Genome-wide pleiotropy and shared biological pathways for resistance to bovine pathogens

<div><p>Host genetic architecture is a major factor in resistance to pathogens and parasites. The collection and analysis of sufficient data on both disease resistance and host genetics has, however, been a major obstacle to dissection the genetics of resistance to single or multiple pathogens. A severe challenge in the estimation of heritabilities and genetic correlations from pedigree-based studies has been the confounding effects of the common environment shared among relatives which are difficult to model in pedigree analyses, especially for health traits with low incidence rates. To circumvent this problem we used genome-wide single-nucleotide polymorphism data and implemented the Genomic-Restricted Maximum Likelihood (G-REML) method to estimate the heritabilities and genetic correlations for resistance to 23 different infectious pathogens in calves and cows in populations undergoing natural pathogen challenge. Furthermore, we conducted gene-based analysis and generalized gene-set analysis to understand the biological background of resistance to infectious diseases. The results showed relatively higher heritabilities of resistance in calves than in cows and significant pleiotropy (both positive and negative) among some calf and cow resistance traits. We also found significant pleiotropy between resistance and performance in both calves and cows. Finally, we confirmed the role of the B-lymphocyte pathway as one of the most important biological pathways associated with resistance to all pathogens. These results both illustrate the potential power of these approaches to illuminate the genetics of pathogen resistance in cattle and provide foundational information for future genomic selection aimed at improving the overall production fitness of cattle.</p></div

The identification of gene ontologies and candidate genes for digital dermatitis in beef cattle from a genome-wide association study

Bovine Digital Dermatitis (DD) is an infectious disease causing severe lameness in cattle. The aim of this study was to perform a Genome Wide Association Study (GWAS) and a Gene-Set Enrichment Analysis (GSEA) to identify candidate genes, instead of an individual Single Nucleotide Polymorphism (SNP), associated with DD traits in beef cattle. Beef cattle (n= 307) were genotyped with the Illumina GGP-HD bovine 150K SNP chip. The M-scores of the cattle over the observation period were used to define the DD traits with different complexities, the distinction between affected (1) and unaffected (0) cattle, regarding the general DD-status (DD AFFECTED), acute disease events (DD ACUTE), visible signs of chronicity (DD CHRONICITY) and proliferation of the skin (DD PROLIFERATION). The gene-set enrichment analysis revealed 30 Gene Ontology (GO) terms associated with the DD AFFECTED trait and 17, 31, and 16 GO terms were associated with DD ACUTE, DD CHRONICITY, and DD PROLIFERATION traits, respectively. By searching the significantly enriched GO terms from the ontology categories, biological process and cellular components, and molecular function, 25 functional genes were identified that were highly involved in cellular and membrane function pertaining to adhesion, migration and proliferation which could contribute to DD traits. These results could provide insight into the genetic framework of this complex trait and disease in beef cattle to aid the development of potential genetic therapies as well as selective breeding strategies to decrease DD prevalence in cattle.</p

Test-day milk yield as a selection criterion for dairy buffaloes (Bubalus bubalis Artiodactyla, Bovidae)

Due to the great demand for buffalo milk by-products the interest in technical-scientific information about this species is increasing. Our objective was to propose selection criteria for milk yield in buffaloes based on total milk yield, 305-day milk yield (M305), and test-day milk yield. A total of 3,888 lactations from 1,630 Murrah (Bubalus bubalis) cows recorded between 1987 and 2001, from 10 herds in the State of São Paulo, Brazil, were analyzed. Covariance components were obtained using the restricted maximum likelihood method applied to a bivariate animal model. Additive genetic and permanent environmental effects were considered as random, and contemporary group and lactation order as fixed effects. The heritability estimates were 0.22 for total milk yield and 0.19 for M305. For test-day yields, the heritability estimates ranged from 0.12 to 0.30, with the highest values being observed up to the third test month, followed by a decline until the end of lactation. The present results show that test-day milk yield, mainly during the first six months of lactation, could be adopted as a selection criterion to increase total milk yield