Phenotypic characterization and genome-wide association studies of digital cushion thickness in Holstein cows

The bovine digital cushion is a compression pad between the distal phalanx and sole and has been associated with claw horn disruption lesions. Digital cushion thickness (DCT) is estimated to be moderately heritable. Therefore, the objectives of our study were to examine influences of management and environment on DCT and to identify genetic markers and candidate genes associated with DCT. In a cohort of 502 Holsteins from 5 farms in New York State, DCT and body condition score (BCS) were collected twice, at <137 d prepartum and from 86 to 127 d in milk, corresponding to periods when the digital cushion is thickest and thinnest, respectively, as determined by previous research. Cows underwent sonographic examination of the digital cushion evaluated at the typical sole ulcer site for the right front and hind foot. Linear mixed models were conducted on DCT with the fixed effects of time point, digit, wither height, sacral height, BCS group, and multiple farm system variables separately and included random effects to control for the random subset of cows per farm, repeated measures, and multiple measurements from each cow. The phenotypic results indicated that DCT varied by sample time point, sacral height, parity, digit, BCS group, and wither height. For the genotypic study, 447 DNA samples were genotyped on the Illumina BovineHD 777K BeadChip (Illumina Inc., San Diego, CA). Quality assessment of markers and samples provided a final data set of 431 samples and 579,449 markers. Genome-wide association studies were conducted for DCT testing inheritance models and genetic variation of digit, foot, time point, and average thickness. One marker passed the Bonferroni correction threshold and 26 passed false discovery rate from 4 genome-wide association studies with covariates of sequencing batch plate, parity group, BCS, wither height, and sacral height. Ten candidate genes were identified, with 2 genes on Bos taurus autosomes 24 and 29 involved in biological functions related to the digital cushion: MC4R and DLG2 were related to fat deposition and bone growth, respectively. The genetic markers discovered in this study have the opportunity to be used in breeding programs using genomic selection to select against claw horn disruption lesions and lameness due to associations between the markers and DCT. Further studies on the biologically plausible candidate genes may identify causative genetic variants and how they relate to DCT through gene regulation, expression, structure, or copy number variation.