Next Generation Sequencing (NGS) based variation analysis: A new practical biomarker for beef tenderness assessment

Abstract

Evaluation of some meat quality attributes using genetic analysis is steadily increasing. PCR based targeted variationanalysis is one of the most commonly preferred techniques for this purpose. Recently, Next Generation Sequencing(NGS) method has drawn considerable attention because of its’ high analysis capacity. The purpose of the currentstudy was to determine variations in CAST gene from Brangus and Simmental cattle by performing whole genesequencing using NGS, and to investigate the potential of NGS method in evaluating meat tenderness based on thehigh genomic data it provides. Whole gene sequence analysis was performed on Calpastatin (CAST) gene of samples acquired from 52 Brangus and 52 Simmental beef cattle breeds using NGS method, and the variations detectedwere evaluated in terms of their potential in measuring meat tenderness and quality. NGS outputs were analyzed inEnsemble “cow” database platform and 13 variations were detected. One of these variations (EXON 8 c.439C>G/p.L147LV ) was evaluated as undeclared before. In 20 Brangus cattle and in 9 Simmental cattle, no variations weredetected whereas 6 variations (V1, V2, V5, V8, V10 and V13) were found significantly different (p<0.05) based ontheir distribution in breeds. Bearing in mind the developments in bioinformatics and NGS method which provideshigh volume of genomic data, use of these methods in evaluating tenderness of meat was thought to be more practicalthan assessment based on sensory analyses and instrumental texture evaluations.