Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Abstract

Background: Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs.Results: Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genomewise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5

Fast Bayesian fine-mapping of 35 production, reproduction and body conformation traits in dairy cattle

“…has been associated with teat length 23 , and our fine-mapping showed that it had an effect on six type traits (including teat length, fore udder attachment, front teat placement, rear teat placement, rear udder height, and final score), with PPC being ≥ 0.95 for all those traits. Abo-Ismail et al…”

“…reported CCND2 was associated with stature 23 . Our fine-mapping results determined its association with four type traits (PPC >0.95 for body depth, rump width, and stature).…”

“…For example, ABCG2 and DGAT1 are known to affect milk production in dairy cattle 19,20 . The ARRDC3 gene has been associated with body confirmation traits and calving traits in beef and dairy cattle [21][22][23] . Our fine-mapping study also revealed novel gene/association combinations for dairy traits.…”

Genetic selection for bovine chromosome 18 haplotypes associated with divergent somatic cell score affects postpartum reproductive and metabolic performance

“…Genetic selection offers a sustainable tool to improve dairy cattle farming via the selection of animals with reduced susceptibility toward diseases, which in turn results in improved periparturient health. Until now, association and linkage studies have revealed promising results concerning bovine chromosome 18 (BTA18) and performance traits (Mao et al, 2016;Abo-Ismail et al, 2017;Müller et al, 2017;Wu et al, 2017). Concerning udder health, Kühn et al (2008) showed that the prediction of half-sib heifers with a high or low SCS was possible through marker-assisted selection regarding a confirmed QTL for SCS in the telomeric region of BTA18.…”

In vivo model to study the impact of genetic variation on clinical outcome of mastitis in dairy uniparous cows

“…Genetic selection offers a sustainable tool to select animals with decreased susceptibility towards postpartum diseases. Several groups have reported promising associations between Bos taurus autosome 18 (BTA 18) and performance traits [26][27][28][29]. Our own studies revealed differing immune competence of primary mammary epithelial cells (MEC) originating from two BTA 18 haplotypes: half sib uniparous cows inheriting an alternative haplotype of a confirmed quantitative trait locus (QTL) for somatic cell score (SCS) in the telomeric region of BTA 18 showed different somatic cell scores in vivo [30].…”