Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle

Abstract

The goal of our study was to identify the SNPs, metabolic pathways (KEGG), and gene ontology (GO) terms significantly associated with calving and workability traits in dairy cattle. We analysed direct (DCE) and maternal (MCE) calving ease, direct (DSB) and maternal (MSB) stillbirth, milking speed (MSP), and temperament (TEM) based on a Holstein-Friesian dairy cattle population consisting of 35,203 individuals. The number of animals, depending on the trait, ranged from 22,301 bulls for TEM to 30,603 for DCE. We estimated the SNP effects (based on 46,216 polymorphisms from Illumina BovineSNP50 BeadChip Version 2) using a multi-SNP mixed model. The SNP positions were mapped to genes and the GO terms/KEGG pathways of the corresponding genes were assigned. The estimation of the GO term/KEGG pathway effects was based on a mixed model using the SNP effects as dependent variables. The number of significant SNPs comprised 59 for DCE, 25 for DSB and MSP, 17 for MCE and MSB, and 7 for TEM. Significant KEGG pathways were found for MSB (2), TEM (2), and MSP (1) and 11 GO terms were significant for MSP, 10 for DCE, 8 for DSB and TEM, 5 for MCE, and 3 for MSB. From the perspective of a better understanding of the genomic background of the phenotypes, traits with low heritabilities suggest that the focus should be moved from single genes to the metabolic pathways or gene ontologies significant for the phenotype.

Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations

“…Modulation of synaptic transmission, a significantly enriched BP for FY candidate genes, plays a crucial role in neuronal signaling and information processing in the nervous system ( https://www.ebi.ac.uk/QuickGO/term/GO:0050804 ). Modulation of synaptic transmission was associated with maternal calving ease in Holstein cows [ 47 ].…”

Contemporary Knowledge on the Assessment of Temperament in Cattle and Its Impact on Production and Reproduction Including Some Immunological, Genetic and Metabolic Parameters

“…Furthermore, the gene associated with the most traits in the novel subject test (SESTD1) was highly expressed in domestic cattle brains. Additionally, it was shown that at least seven SNPs connected with temperament determined in the studies by Jakimowicz et al [ 58 ] were localized on the X chromosome. Moreover, in Brahman cattle, genomic regions and genes related to temperament have recently been identified [ 59 ].…”

Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment

“…Estimated pedigree-based heritabilities for milking temperament ranged from 0.04-0.47 in dairy cattle milked in conventional milking systems [3,135]. For milking speed or milk flow, heritabilities ranged from 0.12 to 0.44 [136][137][138] when calculated using pedigrees or a genomic relationship matrix. Ebinghaus et al [9,76] evaluated the suitability of different behaviour tests describing cow-human relationships for breeding (e.g., avoidance or distance toward an unfamiliar person, tolerance to tactile interaction).…”

“…Chen et al [167] detected 40 and 35 significantly associated SNPs with milking temperament and milking speed respectively in a population of ~4000 North American HF dairy cows (Table S1). Jakimowicz et al [136] associated seven SNPs located on chromosome X (explaining 1.9% of the phenotypic variance) with milking temperament, and 24 SNPs with milking speed (explaining 5.8% of the phenotypic variance) (Table S1).…”