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Background  Production and health traits are central in cattle breeding. Advances in next-generation sequencing technologies and genotype imputation have increased the resolution of gene mapping based on genome-wide association studies (GWAS). Thus, numerous candidate genes that affect milk yield, milk composition, and mastitis resistance in dairy cattle are reported in the literature. Effect-bearing variants often affect multiple traits. Because the detection of overlapping quantitative trait loci (QTL) regions from single-trait GWAS is too inaccurate and subjective, multi-trait analysis is a better approach to detect pleiotropic effects of variants in candidate genes. However, large sample sizes are required to achieve sufficient power. Multi-trait meta-analysis is one approach to deal with this problem. Thus, we performed two multi-trait meta-analyses, one for three milk production traits (milk yield, protein yield and fat yield), and one for milk yield and mastitis resistance.    Results  For highly correlated traits, the power to detect pleiotropy was increased by multi-trait meta-analysis compared with the subjective assessment of overlapping of single-trait QTL confidence intervals. Pleiotropic effects of lead single nucleotide polymorphisms (SNPs) that were detected from the multi-trait meta-analysis were confirmed by bivariate association analysis. The previously reported pleiotropic effects of variants within the  DGAT1  and  MGST1  genes on three milk production traits, and pleiotropic effects of variants in  GHR  on milk yield and fat yield were confirmed. Furthermore, our results suggested that variants in  KCTD16 ,  KCNK18  and  ENSBTAG23629  had pleiotropic effects on milk production traits. For milk yield and mastitis resistance, we identified possible pleiotropic effects of variants in two genes,  GC  and  DGAT1 .    Conclusions  Multi-trait meta-analysis improves our ability to detect pleiotropic interactions between milk production traits and identifies variants with pleiotropic effects on milk production traits and mastitis resistance. In particular, this should contribute to better understand the biological mechanisms that underlie the unfavorable genetic correlation between milk yield and mastitis.

Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle