Equine trait mapping: from disease loci to the discovery of a major gene controlling vertebrate locomotion

Assigning function to genes is essential for a better understanding of biological systems. To date, approximately half of the genes in the vertebrate genome have known function. Domestic animals are a rich source for trait mapping and in this thesis we have mapped three distinct equine phenotypes. The result provides increased knowledge regarding gene function and importantly, practical implications for horse welfare. In paper I and IV, we confirm that Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome is inherited as an incompletely dominant trait (p= 2.2x10-16). By first identifying a 208 kb identity-by decent (IBD) region and subsequently excluding polymorphic sites identified through Illumina sequencing, we conclude that the gene PMEL causes these defects in horse. Our findings, together with functional analyses recently published, support that the cause of MCOA syndrome is a missense mutation (Arg625Cys) near the transmembrane region of PMEL that results in altered biochemical properties. In paper II we show that variants in the MHC-II region influence the susceptibility to equine Insect Bite Hypersensitivity with the same marker risk allele identified in two distinct populations, OR 4.19 (p= 2.3x10-5) and 1.48 (p= 0.04) for Icelandic horses and Exmoor ponies respectively. In addition, homozygosity across the MHC-II region confers a higher risk of developing disease, OR= 2.67 (p= 1.3x10-3). Finally, in paper III we utilize the EquineSNP50 BeadChip to identify the first Gait locus in horse. A highly significant SNP (EMP2= 2.0x10-4) was identified to be consistent with a recessive mode of inheritance for the lateral gait pace in Icelandic horses, and confirmed in an independent sample set (p= 2.4x10-14). Illumina sequencing of an established IBD region identified a nonsense mutation in the gene DMRT3. A clearly dichotomous distribution in a panel of gaited and non-gaited breeds revealed that the DMRT3 mutation is permissive for a variety of alternate gaits. The mutation also has a favorable effect in harness racing horses. Functional characterization of the truncated protein demonstrated correct localization and an intact DNA binding profile. mRNA expression in a small population of commissural neurons from the spinal cord was confirmed in mutant and wild type horses. Further, a DMRT3 null mouse displayed a change in spinal cord circuit signaling and locomotion. These findings reveal a new molecule involved in the regulation of limb movement.