Genome‐wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12

Abstract

Reproductive performance is a critical trait in dairy cattle. Poor reproductive performance leads to prolonged calving intervals, higher culling rates and extra expenses related to multiple inseminations, veterinary treatments and replacements. Genetic gain for improved reproduction through traditional selection is often slow because of low heritability and negative correlations with production traits. Detection of DNA markers associated with improved reproductive performance through genome-wide association studies could lead to genetic gain that is more balanced between fertility and production. Norwegian Red cattle are well suited for such studies, as very large numbers of detailed reproduction records are available. We conducted a genome-wide association study for non-return rate, fertility treatments and retained placenta using almost 1 million records on these traits and 17 343 genome-wide single-nucleotide polymorphisms. Genotyping costs were minimized by genotyping the sires of the cows recorded and by using daughter averages as phenotypes. The genotyped sires were assigned to either a discovery or a validation population. Associations were only considered to be validated if they were significant in both groups. Strong associations were found and validated on chromosomes 1, 5, 8, 9, 11 and 12. Several of these were highly supported by findings in other studies. The most important result was an association for non-return rate in heifers in a region of BTA12 where several associations for milk production traits have previously been found. Subsequent fine-mapping verified the presence of a quantitative trait loci (QTL) having opposing effects on non-return rate and milk production at 18 Mb. The other reproduction QTL did not have pleiotropic effects on milk production, and these are therefore of considerable interest for use in marker-assisted selection.

Tissues, Metabolic Pathways and Genes of Key Importance in Lactating Dairy Cattle

“…This gene has also been reported to be associated with protein yield in dairy cattle in Holstein cattle [28,111]. Olsen et al [113], reported a region on chromosome 12 significant for nonreturn rate in Norwegian Red cattle previously reported to be associated with several milk production traits (milk, fat and protein yield). They showed that the most significant SNP in this region had a positive effect on milk traits and a negative effect on non-return rate (mainly for cows returning to oestrus after insemination) [113].…”

“…Olsen et al [113], reported a region on chromosome 12 significant for nonreturn rate in Norwegian Red cattle previously reported to be associated with several milk production traits (milk, fat and protein yield). They showed that the most significant SNP in this region had a positive effect on milk traits and a negative effect on non-return rate (mainly for cows returning to oestrus after insemination) [113]. A GWAS of fertility and production traits in Italian Holstein cattle revealed one SNP on chromosome 5 (at 199 Mb) associated with protein yield, calving interval, fertility index, angularity and days to first service [107].…”

A mixed-model approach for genome-wide association studies of correlated traits in structured populations

“…, due to population structure). As designs like cohort studies become more prevalent, the need for modeling correlated traits as well as population structure will grow 2,11,12 , and the same is true for the increasing number of non-human GWAS 13,14,15,16,17 .…”

It's more than stamp collecting: how genome sequencing can unify biological research

“…Genome-wide association studies (GWAS) based on SNP, exome, and genome sequencing of cohorts have contributed to our understanding of complex disease genetics identifying over 15,000 regions associated with the majority of common human diseases [11]. GWAS is also applicable to quantitative traits in non-model species including crops [12] and farm animals for agricultural traits such as fertility and milk production [13, 14]. Single-cell sequencing and alignment of resultant short reads to the human reference has primarily been used to understand how mutation variation and mutant cell lineage within human tumors affects cancer treatment [15].…”