mRNA-seq on leg muscle, submandibular lymph node, and liver tissues was performed to identify differences in APA events between inbred and outbred Luchuan pigs. We revealed different tissue-specific APA usage caused by inbreeding, which were associated with different biological processes. Furthermore, we explored the role of polyadenylation signal (PAS) SNPs in APA regulation under inbreeding and identified key genes such as PUM1, SCARF1, RIPOR2, C1D, and LRRK2 that are involved in biological processes regulation. This study provides resources and sheds light on the impact of genomic homozygosity on APA regulation, offering insights into genetic characteristics and biological processes associated with inbreeding.
摘要：
近交可导致基因组中纯合单核苷酸多态性（SNPs）的积累，能显著影响基因表达和表型。在这项研究中,我们使用近交陆川猪研究了近交产生的纯合SNP对选择性聚腺苷酸化（APA）位点选择的影响以及潜在的遗传机制。基因组重新测序显示近交导致纯合SNP在猪基因组中的高积累。3腿部肌肉上的mRNA-seq，颌下淋巴结,并进行肝脏组织以确定近交和近交陆川猪之间APA事件的差异。我们揭示了近亲繁殖引起的不同组织特异性APA用法，与差异生物学过程有关。此外，我们探索了聚腺苷酸化信号（PAS）SNP在近交条件下APA调控中的作用，并鉴定了PUM1，SCARF1，RIPOR2，C1D，和参与生物过程调节的LRRK2。本研究为基因组纯合性对APA调控的影响提供了资源和启示。提供与近亲繁殖相关的遗传特征和生物学过程的见解。
