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Abril-Parreño L, Carthy TR, Keogh K, Štiavnická M, O'Meara C, Lonergan P, Kenny DA, Fair S. Genome-wide association study reveals candidate markers related to field fertility and semen quality traits in Holstein-Friesian bulls. Animal 2023; 17:100841. [PMID: 37224615 DOI: 10.1016/j.animal.2023.100841] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023] Open
Abstract
In vitro assessment of bull semen quality is routinely used in bull semen processing centres in order to ensure that semen destined to be used in the field has passed minimum standards. Despite these stringent quality control checks, individual bulls that pass the quality control checks can still vary in field fertility by up to 25%. A genome-wide association study was undertaken to determine genetic markers associated with prefreeze and post-thaw bull sperm quality traits as well as field fertility. Genome-wide association analysis was performed using a single nucleotide polymorphism (SNP) regression mixed linear model in WOMBAT. Genes within a 250 Kb span of a suggestive (P ≤ 1 × 10-5) SNP were considered as candidate genes. One SNP was associated with adjusted pregnancy rate, and 21 SNPs were associated across the seven semen quality traits (P ≤ 1 × 10-5). Functional candidate genes include SIPA1L2 which was associated with adjusted pregnancy rate. This encodes a Rap GTPase-activating protein involved in Rap1 signalling pathway and was previously found to play a role in the process of sperm differentiation. Gene ontology (GO) analysis also identified significantly enriched biological processes involved protein tyrosine kinase activity including genes such as DYRK1A, TEC and TXK that were associated with sperm motility prior to freezing. Another candidate gene associated with post-thaw sperm motility was FHDC1 which coordinates actin filament and microtubule dynamics. The induced 11 GO terms in the ejaculates rejected after freezing trait were related to ATPase, phosphatase and hydrolase activity. These results reveal novel specific genomic regions and candidate genes associated with economically important phenotypes such as field fertility and semen quality traits.
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Affiliation(s)
- Laura Abril-Parreño
- Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, Faculty of Science and Engineering, University of Limerick, Limerick V94 T9PX, Ireland
| | - Tara R Carthy
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Co. Meath C15 PW93, Ireland
| | - Kate Keogh
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Co. Meath C15 PW93, Ireland
| | - Miriama Štiavnická
- Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, Faculty of Science and Engineering, University of Limerick, Limerick V94 T9PX, Ireland
| | - Ciara O'Meara
- National Cattle Breeding Centre, Naas, Co. Kildare W91 WF59, Ireland
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, D04 W6F6, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Co. Meath C15 PW93, Ireland
| | - Sean Fair
- Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, Faculty of Science and Engineering, University of Limerick, Limerick V94 T9PX, Ireland.
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