Genomic Study for Beef Tenderness in a Polled Nelore Cattle Population

This study was carried out to identify genomic regions associated with beef tenderness (Warner-Bratzler Shear Force - WBSF) and to evaluate the prediction ability using preselected markers based on the genome wide association study (GWAS) results in an experimental Nelore cattle population. The dataset was provided by Guaporé Agropecuária S/A – OB Ranch, located in Mato Grosso State, Brazil, and by the Brazilian Agriculture Research Corporation (EMBRAPA- Cerrados), located in Goiás State, Brazil. The animals, born from 2002 to 2010, were slaughtered at 25 months of age. Twenty-four hours after the slaughter, 436 samples with 2.5 cm of longissimus dorsi muscle, from the 10th - 13th rib of the left half-carcasse were obtained to measure WBSF. Part of the studied animals (61) were genotyped using a high-density SNP panel (BovineHD BeadChip assay 777k, Illumina Inc., San Diego, CA) and part (548) were genotyped with a lower-density 80k BeadChip (GeneSeek Genomic Profiler HD BeadChip) and then imputed for a 777k chip through FImpute v. 2.215 software using pedigree and genomic information. After genomic data quality control, there were available 375,678 SNP and 599 genotyped animals. The single-step GWAS was used to identify genomic regions associated to the phenotypes. The traditional genetic evaluation and the single-step genomic BLUP were run using a single-trait animal model that included the fixed effect of sex, slaughter control number, and the linear effect of age of slaughter and the random effect of animal. Confirming the polygenic nature of WBSF, 17 windows (located in 9 different chromosomes) were found to be associated with WBSF. Several genes that have their functions related to energy metabolism and fat, and calcium ion were found in the associated windows. As meat quality is a multidimensional concept and fat enriches tenderness, it is important to highlight these genes that act on energy metabolism and fat. Also, the associated window that explained more than 12% of the additive genetic variance is very close to the region where the CAST gene is located. The inclusion of genomic information into the traditional genetic evaluation increased 8.11% the accuracy of the evaluation. In addition, using only the preselected markers (5k) increased 21.62% and 74% of the ability to predict EBV and phenotype, respectively, compared to using high density markers. The results showed that using genomic information could help to better understand the genetic architecture of beef tenderness and increase prediction ability of genetic evaluation.