Dairy cattle

Genomic and transcriptional characterisation of bovine digital dermatitis using long and short read whole genome sequencing and total bulk and single cell RNA-seq

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Abstract

Bovine Digital Dermatitis (BDD) is a polybacterial infectious disease that significantly impacts dairy and beef cattle worldwide, causing lameness, reduced milk yield, and premature culling, leading to major economic losses and environmental footprint. The disease is primarily associated with spirochetes of the Treponema genus, which are also implicated in chronic human conditions such as syphilis and periodontal infections. Previous studies, including our own, have demonstrated that host resistance to BDD is a complex heritable trait. Consequently, the UK introduced the Digital Dermatitis Index (DDI) in the national genetic evaluation to support selective breeding for BDD resistance. The present study aimed to elucidate the molecular mechanisms underlying BDD susceptibility. A cohort of 323 heifers was monitored monthly for BDD lesions using the M-scoring system. Animals were classified into three genetic merit groups based on DDI : high (HG) implying genetic resistance, medium (MG), and low (LG). Subsequently, three study groups were defined for detailed analysis: (1) healthy HG heifers (HGH), (2) chronically infected LG heifers (LGC), and (3) previously infected but healed LG heifers (LGH). Blood samples were collected to perform high-coverage (more than 40X) whole genome sequencing (WGS) on 36 animals, with 12 samples representing each study group. In addition, Nanopore long-read sequencing (approximately 40X coverage) was conducted on a subset of 9 samples (3 per group). Foot skin biopsies were used for transcriptomic analyses: a total of 72 biopsies were processed for bulk RNA sequencing (including long non-coding RNAs and small RNAs) across all study groups, while 12 biopsies were used for single-nucleus RNA sequencing (snRNA-seq) and 4 for single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform, followed by sequencing on an Illumina system. Short-read WGS data was analysed with GATK best-practices pipeline. Joint genotyping resulted in 13.1 million SNPs, 45% of which were novel. Single-cell RNAseq data processing through CellRanger and Seurat tools resulted in high-quality transcriptomic profiles from over 10,000 individual cells. Notably, scRNA-seq yielded fewer viable cells than snRNA-seq, likely due to challenges in dissociating bovine skin tissues. Analysis identified multiple cell clusters annotated as keratinocytes, fibroblasts, epithelial cells, smooth muscle cells and myeloid cell populations based on marker gene expression. Study group-specific differences were evident; for example, LGC samples showed higher proportions of immune and myeloid cells, consistent with active lesions. These initial findings will be integrated with forthcoming results from ongoing bulk RNA-seq and WGS analyses to yield deeper insights into the molecular basis of BDD resistance. This research provides novel insights into cellular and genetic factors influencing BDD resistance. By linking host genetic merit to immune function and tissue-specific transcriptional landscapes, our findings lay the groundwork for precision breeding strategies to enhance cattle health, welfare, and productivity.

Keywords: 2026

How to Cite:

Hinsu, A., Sato, A., Attree, E., Bao, K., Anagnostopoulos, A., Siachos, N., Gillespie, A., Guest, D., Evans, N., Xia, D., Banos, G., Oikonomou, G., Werling, D. & Psifidi, A., (2026) “Genomic and transcriptional characterisation of bovine digital dermatitis using long and short read whole genome sequencing and total bulk and single cell RNA-seq”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285565. doi: https://doi.org/10.31274/wcgalp.23741

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