Transcriptomics of Innate Immune Response in the Domestic Goat and Comparative Analysis with Other Ruminants

Goats are common with small-scale farmers and play an important role in livestock economics. Despite being genetically similar, ruminants vary in susceptibility to similar pathogens but the underlying molecular mechanisms remain largely unknown. By studying innate immune signatures in the goat and comparing to other ruminants, we will begin to elucidate the molecular basis of disease response.

We collected 12 tissues from 4 male, 5-day old (alpine x toggenburg x saanen) dairy goats to study gene expression profiles using RNAseq. TruSeq 75bp paired-end libraries are being generated on the Illumina platform, at 25 million reads depth, for comparison with sheep and water buffalo. In parallel, we have performed whole genome resequencing on each goat at 30X coverage. We are also differentiating bone-marrow derived macrophages and stimulating these with lipopolysaccharide, to mimic pathogen challenge. We will compare expression of macrophage specific transcripts in goat with equivalent datasets from cattle, water buffalo and sheep. We intend to transfer these techniques to build capacity in Africa and using goats from UK and Africa, we will investigate mechanisms of response to infection, breed and ecotype specific variation.

The data obtained will contribute to characterization of macrophage specific genes in goat, highlight key immune signatures across tissues and improve annotation of the reference assembly (ASM170441v1). In addition, understanding molecular mechanisms of variation in disease resistance across ruminants will provide a valuable resource for study of functional ruminant genomics, and enhance breeding strategies being implemented to meet the rising demand for livestock products across the globe.