Identification of quantitative trait loci affecting wet carcass syndrome in sheep using high density snp genotypes

[摘要] English: Wet carcass syndrome (WCS) is a condition predominantly found in sheep, which negatively affects the quality of their carcasses. The Northern Cape Province in South Africa and the southern part of Namibia have been identified as geographic regions with a high occurrence rate of WCS. During the pre-slaughter period, the animal appears to be clinically normal, showing no symptoms of an abnormality. However, after the removal of the skin during the slaughter process the carcass appears to be 'wet. The condition is phenotypically described as a subcutaneous accumulation of watery fluid. The areas on the carcass most affected are the brisket, flanks, hindquarters, sides, and back. The watery fluid is also found in the intramuscular connective tissue layers of both the flank and subscapular area. Unfortunately, WCS results in sheep carcasses that are deemed to be unacceptable by the end consumer from both an appearance point of view and an apparent reduced shelf life. When the description and results of previous research are considered, no physiological-, environmental- or management system was conclusively identified as a causative agent of WCS. However, stress experienced by the animals during the pre-slaughter period was identified as a possible cause and is continuously discussed throughout the current research to date. The tentative breed-specificity, i.e. Dorper sheep breed, of the condition lends some credence to a potential genetic basis for it. However, previous research has not considered a genetic variant as a causal agent of WCS. The current study employed the Ovine Infinium® HD SNP BeadChip and a genome-wide association analysis (GWAS) approach to scan the genomes of both afflicted- and unafflicted sheep in search of putative quantitative trait loci associated with the WCS phenotype. This study was not only one of the first in Southern Africa to make use of this specific BeadChip but also the first to investigate the role of genetics as a causative factor of WCS. Muscle samples from sheep carcasses (33 afflicted and 36 unafflicted) were collected from three different abattoirs in the Northern Cape Province of South Africa and Southern Namibia.By using a candidate gene approach it was possible to map genetic loci, RYR1 and PRKAG3 (RN¯) causative of phenotypically similar conditions such as porcine stress syndrome and red, soft and exudative meat to the ovine genome. The positions of these loci (RYR1 on Chromosome 14 and PRKAG3 on Chromosome 2) mapped to the ovine genome were not in accordance with the loci showing significant association with the WCS phenotype; and no relationship was found between single nucleotide polymorphisms located within these genes and WCS. Furthermore, along with the latter approach the test of runs of homozygosity presented similar results as well as providing plausible evidence that WCS is not a recessive inherited condition. To test for an association between the phenotype (WCS) and an autosomal genetic marker(s) i.e. SNPs, a case-control study design was implemented. Given the relatively small sample size of the current study, the results obtained from the GWAS attested strong evidence of at least two loci, oar3_OARX_29903534 and oar3_OARX_113973214 positioned within the non-homologous region of the X chromosome for WCS carcasses. All afflicted animals, both males and females, carried at least one G2 allele for marker oar3_OARX_113973214, which was shown to be related to the WCS phenotype. Given the apparent influence of stress on WCS, these unafflicted males and females in all likelihood did not experience adequate levels of stress to manifest the WCS condition post-slaughter. The results of the current study also indicated that WCS may possibly be a rare X-linked inherited condition, provided only female individuals are considered. Finally, two possible major loci involving two major genes, HTR2C and DMD, positioned on the non-homologous region of the X chromosome have been identified as novel positional and functional candidate genes for WCS in sheep.

[发布机构] University of the Free State