Gene Expression Profiling of Grass Carp (Ctenopharyngodon idellus) and Crisp Grass Carp

Abstract

Grass carp (Ctenopharyngodon idellus) is one of the most important freshwater fish that is native to China, and crisp grass carp is a kind of high value-added fishes which have higher muscle firmness. To investigate biological functions and possible signal transduction pathways that address muscle firmness increase of crisp grass carp, microarray analysis of 14,900 transcripts was performed. Compared with grass carp, 127 genes were upregulated and 114 genes were downregulated in crisp grass carp. Gene ontology (GO) analysis revealed 30 GOs of differentially expressed genes in crisp grass carp. And strong correlation with muscle firmness increase of crisp grass carp was found for these genes from differentiation of muscle fibers and deposition of ECM, and also glycolysis/gluconeogenesis pathway and calcium metabolism may contribute to muscle firmness increase. In addition, a number of genes with unknown functions may be related to muscle firmness, and these genes are still further explored. Overall, these results had been demonstrated to play important roles in clarifying the molecular mechanism of muscle firmness increase in crisp grass carp.

Partial substitution of soybean meal with faba bean meal in grass carp (Ctenopharyngodon idella) diets, and the effects on muscle fatty acid composition, flesh quality, and expression of myogenic regulatory factors

“…These findings suggested that dietary nutritional factors may affect fish growth by modulating the MRFs expression. Yu et al (2014) indicated that the relative genes expression of muscle differentiation were strongly correlated with muscle firmness of grass carp by using microarray sequencing technique to research the difference between grass carp and crisp grass carp, which was in agreement with the present study. Besides, L. M. Valente et al (2016) reported that dietary incorporation of plant protein would modulate the expression of muscle growth-related genes and would thereby alter muscle cellularity and textural profile of Senegalese sole.…”

Proteomic signature of muscle fibre hyperplasia in response to faba bean intake in grass carp

“…The proteomic data obtained in the current study indicated that two enzymes involved in the intermediate process of glycolysis were significantly upregulated in the muscle of crisp grass carp, with the protein expression of the aldehyde dehydrogenase 9 family, for example, increasing 87.90-fold. In the expression profile of crisp grass carp, we also found that the gene expression of aldehyde dehydrogenase increased 5.51-fold8. Under anaerobic conditions, aldehyde dehydrogenase can oxidise glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate, and reduce NAD + to NADH.…”

“…This study showed significantly decreased protein expression of pyruvate dehydrogenase, which is associated with the decomposition of pyruvate. In our previous study, the gene expression of pyruvate dehydrogenase also decreased 0.15-fold in the crisp grass carp8. This indicated that during muscle hardening of grass carp, pyruvate less efficiently entered the mitochondria, to undergo oxidative decomposition via the citric acid cycle pathway.…”

“…In this study, a total of 99 differentially expressed proteins (ratio <0.5 or >2) were detected in the muscle of crisp grass carp and ordinary grass carp, and the greatest increase in expression was 88-fold. In our previous transcriptome results, the largest difference in mRNA expression was 11-fold, indicating that the proteome had more significant differential expression than that of the transcriptome8. In this study, a protein–protein interaction network of 56 differentially expressed proteins was generated.…”

“…Despite the complex nutrients in faba bean, it has the same effect on muscle regulation in many different animals, indicating that the signalling pathway for the nutrition regulation of faba bean exhibits a relatively convergent molecular mechanism. In view of this, we previously compared the gene expression profiles of crisp grass carp and ordinary grass carp, and found 241 differentially expressed genes in the muscle of crisp grass carp, including six collagen genes, four myocyte differentiation genes and fourteen cytoskeletal organisation genes8. However, only 20–40% of the protein concentrations are determined by the corresponding mRNA concentrations9.…”