Multi-breed genome-wide association studies across countries for electronically recorded behavior traits in local dual-purpose cows

Abstract

Basic bovine behavior is a crucial parameter influencing cattle domestication. In addition, behavior has an impact on cattle productivity, welfare and adaptation. The aim of the present study was to infer quantitative genetic and genomic mechanisms contributing to natural dual-purpose cow behavior in grazing systems. In this regard, we genotyped five dual-purpose breeds for a dense SNP marker panel from four different European countries. All cows from the across-country study were equipped with the same electronic recording devices. In this regard, we analyzed 97,049 longitudinal sensor behavior observations from 319 local dual-purpose cows for rumination, feeding, basic activity, high active, not active and ear temperature. According to the specific sensor behaviors and following a welfare protocol, we computed two different welfare indices. For genomic breed characterizations and multi-breed genome-wide association studies, sensor traits and test-day production records were merged with 35,826 SNP markers per cow. For the estimation of variance components, we used the pedigree relationship matrix and a combined similarity matrix that simultaneously included both pedigree and genotypes. Heritabilities for feeding, high active and not active were in a moderate range from 0.16 to 0.20. Estimates were very similar from both relationship matrix-modeling approaches and had quite small standard errors. Heritabilities for the remaining sensor traits (feeding, basic activity, ear temperature) and welfare indices were lower than 0.09. Five significant SNPs on chromosomes 11, 17, 27 and 29 were associated with rumination, and two different SNPs significantly influenced the sensor traits “not active” (chromosome 13) and “feeding” (chromosome 23). Gene annotation analyses inferred 22 potential candidate genes with a false discovery rate lower than 20%, mostly associated with rumination (13 genes) and feeding (8 genes). Mendelian randomization based on genomic variants (i.e., the instrumental variables) was used to infer causal inference between an exposure and an outcome. Significant regression coefficients among behavior traits indicate that all specific behavioral mechanisms contribute to similar physiological processes. The regression coefficients of rumination and feeding on milk yield were 0.10 kg/% and 0.12 kg/%, respectively, indicating their positive influence on dual-purpose cow productivity. Genomically, an improved welfare behavior of grazing cattle, i.e., a higher score for welfare indices, was significantly associated with increased fat and protein percentages.

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

“…The rather small number of detected SNP for the moderately to highly heritable polygenic traits is in line with our small sample size and its diversity (multi-breed), and is most likely due to a lack of power to detect variants with smaller effects. However, with regard to the functional annotations of the identified genomic regions, our study confirms the potential of multi-breed GWAS in detecting fewer variants, but more precise functional loci or causative mutation across breeds [75,132]. In this context, the SNP associated with morphometric traits in the present study may represent novel common variants for linear body traits in African breeds, suggesting further investigations.…”

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

“…Recent studies provided insight into the body size variation in cetaceans, indicating that this gene was related to tall stature and overgrowth [ 47 ], and a genome-wide scan for selection signatures revealed that this gene was related to cardiac structure and function in Atlantic killifish [ 48 ]. Another multi-breed GWASs on dual-purpose bovine behavior traits identified this gene as related to rumination [ 49 ].…”

Research progress and applications of genome‐wide association study in farm animals

“…In a Tan et al study, it was reported that the causal effect of SOX6 on breast muscle development was proved by summary-data-based MR (combined eQTL and GWAS results) and a similar role in muscle compression force and drip loss was observed [11]. Yin et al proved that cattle rumination and feeding had a positive influence on productivity and the improvement of welfare indices was significantly associated with increased fat and protein percentages [158].…”

“…Yin et al. proved that cattle rumination and feeding had a positive influence on productivity and the improvement of welfare indices was significantly associated with increased fat and protein percentages [158].…”