Transcriptional alterations due to sole ulcer revealed via RNA-seq analysis of corium tissue in lactating dairy cows

Document Type


Publication Date



American Dairy Science Association


Journal of Dairy Science




Suppl. 1






dairy cow, hoof, transcriptome


Ulceration of the sole can damage the corium and affect the keratinization of the hoof tissue. An RNA-seq analysis was performed in corium tissue biopsies to provide a comprehensive transcriptome profile of the hoof. Multiparous Holstein dairy cows were selected based on their condition as clinically healthy (HSU, n = 7), or diagnosed with sole ulcers (SU, n = 7). Lameness was assessed based on a locomotion score (1–5 scale). Hoof hardness was assessed using a durometer (Shore A 0–100HA). Locomotion scores were 1 ± 0 and 2.5 ± 0.5 (mean ± SD) for HSU and SU, respectively. Hoof hardness was 79.8 ± 6.1 and 69.9 ± 4.4 for HSU and SU, respectively. Hoof biopsies were performed according to Osorio et al., 2012; J Dairy Sci, 95:6388. All corium samples were immediately flash-frozen in liquid nitrogen. The RNA integrity number for all samples was 8.0 ± 1.0. The RNA samples were sequenced (NGS; Illumina, NovaSeq S4) at the University of Minnesota Genomics Center. Processed reads were aligned to the bovine genome using HISAT2. Differential transcript analysis was performed using a quasi-likelihood test in R-package (EdgeR) and False Discovery Rate < 0.05 correction was applied. Among the 500 differentially expressed genes identified, SU upregulated the expression of genes related to the Toll-like receptor (TLR) pathway including TLR2, 5, and 6 (P < 0.01) in comparison to HSU. Genes mediators of pro-inflammatory response IL1R1, IL18R1, and IL18RAP (P ≤ 0.03) were upregulated in the SU in comparison to HSU. Keratin-associated proteins (KRTAP) including KRTAP11–1, KRTAP15–1, KRTAP19–3, and KRTAP27–1 were downregulated (P < 0.002) in SU than HSU. The greater (P = 0.005) expression of COL6A2 in hoof tissue of SU cows than HSU can be associated with extracellular matrix structural function impacted by sole ulcer. Our preliminary data further confirms that ulcerations can develop inflammatory-like conditions while decreasing keratinization of the hoof. Further analysis of this RNA-seq data can provide novel molecular targets for nutritional interventions to reduce sole ulcer incidence and prevalence in dairy herds.