Sequencing & Pangenomes

Genome-wide association for fertility traits in Holstein cattle using whole-genome sequence data

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Abstract

Reproductive efficiency has a significant positive impact on dairy cattle systems; however, improving cows' reproductive ability is challenging as the selection criteria typically exhibit low heritability. The primary objective of this study was to perform genome-wide association analyses (GWAS) for age at first service (AFS), days between calving and first service (CTFS), and days open (DO) in Canadian Holstein cows, using imputed whole-genome sequence data. Phenotypes and genomic data were available for 2,327 (AFS), 1,107 (CTFS), and 939 (DO) cows. Quality control of the genotypic data excluded individuals and markers with a call rate below 90%, single nucleotide polymorphisms (SNPs) with a minor allele frequency below 5%, and SNPs showing extreme deviations from Hardy-Weinberg equilibrium (p 0.90. Multiple test correction consisted of dividing the global significance threshold (0.05) by the number of independent chromosomal segments, resulting in a genome-wide p-value threshold of 2.512à— 10⁻⁵. Annotation of the significant SNPs was performed using the GALLO R package, and functional analyses of the genes was conducted with the DAVID tool. A total of 140 significant associations were identified, including 88 for AFS (BTA2, BTA5, and BTA17), 19 for CTFS (BTA19, BTA20, BTA27, BTA29), and 33 for DO (BTA1, BTA3, BTA4, BTA11). Candidate genes were found for all traits, including PID1, SPHKAP, AP1S3, DOCK10, NEL2, FAT4, JADE1, PABPC4L, ELF2 (for AFS); MSI2, CCDC182, VEZF1, SRSF1, DYNLL2, OR4D2B, OR4D1B, RNF43, HSF5, GAPT, DLG2 (for CTFS), and USP24, DHCR24, SHISAL2A, GPX7, STEAP2, CFAP69, FAM237B, GTPBP10, HUS1, TNS3, SH3RF3, EDAR (for DO). These genes were previously associated with key biological processes such as spermatogenesis, follicle formation, meiotic regulation, and muscle development. Moreover, many QTL were previously reported in the genomic regions identified, including QTL for calving ease, stillbirth, pregnancy rate, and luteal activity. This study reveals new candidate genes for fertility traits in Holstein cattle, which may serve as targets for future studies investigating the genomic background of reproductive traits in dairy cattle.Acknowledgements: The first author acknowledges the "Fundação de Amparo à  Pesquisa da Bahia" (grant number:00114867478) for providing its Master Science scholarship, and the National Council for Scientific and Technological Development (grant number:445295/2024-4) for the financial support to this project. Luís F.B. Pinto is a recipient of research productivity fellowships from CNPq.

Keywords: 2026

How to Cite:

de Lima, M., Cortez de Souza, T., Batista Pinto, L., Miglior, F., Schenkel, F. & Brito, L., (2026) “Genome-wide association for fertility traits in Holstein cattle using whole-genome sequence data”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286579. doi: https://doi.org/10.31274/wcgalp.24054

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