Polymorphism analysis in genes associated with meat tenderness in Nelore cattle

The aims of this study were to identify haplotyped loci associated with meat tenderness (WBSF) in candidate genes and to search for new polymorphisms in these regions that influence such trait in Nelore cattle. Fifty-two genes that had previously been associated with WBSF or that have biological functions that may influence tenderness were chosen for the haplotype association analysis in 1657 animals. Of the 52 tested candidate genes, two haplotyped loci located in ASAP1 and CAPN1 were significantly associated with WBSF. The effect of the significant haplotype alleles varied from −0.44 to 0.80 and −1.03 to 1.52 kg in CAPN1 and ASAP1, respectively. Exonic regions near and within these loci were chosen for sequencing to search for new polymorphisms. Four SNPs were identified in ASAP1 and seventeen in CAPN1. All SNPs detected in the sequenced regions in ASAP1 showed no association with WBSF even though two of them (rs714391435 and rs109256712) were in strong linkage disequilibrium (LD) with most SNPs that composed the significant haplotyped locus. Four SNPs located in CAPN1 were found for the first time in this study. One of them (rs1121961662) showed significant association with WBSF and is also in strong LD with all SNPs within the significant haplotyped locus in CAPN1 gene. The SNP rs1121961662 could be used as a molecular marker for this QTL and may be included in low-density arrays to improve the selection of meat tenderness in Bos indicus animals.