Genomic analysis of claw lesions in Holstein cows: Opportunities for genomic selection, quantitative trait locus detection, and gene identification.

Claw lesions are the third most important health issue in dairy cattle, after mastitis and reproductive disorders, and genomic selection is a key component for long-term improvement of claw health. The objectives of this study were to assess the feasibility of a genomic evaluation for claw health in French Holstein cows, explore possibilities to increase evaluation accuracy, and gain a better understanding of the genetic determinism of claw health traits. The data set consisted of 48,685 trimmed Holstein cows, including 9,646 that were genotyped; 478 genotyped sires were also used. Seven claw lesion traits were evaluated using BLUP, genomic BLUP, BayesC, and single-step genomic BLUP, and the accuracies obtained using these approaches were measured through a validation study. The BayesC approach was used to detect quantitative trait locus (QTL) regions associated with the 7 individual traits (digital dermatitis, heel horn erosion, interdigital hyperplasia, sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure) based on their Bayes factor. Annotated genes on these regions were reported. Genomic evaluation approaches generally did not allow for greater accuracies than BLUP, except for single-step genomic BLUP. Accuracies were moderate, but best and worst validation animals were correctly discriminated and showed significant differences in lesion frequencies. A total of 192 QTL regions were identified, including 13 with major evidence or involved for 2 of the traits. A high number of genes were present on these regions, and several had functions associated with the immune system. In particular, the EPYC gene is located close to a major evidence QTL for resistance to digital dermatitis that is also a QTL for interdigital hyperplasia (on chromosome 5, around 20.9 MB) and has been associated with Ehlers-Danlos syndrome in cattle. Genomic selection can be used to improve resistance to individual claw lesions, and several possibilities exist to improve accuracies of genomic evaluations.

Genetic evaluation of claw health traits accounting for potential preselection of cows to be trimmed.

Claw lesions are one of the most important health issues in dairy cattle. Although the frequency of claw lesions depends greatly on herd management, the frequency can be lowered through genetic selection. A genetic evaluation could be developed based on trimming records collected by claw trimmers; however, not all cows present in a herd are usually selected by the breeder to be trimmed. The objectives of this study were to investigate the importance of the preselection of cows for trimming, to account for this preselection, and to estimate genetic parameters of claw health traits. The final data set contained 25,511 trimming records of French Holstein cows. Analyzed claw lesion traits were digital dermatitis, heel horn erosion, interdigital hyperplasia, sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure. All traits were analyzed as binary traits in a multitrait linear animal model. Three scenarios were considered: including only trimmed cows in a 7-trait model (scenario 1); or trimmed cows and contemporary cows not trimmed but present at the time of a visit (considering that nontrimmed cows were healthy) in a 7-trait model (scenario 2); or trimmed cows and contemporary cows not trimmed but present at the time of a visit (considering lesion records for trimmed cows only), in an 8-trait model, including a 0/1 trimming status trait (scenario 3). For scenario 3, heritability estimates ranged from 0.02 to 0.09 on the observed scale. Genetic correlations clearly revealed 2 groups of traits (digital dermatitis, heel horn erosion, and interdigital hyperplasia on the one hand, and sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure on the other hand). Heritabilities on the underlying scale did not vary much depending on the scenario: the effect of the preselection of cows for trimming on the estimation of heritabilities appeared to be negligible. However, including untrimmed cows as healthy caused bias in the estimation of genetic correlations. The use of a trimming status trait to account for preselection appears promising, as it allows consideration of the exhaustive population of cows present at the time a trimmer visited a farm without causing bias in genetic parameters.