Genome-wide association study for milking speed in French Holstein cows

Abstract

Using a combination of data from the BovineSNP50 BeadChip SNP array (Illumina, San Diego, CA) and a EuroGenomics (Amsterdam, the Netherlands) custom single nucleotide polymorphism (SNP) chip with SNP pre-selected from whole genome sequence data, we carried out an association study of milking speed in 32,491 French Holstein dairy cows. Milking speed was measured by a score given by the farmer. Phenotypes were yield deviations as obtained from the French evaluation system. They were analyzed with a linear mixed model for association studies. We identified SNP on 22 chromosomes significantly associated with milking speed. As clinical mastitis and somatic cell score have an unfavorable genetic correlation with milking speed, we tested whether the most significant SNP on these 22 chromosomes associated with milking speed were also associated with clinical mastitis or somatic cell score. Nine hundred seventy-one genome-wide significant SNP were associated with milking speed. Of these, 86 were associated with clinical mastitis and 198 with somatic cell score. The most significant association signals for milking speed were observed on chromosomes 7, 8, 10, 14, and 18. The most significant signal was located on chromosome 14 (ZFAT gene). Eleven novel milking speed quantitative trait loci (QTL) were observed on chromosomes 7, 10, 11, 14, 18, 25, and 26. Twelve candidate SNP for milking speed mapped directly within genes. Of these, 10 were QTL lead SNP, which mapped within the genes HMHA1, POLR2E, GNB5, KLHL29, ZFAT, KCNB2, CEACAM18, CCL24, and LHPP. Limited pleiotropy was observed between milking speed QTL and clinical mastitis.

A Meta-Analysis Including Pre-selected Sequence Variants Associated With Seven Traits in Three French Dairy Cattle Populations

“…Another very significant QTL for milk yield in Holstein was identified on BTA20 at ~38 Mb. The lead SNP of this QTL was located near the PRLR gene which has previously been associated with fertility in Holstein cows (Leyva-Corona et al, 2018 ; Marete et al, 2018b ). The majority of the associated SNP with fertility, a low heritability trait, were 50 k chip variants.…”

Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population

“…Within the AA population, a strong association for carcass weight was detected within 160 kb from the ZFAT gene on BTA14. ZFAT , which was the closest gene to the strongest associated SNP, has been previously associated with stature in both humans [30, 31] and horses [32, 33], and milking speed in French Holstein cows [34], but most interestingly is the fact that it was identified as the likely candidate gene within a lethal recessive haplotype detected in the AA population in Ireland [35]. The putatively lethal haplotype occurred at a frequency of 15.2% in the Irish AA population [35] and was also shown to be positively associated with weight-related traits and feed intake, thus providing further evidence for ZFAT as a likely breed-specific candidate gene for carcass weight within the AA population.…”

Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle

“…The possible signals detected in this study were associated with betaine, L-alanine and L-lactic acid, and the peaks for significant additive SNPs including rs109862186, rs81117935, and rs42009425 were on chromosome 5, 11, and 22. Two of the SNPs rs109862186 and rs42009425 showed no evidence of a candidate gene within 200-kbp distance, however, SNP rs42009425 associated with L-lactic acid was reported to be associated with clinical mastitis in French Holstein cattle (Marete et al, 2018). The SNP rs81117935 associated with L-alanine was found to be located within the candidate gene CTNNA2 which is one of three human alpha-catenin genes.…”