Transcriptome analysis of muscular tissue in Nelore cattle divergent for meat tenderness

Meat tenderness is the consumer's most required sensory attribute. With the high rate of Zebu genes in the Brazilian cattle population, improving meat tenderness becomes more important, because increasing the proportion of Zebu genes in the population decreases meat tenderness. New technologies, such as RNA-Seq, have been used for understanding the genetic processes that regulate quantitative traits. Thus, the objective of this study was to identify differentially expressed (DE) genes related to meat tenderness in Nellore cattle in order to better understand the genetic factors that are related to meat quality. For this, we sequenced 40 longissimus dorsi muscle samples from Nellore cattle divergently ranked on meat tenderness (20 with hard and 20 with tender meat). These samples were chosen based on shear force analysis of 132 Nellore cattle longissimus dorsi muscle samples. All animals belonged to the same management group and were slaughtered on the same day. RNA-Seq data were analyzed by the Tuxedo protocol in the CyVerse Discovery Environment. We found 40 DE genes related to meat tenderness, 17 with described functions. Among them, there were 14 up and 3 down-regulated genes with respect to the tender meat group, including genes related to: ubiquitin metabolism; molecular transport, e.g. for calcium and oxygen and acid-base balance; collagen production; actin; myosin; and fat were identified in the analysis. The PCP4L1 (Purkinje cell protein 4 like 1) and Bola-DQB (major histocompatibility complex, class II, DQ beta) genes were validated by qRT-PCR and showed similar relative expression values compared to those obtained by RNA-Seq (i.e., PCP4L1 gene was more expressed in tender meat samples and Bola-BQD was more expressed in hard meat samples in both techniques). Therefore, this study reveals DE genes that could be used as genetic markers in Nellore for early selection for meat tenderness after more studies.