Analysis of the Sheep Genome, with a Focus on the Evolution and Function of the Rumen and Implications for Methane Production by Ruminants

Analysis of the sheep genome and transcriptome identified a number of novel genes in the sheep epidermal differentiation complex (EDC) locus. One of these genes (TCHHL2), highly expressed in the sheep (and cattle) rumen wall but not observed in non-ruminants, encodes a long protein containing a large array of variable 15 amino acid repeats. Also in the EDC and highly expressed in the rumen were new members of a ruminant-specific gene family (PRD-SPRRII) encoding proteins of generally less than 100 amino acids. By analogy with other keratinized and cornified tissues, such as the skin, these proteins are predicted to play a major role in the heavily cross-linked proteinaceous complex on the surface of the rumen. The rumen specific components presumably generate a surface specialized for the abrasive diet and extremely high density of microbes in the rumen. Only a small number of additional genes were much more highly expressed in the rumen than in all the tissues examined: skin and tonsil (both cornified), the abomasum and intestinal tissues, and the spleen, liver and muscle. These genes included CA1, encoding a carbonic anhydrase putatively involved in the uptake of volatile fatty acids. In contrast to the EDC locus, no rumen specific keratins were identified. Methane, produced by archaea in the rumen is a moderately heritable trait. By combining the genomics data with a time course of “rumen” wall gene expression across prenatal development and from sheep with divergent methane production we are investigating the mechanisms by which sheep affect methane production.