Proceedings of the World Congress on Genetics Applied to Livestock Production, 11.568 A case-control study to identify a genetic component contributing to wet carcass syndrome in sheep L. van der Westhuizen 1,2 , M.D. MacNeil 1,2,3 , M.M. Scholtz 1,2 & F.W.C. Neser 2 1 ARC-Animal Production Institute, Private Bag X2, 0062, Irene, South Africa PienaarL@arc.agric.za (Corresponding Author) 2 Department of Animal, Wildlife and Grassland Sciences, UFS, P.O. Box 339, Bloemfontein, 9300, South Africa 3 Delta G, 145 Ice Cave Road, MT 59301, Miles City, USA Summary Wet carcass syndrome (WCS) is a condition predominantly found in lambs which negatively affects the quality of carcasses. During the pre-slaughter period, the animal appears to be clinically normal, showing no symptoms of an abnormality. However, after slaughter and removal of the skin the carcass appears to be “wet”. The condition is described phenotypically as a subcutaneous accumulation of watery fluid. Therefore, the objective of this investigation was to scan the genomes of afflicted and unafflicted lambs in search of putative quantitative trait loci associated with the WCS phenotype in sheep. Muscle samples from lamb carcasses (43 afflicted and 41 unafflicted) were collected from three different slaughterhouses in the Northern Cape Province of South Africa and Southern Namibia. To test for an association between the phenotype (WCS) and an autosomal genetic marker, a case-control study design was implemented. Separate analyses for each sex were motivated by individual SNP on the X chromosome being suggestive of a QTL. These analyses revealed significant associations between SNP and WCS in males, but not in females. The three SNPs reaching genome-wide significance in males are in strong linkage disequilibrium (LD) with the HTR2C and TENM1 genes. Keywords: association analysis, carcass, single nucleotide polymorphisms Introduction Wet carcass syndrome (WCS) is a condition predominantly found in lambs which negatively affects the quality of their carcasses. It is most frequently observed in Dorper and crosses of Dorper with indigenous and locally developed breeds of South Africa and Namibia (Brock et al., 1983; Webb & van Niekerk, 2011). During the pre-slaughter period, the animal appears to be clinically normal, showing no symptoms of an abnormality. However, after slaughter and removal of the skin the carcass appears to be “wet” (Hattingh et al., 1983). The condition is described phenotypically as a subcutaneous accumulation of watery fluid (Brock et al., 1983). Afflicted carcasses pose difficulties during meat processing and the meat has a reduced shelf life (Joubert et al., 1985). Therefore, these carcasses are deemed unacceptable and are condemned by the meat inspectors. In South Africa, economic losses stemming from WCS were approximately 27 million Rand in 2010 (Webb & van Niekerk, 2011; le Roux, 2012). While WCS has been recognized since 1981 and the subject of research since that time (Brock et al., 1983; Hattingh et al., 1983), its ethology remains undetermined. Not all animals within a flock sent to slaughter at one time are afflicted and inducing the condition