Investigating the genetic architecture of dairy calf disease traits and their relationships with traits of economic importance in Canadian Holstein cattle

Calf health is becoming an increasingly important consideration for genetic selection in modern dairy cattle. However, the impact of calf diseases on other economically important traits and the genetic architecture underlying these traits remain poorly understood. This study aimed to (1) determine the impact of including calf disease traits into Canadian national genetic evaluation by estimating genetic and phenotypic correlations with other economically important traits, and (2) conduct a genome-wide association study and functional analysis to identify and understand genomic regions associated with calf disease traits in Holstein breed. The majority of genetic correlation estimates between calf diseases and other economically important traits were close to zero. However, notable correlations were found between respiratory problems and both fertility traits and clinical mastitis, which showed a favorable relationship. Similarly, estimated phenotypic correlations were generally small, suggesting limited phenotypic impact of calf disease on later life performance. These results highlight the importance of including calf disease traits within national evaluations to ensure improvements can be made on the genetic level. From the genome-wide association study, 17 single nucleotide polymorphisms (SNP) across 5 chromosomes were significantly associated with diarrhea, and 20 SNP across 5 chromosomes were significantly associated with respiratory problems. The enrichment analysis revealed 7 candidate genes that were co-localized with the SNP significantly associated with diarrhea (ACER3, CAPN5, ILK, LIPT2, PGM2L1, and PPME1). For respiratory problems, the enrichment analysis revealed 4 candidate genes that were co-localized with the significant SNP (SYNPO, DCTN4, ANXA6, and MYOZ3). Several potential candidate genes were identified, although further work is required to determine the exact association between identified genes and calf disease traits.