Sheep (Ovis aries) are a major source of meat, milk and fiber in the form of wool, and represent a distinct class of animals that have a specialized digestive organ, the rumen, which carries out the initial digestion of plant material. We have developed and analyzed a high quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants, compared to non-ruminant animals.

MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small regulatory RNAs characterized in chickens we used a deep sequencing approach developed by Solexa (now Illumina Inc.). We sequenced three small RNA libraries prepared from different developmental stages of the chicken embryo (days five, seven, and nine) to produce over 9.5 million short sequence reads. We developed a bioinformatics pipeline to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected almost all of the previously known chicken miRNAs and their respective miRNA* sequences. In addition we discovered 449 new chicken miRNAs including 88 miRNA candidates. Of these, 430 miRNAs appear to be specific to the avian lineage. Another six new miRNAs had evidence of evolutionary conservation in at least one vertebrate species outside of the bird lineage. The remaining 13 putative miRNAs appear to represent chicken orthologs of known vertebrate miRNAs. We discovered 39 additional putative miRNA candidates originating from miRNA generating intronic sequences known as mirtrons.

The genetic factors that contribute to efficient food conversion are largely unknown. Several physiological systems are likely to be important, including basal metabolic rate, the generation of ATP, the regulation of growth and development, and the homeostatic control of body mass. Using whole-genome association, we found that DNA variants in or near proteins contributing to the background use of energy of the cell were 10 times as common as those affecting appetite and body-mass homeostasis. In addition, there was a genic contribution from the extracellular matrix and tissue structure, suggesting a trade-off between efficiency and tissue construction. Nevertheless, the largest group consisted of those involved in gene regulation or control of the phenotype. We found that the distribution of micro-RNA motifs was significantly different for the genetic variants associated with residual feed intake than for the genetic variants in total, although the distribution of promoter sequence motifs was not different. This suggests that certain subsets of micro-RNA are more important for the regulation of this trait. Successful validation depended on the sign of the allelic association in different populations rather than on the strength of the initial association or its size of effect.