Search for Causal Mutations in Meat Tenderness Candidate Genes in Nellore Cattle

The objective of this study was to identify genes with significant effects on meat tenderness and to search for the causal mutations in Nellore cattle. Phenotypic and genotypic data on 1,616 animals from two Brazilian animal breeding programs were used. All animals were genotyped with the Illumina BovineHD panel. Association analyses were performed to identify significant genes. Two haplotypes located in the ASAP1 and CAPN1 genes were significant after Bonferroni correction. To find new SNPs, six regions spanning these genes were sequenced from 298 animals. Seven new SNPs were found in CAPN1 and four in ASAP1. The new SNPs were imputed into the 1,318 remaining animals using BEAGLEv3.3.2. FastPhase and HaploView were used for haplotype reconstruction and linkage disequilibrium analyses, respectively. Statistical analyses were performed using the MIXED procedure of SAS 9.3. Statistical model included fixed effects for contemporary groups (farm, year of birth, management group, month and year of slaughter), number of alleles in each haplotype as covariable (linear effect) and sire as random effect. For ASAP1, the haplotypes had no effect on tenderness. For CAPN1, 14 SNPs were found to be in strong linkage disequilibrium with the most significant haplotype region (exon 14 to intron 19). The SNP rs17871051 is located in exon 14 and results in a substitution of valine for isoleucine. This SNP is known from other studies to influence meat tenderness and may also be a causal mutation in Nellore cattle. However, following Bonferroni correction, the haplotype was not found to significantly affect meat tenderness. Acknowledgements: FAPESP #2013/00035-9, #2014/23013-3 and #2009/16118-5.