Genomic analysis of bovine respiratory disease and lung consolidation in preweaned Holstein calves using clinical scoring and lung ultrasound

Abstract

Bovine respiratory disease (BRD) is a leading cause of morbidity and mortality in dairy calves, with detrimental long-term effects that include stunted growth, increased age at first calving, and decreased milk production in first lactation. The objectives of this study were to establish a protocol for objective and efficient assessment of BRD phenotypes in preweaned dairy calves, develop a genomic reference population with well-defined clinical and subclinical phenotypes, identify chromosomal regions associated with BRD in a genome-wide association study, estimate genetic parameters of BRD, and predict genomic breeding values of dairy calves. A total of 1,107 Holstein calves from 6 dairy farms in southern Wisconsin were examined using clinical respiratory scoring and lung ultrasound at 3 and 6 wk of age. The clinical respiratory score was based on visual appraisal of eyes, nose, ears, cough, and temperature. Lung ultrasound scores were assigned based on the amount of consolidation present. Calves were genotyped with a commercially available SNP array and after quality control and imputation to higher density, 690,291 SNP markers and 1,014 individuals remained. Single-step genome-wide association study and single-step genomic best linear unbiased prediction were applied to binary 3- and 6-wk phenotypes considered as overall respiratory healthy versus affected (RESP3, RESP6) or as presence or absence of lung consolidation (CON3, CON6). Lung ultrasound combined with a clinical scoring system allowed for efficient and objective assessment for the prevalence of BRD. Proportions of variance attributed to 1-Mb non-overlapping windows suggested genomic regions that may contain putative candidate genes, most notably regions on Bos taurus autosomes 1, 6, 7, 10, 11, 12, 15, 17, 18, 27, and 28 that explained 0.70 to 1.45% of the genetic variance. Heritability estimates were higher at 3 wk (0.214 and 0.241 for CON3 and RESP3, respectively) than 6 wk (0.084 and 0.111 for CON6 and RESP6, respectively), and mean reliabilities of genomic estimated breeding vales for calves with genotypes and phenotypes ranged from 0.12 for CON6 to 0.30 for RESP3.