1. Genome-wide association analyses reveal copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle.
- Author
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Rojas de Oliveira H, Chud TCS, Oliveira GA Jr, Hermisdorff IC, Narayana SG, Rochus CM, Butty AM, Malchiodi F, Stothard P, Miglior F, Baes CF, and Schenkel FS
- Subjects
- Animals, Cattle genetics, Genotype, Cattle Diseases genetics, Female, Phenotype, Canada, Gene Frequency, Genome-Wide Association Study veterinary, Reproduction genetics, DNA Copy Number Variations, Polymorphism, Single Nucleotide
- Abstract
This study aimed to evaluate the impact of copy number variants (CNV) on 13 reproduction and 12 disease traits in Holstein cattle. Intensity signal files containing log R ratio and B allele frequency information from 13,730 Holstein animals genotyped with a 95K SNP panel, and 8,467 Holstein animals genotyped with a 50K SNP panel were used to identify the CNVs. Subsequently, the identified CNVs were validated using whole-genome sequence data from 126 animals, resulting in 870 high-confidence copy number variant regions (CNVR) on 12,131 animals. Out of these, 54 CNVR had frequencies higher than or equal to 1% in the population and were used in the genome-wide association analysis (one CNVR at a time, including the G matrix). Results revealed that 4 CNVR were significantly associated with at least one of the traits analyzed in this study. Specifically, 2 CNVR were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and nonreturn rate), and 2 CNVR were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVR harbored genes implicated in immune response, cellular signaling, and neuronal development, supporting their potential involvement in these traits. Further investigations to unravel the mechanistic and functional implications of these CNVR on the mentioned traits are warranted., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)
- Published
- 2024
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