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Wool is composed primarily of proteins belonging to the keratin family. These include the keratins and keratin-associated proteins (KAPs) that are responsible for the structural and mechanical properties of wool fibre. Although all human keratin and KAP genes have been annotated, many of their ovine counterparts remain unknown and even less is known about their genomic organisation. The aim of this study was to use a combinatory approach including comprehensive cDNA and de novo genomic sequencing to identify ovine keratin and KAP genes and their genomic organisation and to validate the keratins and KAPs involved in wool production using ovine expressed sequence tag (EST) libraries and proteomics. The number of genes and their genomic organisation are generally conserved between sheep, cattle and human, despite some unique features in the sheep. Validation by protein mass spectrometry identified multiple keratins (types I and II), epithelial keratins and KAPs. However, 15 EST-derived genes, including one type II keratin and 14 KAPs, were identified in the sheep genome that were not present in the NCBI gene set, providing a significant increase in the number of keratin genes mapped on the sheep genome.

An interspecies deer hybrid resource population developed from a cross of Pere David's and red deer was used to detect QTL that account for species differences. A genome scan, coupled with composite interval mapping, was conducted to search for QTL controlling body measurements at pre-pubescent age (6 months of age) and puberty (15 months of age) in this interspecies hybrid. Five linkage groups that harbour QTL affecting morphology were identified. A joint-traits analysis was used to search for putative pleiotropic QTL on four of these linkage groups, and three were significantly associated with pleiotropic QTL for nose width and foot length (metacarpal and phalanges), which collectively accounted for 29-58% of the phenotypic difference between the two deer species. This study suggests that a few loci with large pleiotropic effects may be responsible for species-specific differences in growth and structure-related traits.