Abstract

Genetic analysis of respiratory disorders in Holstein calves have been developed using producer-recorded data and the single-step GBLUP (ssGBLUP) methodology. Phenotypic data on respiratory events up to one year of age have been obtained from herd management software backup files provided directly from about 300 dairies upon obtaining owners’ permission. The following traits were included in the analysis: respiratory diseases from 0-3 (RESP1), 4-14 (RESP2), 15-50 (RESP3), 51-365 (RESP4) and 0-365 days of age (RESPA). Each trait was defined as a binary event, having a value of one if an animal has been recorded with a disorder, and zero otherwise. The number of phenotypic records ranged from about 224,000 for RESP1 to approximately 874,000 for RESPA, with the prevalence ranging from 4.6% (RESP1) to 20.2% (RESPA). All traits were analyzed using a univariate threshold animal model, including fixed effect of year of birth x calving season x region and random effects of herd x year of birth and animal. Heritabilities, estimated on the liability scale, ranged from 0.039 (RESP4) to 0.097 (RESP1). A total of 45,425 SNPs were used in genomic analyses. Over 292K genotyped animals were included in the evaluation. Animals genotyped with low density chips were imputed to the required number of SNPs using Fimpute software. All analyses were performed using the ssGBLUP implementing the ‘algorithm for proven and young animals’ (APY) designed to accommodate very large number of genotypes. Predicted transmitting abilities (PTA) were expressed in percentage points as deviations from the average estimated probability of a disorder in the base population. Reliabilities of breeding values were obtained by approximation in which the genotype contribution was approximated using the diagonal values of the genomic relationship matrix. Estimated genomic PTAs and reliabilities were approximately normally distributed for all traits, with reliabilities for genotyped animals without own phenotypes reaching average values between 38% (RESP4) and 50% (RESP1). Genome-wide association analyses were conducted with a subset of genotyped animals using single-step GWAS (ssGWAS) approach with a 10 SNP sliding window. Regions explaining most genetic variance were found on chromosomes 1, 2, 9, 14, 27, and X. Some of those regions contained genes that may be involved in physiological pathways affecting respiratory health of dairy calves. Keywords: calf health, respiratory diseases, genomic selection, GWAS

Natascha Vukasinovic, Dianelys Gonzalez-Peña, Jordan Brooker, Prerak Desai, Sue DeNise

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Biology & Species - Bovine (dairy) 2, , 597, 2018
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