Genome-wide association analysis for beef traits in Marchigiana cattle breed

Abstract Text: Genome-wide association studies (GWAs) are procedures that enable to correlate huge amounts of genetic and phenotypic data to find genomic regions that affect traits of economic importance. Several studies have been conducted for dairy cattle while few reports are available for beef cattle. In this study  a GWAs was performed on Marchigiana  breed cattle, one of the most important beef breeds farmed in Italy. Phenotypes were  body weight (BW), average daily gain (ADG), carcass weight (CW), dressing percentage (DP), pH at slaughtering (pH), shank circumference (SC) and head weight (HW) measured on 408 Marchigiana young bulls slaughtered between 16 and 24 months of age. Animals were genotyped with the Illumina 54K bead -chip. Edits were on the call rate (>0.99), number of missing (>2,5%), MAF (>0.01). Data were analyzed with a mixed linear  model that included the fixed effects of herd, date of slaughtering, fixed covariables of age at slaughtering, SNP genotype (coded as 0,1,2), and the random effect of the sire to account for population stratification. A permutation test with 10,000 replications for each marker was performed in order to account for multiple testing. Significant markers (permutation corrected P<0.05) were 12 for BW, 124 for ADG, 36 for CW, 28 for DP, 9 for pH, 19 for SC, and 41 for  HW, respectively. Annotated genes in genomic regions corresponding to significant SNP were derived from the UCSC Genome Browser Gateway (http://genome.ucsc.edu/) using intervals of 500 Kbp (0,25 Mbp upstream and downstream of the significant region). Among identified genes, some were related to bone metabolism, as the OSTN (Osteocrin), SPARC (secreted protein acid cystein rich), muscle physiology as MEF2C (myocyte enhancer factor 2) and CA3(carbonic anhydrase III, muscle specific) feeding behaviour as HCRTR2 (hypocretin (orexin) receptor 2) and fatty acid biosynthesis as ACACB (acetyl-CoA carboxylase beta) and ACAD8 (Acyl-CoA dehydrogenase family, member 8) respectively. Of interest were also some genes that could be related to meat quality as FPGS  (folylpolyglutammate synthase) on BTA11, TTPA (tocopherol (alpha) transfer protein) on BTA 14 and GGPS1 (geranylgeranyl diphosphate synthase 1) on BTA28. These genes are involved in the metabolism of antioxidants such as vitamins A, E and folate that are effective molecules in preventing oxidative stress.

Keywords: GWAS, beef traits, Marchigiana cattle