Identification of SNPs and changes in protein coding of genes associated with beef quality in Nellore cattle

Abstract

We investigated single nucleotide polymorphisms of four genes (calpain (CAPN-9 and CAPN-14), calpastatin – CAST, diacylglycerol acyltransferase – DGAT, and leptin - LEP) that are related to beef quality, and we examined changes in the synthesis of proteins that they encode in Nellore cattle. Samples from 95 adult males of commercial origin were analyzed. Genomic DNA was extracted from the longissimus dorsi (sirloin) muscle tissue, identified with PCR-single-stranded conformation polymorphism analysis. For each different pattern identified, the products were sent for sequencing and analyzed using sequence scanner software. The data were analyzed by determining the absolute and relative frequencies of the polymorphisms identified in each gene. For the CAPN-9 gene, sequencing showed five polymorphisms (G/A, T/A, T/C, T/C, and A/G), of which two involved amino acid substitutions (c.5861G>A and c.5498A>G). Sequencing of the CAPN-14 gene revealed four polymorphisms (A/C, G/A, T/C, and C/G), with two involving amino acid substitutions (c.11054 T>C and c.11161C>G). Sequencing of the CAST-5 gene revealed five polymorphisms (C/T, T/C, C/A, C/A, and G/T), four of which involved amino acid substitutions (c.29919C>T, c.29963A>C, c.29978C>A, and c.30019G>T). Sequencing of the DGAT gene revealed six polymorphisms (T/A, G/A, A/T, G/C, A/G, and G/A), four of which involved amino acid substitutions (c.11730A>T, c.11809G>C, c.11858A>G, and c.11927G>A). Sequencing of the LEP gene revealed three polymorphisms (C/T, C/T and T/C), with one involving an amino acid substitution (c.14962T>G). These genes had a large number of polymorphisms resulting in amino acid differences in Nellore Cattle. These polymorphisms involving amino acid changes may promote functional changes in beef characteristics of Nellore cattle given that these genes are associated with beef quality parameters.