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Comprehensive analysis of single-nucleotide variants and alternative polyadenylation between inbred and outbred pigs

文献类型： 外文期刊

作者： Han, Yu 1 ; Tu, Weilong 1 ; Zhang, Yingying 1 ; Huang, Ji 1 ; Meng, Xiangge 2 ; Wu, Qingqing 2 ; Li, Songyu 2 ; Liu, Bang 2 ; Michal, Jennifer J. 4 ; Jiang, Zhihua 4 ; Tan, Yongsong 1 ; Zhou, Xiang 2 ; Wang, Hongyang 1 ;

作者机构： 1.Shanghai Acad Agr Sci, Inst Anim Husb & Vet Sci, Key Lab Livestock & Poultry Resources Pig Evaluat, Minist Agr & Rural Affairs, Shanghai 201106, Peoples R China

2.Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Wuhan 430070, Peoples R China

3.Hubei Hongshan Lab, Wuhan 430070, Peoples R China

4.Washington State Univ, Dept Anim Sci, Pullman, WA USA

5.Shanghai Engn Res Ctr Breeding Pig, Shanghai 201106, Peoples R China

关键词： Luchuan pigs; Inbreeding; Homozygosity; Polyadenylation signal; Muscle development; Immune response

期刊名称：INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES （ 影响因子：7.7； 五年影响因子：7.7 ）

ISSN： 0141-8130

年卷期： 2024 年 278 卷

页码：

收录情况： SCI

摘要： 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.

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