Genome-Wide Association Analysis of Boar Semen Traits Based on Computer-Assisted Semen Analysis and Flow Cytometry

Overview

Journal Animals (Basel)

Date 2025 Jan 11

PMID 39794969

Authors

Xiyan Yang

Jingkun Nie

Yaxuan Zhang

Suqing Wang

Xiaoping Zhu

Zhili Li

Yunxiang Zhao

Xiuguo Shang

Affiliations

Soon will be listed here.

Abstract

Semen quality and persistence are critical for evaluating the usability of individual boars in AI, a standard practice in pig breeding. We conducted GWASs on various semen traits of Duroc boars, including MOT, DEN, ABN, MMP, AIR, and ROS levels. These traits were assessed using FCM and CASA. A total of 1183 Duroc boars were genotyped using the GeneSeek GGP Porcine 50 K SNP BeadChip. The GWAS was performed using three different models: GLM, MLM, and FarmCPU. Additionally, trait heritability was estimated using single- and multiple-trait PBLUP models, yielding 0.19, 0.29, 0.13, 0.18, 0.11, and 0.14 heritability for MOT, DEN, ABN, MMP, AIR, and ROS, respectively. All semen traits exhibited low heritability except ABN, which demonstrated medium heritability. Nine candidate genes (, , , , , , , , and ) were potentially associated with semen traits. These genes are associated with antioxidant and mitochondrial functions in porcine sperm. Our findings provide insight into the genetic architecture of semen traits in Duroc boars, and the identified SNPs and candidate genes may enhance economic outcomes in the pig breeding industry while improving sperm quality through targeted breeding strategies.

References

Mei Q, Fu C, Sahana G, Chen Y, Yin L, Miao Y . Identification of new semen trait-related candidate genes in Duroc boars through genome-wide association and weighted gene co-expression network analyses. J Anim Sci. 2021; 99(7). PMC: 8292953. DOI: 10.1093/jas/skab188. View

Dostalova Z, Calvete J, Sanz L, Topfer-Petersen E . Boar spermadhesin AWN-1. Oligosaccharide and zona pellucida binding characteristics. Eur J Biochem. 1995; 230(1):329-36. DOI: 10.1111/j.1432-1033.1995.tb20567.x. View

Zhang X, Lee M, Buckley C, Wilson C, McCarron J . Mitochondria regulate TRPV4-mediated release of ATP. Br J Pharmacol. 2021; 179(5):1017-1032. DOI: 10.1111/bph.15687. View

Gao N, Chen Y, Liu X, Zhao Y, Zhu L, Liu A . Weighted single-step GWAS identified candidate genes associated with semen traits in a Duroc boar population. BMC Genomics. 2019; 20(1):797. PMC: 6822442. DOI: 10.1186/s12864-019-6164-5. View

Li Y, Li C, Lin S, Yang B, Huang W, Wu H . A nonsense mutation in Ccdc62 gene is responsible for spermiogenesis defects and male infertility in repro29/repro29 mice. Biol Reprod. 2017; 96(3):587-597. DOI: 10.1095/biolreprod.116.141408. View

Miyazaki R, Fukuda M, Takeuchi H, Itoh S, Takada M . Flow cytometry to evaluate acrosome-reacted sperm. Arch Androl. 1990; 25(3):243-51. DOI: 10.3109/01485019008987613. View

Liu X, Yin L, Zhang H, Li X, Zhao S . Performing Genome-Wide Association Studies Using rMVP. Methods Mol Biol. 2022; 2481:219-245. DOI: 10.1007/978-1-0716-2237-7_14. View

Ding X, Tan Z, Xing K, Yang T, Wang Y, Sun D . Genome-wide association study for reproductive traits in a Large White pig population. Anim Genet. 2018; 49(2):127-131. PMC: 5873431. DOI: 10.1111/age.12638. View

Hollema B, Zwiers S, Hermesch S . Genetic parameters for haemoglobin levels in sows and piglets as well as sow reproductive performance and piglet survival. Animal. 2019; 14(4):688-696. DOI: 10.1017/S1751731119002532. View

10.

Wang H, Jiang L, Liu X, Yang J, Wei J, Xu J . A post-GWAS replication study confirming the PTK2 gene associated with milk production traits in Chinese Holstein. PLoS One. 2014; 8(12):e83625. PMC: 3873394. DOI: 10.1371/journal.pone.0083625. View

11.

Pearson T, Manolio T . How to interpret a genome-wide association study. JAMA. 2008; 299(11):1335-44. DOI: 10.1001/jama.299.11.1335. View

12.

Kaler A, Gillman J, Beissinger T, Purcell L . Comparing Different Statistical Models and Multiple Testing Corrections for Association Mapping in Soybean and Maize. Front Plant Sci. 2020; 10:1794. PMC: 7052329. DOI: 10.3389/fpls.2019.01794. View

13.

Wang H, Wang X, Li M, Sun H, Chen Q, Yan D . Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population. Genes (Basel). 2022; 13(11). PMC: 9689869. DOI: 10.3390/genes13111990. View

14.

Li X, Acharya A, Farmer A, Crow J, Bharti A, Kramer R . Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing. BMC Genomics. 2012; 13:568. PMC: 3533575. DOI: 10.1186/1471-2164-13-568. View

15.

Chen X, Tian M, Sun R, Zhang M, Zhou L, Jin L . SIRT5 inhibits peroxisomal ACOX1 to prevent oxidative damage and is downregulated in liver cancer. EMBO Rep. 2018; 19(5). PMC: 5934778. DOI: 10.15252/embr.201745124. View

16.

Marques D, Bastiaansen J, Broekhuijse M, Lopes M, Knol E, Harlizius B . Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs. Genet Sel Evol. 2018; 50(1):40. PMC: 6080523. DOI: 10.1186/s12711-018-0412-z. View

17.

Urushima Y, Haraguchi M, Yano M . Depletion of TMEM65 leads to oxidative stress, apoptosis, induction of mitochondrial unfolded protein response, and upregulation of mitochondrial protein import receptor TOMM22. Biochem Biophys Rep. 2020; 24:100870. PMC: 7725676. DOI: 10.1016/j.bbrep.2020.100870. View

18.

Cheng H, Zhang Z, Han H, Wei R, Zhao W, Sun Y . Cross-ancestry meta-genome-wide association studies provide insights to the understanding of semen traits in pigs. Animal. 2024; 18(11):101331. DOI: 10.1016/j.animal.2024.101331. View

19.

Yean R, Dilipkumar M, Rahman S, Song B . A Two-in-One Strategy: Target and Nontarget Site Mechanisms Both Play Important Role in IMI-Resistant Weedy Rice. Int J Mol Sci. 2021; 22(3). PMC: 7863736. DOI: 10.3390/ijms22030982. View

20.

Koketsu Y, Sasaki Y . Boar culling and mortality in commercial swine breeding herds. Theriogenology. 2009; 71(7):1186-91. DOI: 10.1016/j.theriogenology.2008.12.018. View