Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

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.

Transcriptomic profiles of the ruminal wall in Italian Mediterranean dairy buffaloes fed green forage

“…Buffaloes that received green feed showed changes in the expression of many genes encoding factors associated with muscle structure and function. Of particular interest is the increased expression of KCNK10, CACNG4, and ATP2B4 genes, encoding factors that modulate the homeostasis of Ca 2+ [77][78][79][80], a second messenger important for muscle contraction and differentiation, which allows to suppose that green feed might stimulate the ruminal muscular function. Furthermore, green feed modulated, with a different direction, genes encoding structural components of the cytoskeleton, such as MYH11, DES, and LOC102397197 (or TUBA1D), and factors promoting its assembling, such as TPPP, TPPP3, thus suggesting an impact of this diet on muscular structure.…”

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

“…One of the interesting genes was the ANK1 which was found to have a link between polymorphism in its promoter region and the meat quality of porcine 37 and cattle 38 , 39 . Additionally, the HSPA13 gene influences meat quality by affecting the water holding capacity of meat 40 . The results of some studies 41 , 42 have indicated an association between the ANKS1B gene and growth plus body size in sheep.…”