Abstract
Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.
Highlights
ObjectivesThe purpose of this study is to use the RNA-Seq technique, functional enrichment tools, protein–protein interaction (PPI) network, and Quantitative Trait Locus (QTLs) database (QTLdb) to identify the crucial differentially expressed genes (DEGs), significant Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways affecting the regulation of WHC, aiming to improve the WHC trait and enhance beef quality by using molecular breeding technologies
The transcriptome sequencing of LD muscle tissue was conducted by RNA-seq for paired-end strategy on an Illumina NovaSeq 6000 platform
A total of 177,433,007 clean reads were obtained for the eight samples, and the quality values of Q20 and Q30 were above 98.09% and 94.37%, respectively
Summary
The purpose of this study is to use the RNA-Seq technique, functional enrichment tools, protein–protein interaction (PPI) network, and QTL database (QTLdb) to identify the crucial differentially expressed genes (DEGs), significant Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways affecting the regulation of WHC, aiming to improve the WHC trait and enhance beef quality by using molecular breeding technologies
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