Transcriptome Response of Small Intestine of Village Chickens from Two Agro-Ecological Zones of South Africa Naturally Infected with Ascaridia galli parasites

Nematodes of the genus Ascaridia are known to infect many species of birds and cause fatal diseases. Ascaridia galli damages the intestinal mucosa of chickens leading to blood loss and secondary infection. Very little information is available on the genetic resistance to gastrointestinal parasites particularly in village chickens populations. This study investigates the gene expression profiles in chickens from two different agro-ecological zones of South Africa that were naturally infected with A. galli parasites. Cox1 gene of A. galli parasities revealed six diverse haplotypes with no genetic differentiation between A. galli from Limpopo and KZN provinces. The naturally infected A. galli intestines displayed hypertrophy of the intestinal villi and necrosis of the crypt of Lieberkühn gland. Total RNA from small intestines of infected and non-infected village chickens was sequenced using Illumina HiSeq 2500 to generate between 3,908,924 and 3,994,946 reads. An average of 83.50% of trimmed reads were mapped to gallus.galgal4.74 genome using Tophat program. Of 16383 DEGs detected between any two-way comparisons using Cuffdiff, 3057 DEGs were up/down regulated in Limpopo chickens whereas 1417 DEGs were up/down regulated in KZN chickens. A total of 426 DEGs were shared between the comparisons. Gene ontology analysis of DEGs revealed an enrichment of immune response, defense response, inflammatory response and cell signaling genes. T cell receptor signaling pathway was among the most significantly impacted pathways in both comparisons. The functional annotation of DEGs presents an opportunity to understand the molecular network underlying the genetic resistance of village chickens to A. galli infections.