Van Marle-Koster, Este2025-02-182025-02-182025-042024-11*A2025http://hdl.handle.net/2263/101023Thesis (PhD (Animal Science))--University of Pretoria, 2024.Lameness due to claw lesions is a major hurdle for sustainable dairy production worldwide. Hoof trimming is used as a preventative measure, and key to future improvement strategies, providing phenotypic records for genetic interventions. This study aimed to evaluate hoof-trimming data in South African Holstein herds in total mixed ration (TMR) systems to determine the prevalence of claw lesions, investigate phenotypic and genetic parameters thereof, and explore the use of genomic information to provide insight into the underlying genetic architecture of claw lesion traits. Routine hoof-trimming appointments to five dairy herds in the central region of South Africa over a 10-year period, together with genotypes generated during the South African Dairy Genomic Programme provided the data for this study. More than 50% of cows presented with a lesion on any one foot, with digital dermatitis (DD) as the most commonly recorded lesion, followed by the non-infectious lesions sole ulcers (SU), sole haemorrhage (SH), and white line (WL) lesions, most of which occurred in the rear feet. The relationships between housing systems, individual feet, and the different lesions was analysed using chi-square tests as well as correspondence analysis (CA); SU and SH were strongly associated with each other, as were DD and interdigital phlegmon (IP), and SH and WL. These associations between lesions could be used to inform a more simplified approach to lesion recording systems, and contribute to practical prevention strategies on-farm. Phenotypic correlations between individual lesions and groups (infectious, non-infectious, and total lesions) were investigated using Spearman correlation tests. Moderate to strong relationships were observed among non-infectious lesions SH, SU, and WL (0.425–0.576), with the occurrence of SU and WL being strongly positively associated with total non-infectious lesions (0.543–0.576). Similarly, the infectious lesion DD was positively correlated with total infectious lesions (0.984). The estimated heritability of lesion categories varied between 0.008 for total lesions to 0.05 for the total non-infectious lesions category. A genome-wide association study for non-infectious lesions was performed using EMMAX, leading to the identification of one genome-wide significant single nucleotide polymorphism (SNP) and 15 genome-wide suggestive SNP. Candidate genes associated with the significant SNP on chromosome 25 related to abnormal skin morphology, immunity, and inflammation. From the literature, and this study, it is clear that claw lesions are highly polygenic. Differences among definitions and descriptions add to the complexity of the analyses. This study represents the first attempt to investigate claw lesions in South Africa using a combination of phenotypic and genetic data. The results confirmed the lack of adequate phenotypic data for genetic and genomic analyses, due to a lack of consistent farmer recording as well as a lack of coherence among data recording systems. Underlying genetic variability was confirmed and holds potential for further research but this requires consistent and complete phenotypic claw data. The prevalence of lameness remains high and a simplified and standardised recording system will be a first step in improving participation in national recording schemes for applicable research to reduce the incidence of this painful and costly disorder.en© 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria.UCTDSustainable Development Goals (SDGs)Claw-lesion trimmingHolsteinGenome-wide association study (GWAS)Dairy cattleDigital dermatitisAnimal recordingThesisu21038717https://doi.org/10.25403/UPresearchdata.28435658