Global transcriptomic evaluation of the hoof lamina in beef cattle with altered mobility

Objectives

Impaired mobility of cattle arriving at packing plants gained considerable attention in the fall of 2013. In addition to a stiff gait and reluctance to move, cattle presented with increased respiratory rates and muscle tremors. In the most severe cases, animals were observed to slough one or more hooves (claw horn capsules) during transport or while in lairage. Affected animals experience significant discomfort and when hoof sloughing occurs at the packing plant animals, these animals are unable to be processed creating both an animal welfare issue as well an economic loss to the packer. It is believed that a better understanding of possible molecular causes of this condition would help feeders develop better feeding and management practices to prevent the disease. This report describes our observations from an evaluation of the transcriptome of hoof lamina, by differential expression and co-expression network approaches, to identify gene and pathways underlaying the altered mobility scores of beef cattle.

Materials and methods

The lateral claw of each hind limb of 21 animals was sectioned and the sections of the hoof wall/laminar corium/P3 located midway between the coronary band and the sole were collected. The hoof wall and pedal bone were sharply dissected from the lamina and the laminar sample was directed for RNA-Seq analysis. The global transcriptome was evaluated by using DESeq2 (R package) to identify differentially expressed genes (DEG) between animals with unaffected mobility (control group; N = 4; mobility score 1), and those showing any level of alteration in mobility (lameness group; N = 17; mobility score 2, 3 and 4). False discovery rate was controlled using Benjamini and Hochberg methodology (adjusted p < 0.1). To identify groups of genes (modules) exhibiting similar changes in gene expression across different mobility score levels, a co-expression network analysis was conducted (WGNCA). Modules were labelled with color names. We identified modules that were statistically associated with mobility scores (P < 0.05) using PROC Glimmix (SAS), accounting for gender differences. Functional enrichment analysis was performed using the Cytoscape plugin ClueGO to identify over-represented gene function or pathway ontology terms. [...]