Differential gene expression analysis of Dohne Merino sheep naturally infected with Haemonchus contortus

Gastrointestinal nematode (GIN) infections, particularly caused by Haemonchus contortus, are a major concern in sheep farming, resulting in significant economic losses Genetic resistance, used alongside chemical control, nutrition, and pasture management, provides a sustainable strategy to mitigate these infections in industrial livestock systems The South African Dohne Merino sheep, known for their resilience and suitability for both wool and meat production, offer a potential genetic resource for breeding GIN resistance, providing an alternative to chemical control. This study utilised RNA-Seq and differential gene expression (DEG) analysis to investigate the molecular mechanisms underlying H. contortus infection in Dohne Merino sheep. Six adult ewes from Wauldby farm (Eastern Cape Province), naturally exposed to H. contortus, were selected. The animals were categorised into resistant (n = 3) and susceptible (n = 3) groups based on Estimated Breeding Values (EBVs) from faecal egg count (FEC) phenotypes. DEG analysis revealed 34 significantly differentially expressed genes (DEGs) related to immune responses and external stimuli, with involvement in key pathways such as Rap1 and PI3K-Akt signaling, linked to H. contortus resistance. Additionally, segment-specific analysis of the gastrointestinal tract identified DEGs in different regions: 146 in the abomasum, 302 in the ileum, 584 in the jejunum, and 332 in the duodenum. The findings highlight genes and pathways contributing to GIN resistance and tissue-specific response mechanisms. These insights can support the selection and breeding of sheep with enhanced resistance to H. contortus, offering a genetic approach to combating GIN infections.