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Identified Candidate Genes of Semen Trait in Three Pig Breeds Through Weighted GWAS and Multi-Tissue Transcriptome Analysis

文献类型： 外文期刊

作者： Zhang, Xiaoke 1 ; Xu, Zhiting 1 ; Lin, Qing 1 ; Gao, Yahui 1 ; Qiu, Xiaotian 3 ; Li, Jiaqi 1 ; Xie, Shuihua 4 ;

作者机构： 1.South China Agr Univ, Coll Anim Sci, Natl Engn Res Ctr Breeding Swine Ind, State Key Lab Swine & Poultry Breeding Ind,Guangdo, Guangzhou 510642, Peoples R China

2.Chinese Acad Agr Sci, Inst Anim Sci, State Key Lab Anim Biotech Breeding, Beijing 100193, Peoples R China

3.Natl Anim Husb Serv, Beijing 100125, Peoples R China

4.Agr Technol Extens Ctr Guangdong Prov, Guangzhou 510520, Peoples R China

关键词： pig; semen traits; weighted GWAS; multi-tissue transcriptome analysis; candidate genes

期刊名称：ANIMALS （ 影响因子：2.7； 五年影响因子：3.2 ）

ISSN： 2076-2615

年卷期： 2025 年 15 卷 3 期

页码：

收录情况： SCI

摘要： High-quality semen is an essential factor for the success of artificial insemination, and revealing the genetic structure of pig semen traits helps improve semen quality. This study aimed to identify candidate genes associated with semen traits in three pig breeds (Duroc, Landrace, and Yorkshire) through weighted GWAS and multi-tissue transcriptome analysis. In this study, to identify candidate genes associated with semen traits in Duroc, Landrace, and Yorkshire, we performed weighted GWAS in four traits (sperm motility, sperm progressive motility, sperm abnormality rate, and total sperm count) using 936 pigs and multi-tissue transcriptome analysis using 34 tissues RNA-seq data of 5457 pigs from FarmGTEx. It was found that 16, 9, and 12 significant SNPs associated with semen traits were identified in Duroc, Landrace, and Yorkshire, with corresponding 7, 5, and 7 candidate genes in these three breeds, respectively, which may be involved in mammal spermatogenesis, testicular function, and male fertility. Moreover, we not only found the same candidate gene DNAI2 as in previous studies but also found two new candidate genes PNLDC1 and RSPH3, which were identified simultaneously in both Landrace and Yorkshire. By integrating the GWAS and multi-tissue transcriptome analysis results, we found that candidate genes associated with semen traits of three pig breeds were highly expressed in the testis tissue. The three genotypes of rs320928244 had significant effects on the expression of the DYNLT1 gene in the testis tissue of Landrace. These results together showed that these candidate genes were mainly related to sperm motility defects. This study helps deepen the understanding of the genetic basis of semen traits and provides a theoretical foundation for improving the semen quality of Duroc, Landrace, and Yorkshire breeds.

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