Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork

Abstract

BackgroundDrip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss and other meat quality traits of 28 purebred Duroc pigs were measured, muscles of these individuals were RNA sequenced, and eight individuals with extremely low and high drip loss were selected for analyzing their transcriptome differences and identifying potential candidate genes affecting drip loss.ResultsAs a result, 363 differentially expressed (DE) genes were detected in the comparative gene expression analysis, of which 239 were up-regulated and 124 were down-regulated in the low drip loss group. The DE genes were further filtered by correlation analysis between their expression and drip loss values in the 28 Duroc pigs measured and comparison of them with QTLs affecting drip loss. Consequently, of the 363 DE genes, 100 were identified as critical DE genes for drip loss. Functional analysis of these critical DE genes revealed some GO terms (extracellular matrix, cell adhesion mediated by integrin, heterotypic cell-cell adhesion), pathway (ECM-receptor interaction), and new potential candidate genes (TNC, ITGA5, ITGA11, THBS3 and CD44) which played an important role in regulating the variation of drip loss, and deserved to carry further studies to unravel their specific mechanism on drip loss.ConclusionsOur study revealed some GO terms, pathways and potential candidate genes affecting drip loss. It provides crucial information to understand the molecular mechanism of drip loss, and would be of help for improving meat quality of pigs.

Weighted gene co‐expression network analysis reveals potential candidate genes affecting drip loss in pork

“…Each trait was measured in triplicate. Drip loss was determined using the same method as described in our previous study (Zhao et al 2019). Specifically, approximately 10 g of a muscle sample from the third-and fourth-last thoracic vertebrae was weighed and placed into a plastic measuring device shaped like a funnel.…”

“…mRNA, including coding RNA and a small group of lncRNA with a ploy A tail, was isolated from the total RNA. The detailed process of library construction and sequencing is provided in our previous study (Zhao et al 2019).…”

“…The longissimus dorsi muscle transcriptome of the 28 pigs was sequenced using a paired-end mRNA-seq approach. Sequencing data are available in Zhao et al (2019). In total, 26 918 genes were detected through alignment with the S. scrofa reference genome (S. scrofa 11.1, http://asia.ense mbl.org/Sus_scrofa/Info/Index).…”

“…RNA-seq, which has been used to assess gene expression in tissues, provides a new perspective and method to screen candidate genes at the transcriptome level. RNA-seq analysis of high-and low-drip loss individuals revealed new candidate genes affecting drip loss (Ponsuksili et al 2008;Li et al 2016;Zhao et al 2019). In our previous study, we used eight Duroc pigs with extremely high and low drip loss selected from 28 purebred Duroc pigs, to identify differentially expressed genes (DEGs).…”

“…In our previous study, we used eight Duroc pigs with extremely high and low drip loss selected from 28 purebred Duroc pigs, to identify differentially expressed genes (DEGs). Based on the DEG analysis, correlation analysis between gene expression and drip loss values, and comparison between DEGs and QTL related to drip loss, 100 of 363 DEGs were found to be critical ones affecting drip loss (Zhao et al 2019).…”