Genome-wide association analyses reveals copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle.

Oliveira, Hinayah R; Chud, Tatiane C S; Oliveira, Gerson A; Hermisdorff, Isis C; Narayana, Saranya G; Rochus, Christina M; Butty, Adrien M; Malchiodi, Francesca; Stothard, Paul; Miglior, Filippo; Baes, Christine F; Schenkel, Flavio S (2024). Genome-wide association analyses reveals copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle. Journal of dairy science, 107(9), pp. 7052-7063. American Dairy Science Association 10.3168/jds.2023-24295

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This study aimed to evaluate the impact of copy number variants (CNVs) 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 CNV regions (CNVRs) on 12,131 animals. Out of these, 54 CNVRs 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 CNVRs were significantly (p-value < 3.7 × 10-5) associated with at least one of the traits analyzed in this study. Specifically, 2 CNVRs were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and non-return rate), and 2 CNVRs were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVRs 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 CNVRs on the mentioned traits are warranted.

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