Global gene expression patterns of grass carp following compensatory growth

Abstract

BackgroundCompensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome. Most animals, especially fish, are capable of compensatory growth, but the mechanisms remain unclear. Further investigation of the mechanism of compensatory growth in fish is needed to improve feeding efficiency, reduce cost, and explore growth-related genes.ResultsIn the study, grass carp, an important farmed fish in China, were subjected to a compensatory growth experiment followed by transcriptome analysis by RNA-sequencing. Samples of fish from starved and re-feeding conditions were compared with the control. Under starved conditions, 4061 and 1988 differentially expressed genes (DEGs) were detected in muscle and liver tissue when compared the experimental group with control group, respectively. After re-feeding, 349 and 247 DEGs were identified in muscle and liver when the two groups were compared. Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver. Most of these DEGs were involved in metabolic processes, or encoded enzymes or proteins with catalytic activity or binding functions, or involved in metabolic and biosynthetic pathways. A number of the more significant DEGs were subjected to further analysis. Under fasting conditions, many up-regulated genes were associated with protein ubiquitination or degradation, whereas many down-regulated genes were involved in the metabolism of glucose and fatty acids. Under re-feeding conditions, genes participating in muscle synthesis and fatty acid metabolism were up-regulated significantly, and genes related to protein ubiquitination or degradation were down-regulated. Moreover, Several DEGs were random selected for confirmation by real-time quantitative PCR.ConclusionsGlobal gene expression patterns of grass carp during compensatory growth were determined. To our knowledge, this is a first reported for a teleost fish. The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1427-2) contains supplementary material, which is available to authorized users.

Diet Affects Muscle Quality and Growth Traits of Grass Carp (Ctenopharyngodon idellus): A Comparison Between Grass and Artificial Feed

“…Ctenopharyngodon idellus is the principal species in freshwater aquaculture in China (He et al, 2015 ). Intensive farming based on utilization of artificial formulated feed has contributed to the continuous growth in the production of grass carp (Borlongan and Satoh, 2002 ; FAO Yearbook, 2014 ).…”

Dynamic mRNA and miRNA expression analysis in response to intermuscular bone development of blunt snout bream (Megalobrama amblycephala)

“…High-throughput sequencing technologies are being widely used to investigate the complete repertoire of expressed RNA transcripts in specific tissues or cells at specific stages of development, and this knowledge is helping improve our understanding of the molecule mechanism affecting expression 10 , regulatory 11 and development 12 . In fish, independent transcriptome profiling (RNA-seq) of miRNAs or mRNAs has been used to identify gene and miRNA expression related to various physiological functions 13 14 15 16 . As miRNAs has been reported to regulate gene expression by promoting mRNA degradation and repressing translation, the combined analyses of mRNA with miRNA expression data has been conducted in plants and mammals to infer regulatory mechanisms associated with various physiological processes 17 18 19 .…”

Identifying the Related Genes of Muscle Growth and Exploring the Functions by Compensatory Growth in Mandarin Fish (Siniperca chuatsi)

“…In the meantime, because muscle breakdown and muscle protein synthesis were inhibited, muscle contraction and motor function were restrained, which was manifested as a significant decrease in troponin expression (Figure 7, Troponin). After re-feeding, significant up-regulation of Mhc and Mlc was observed (Figure 7, Mhc and Mlc), showing that muscle protein was no longer used as the major energy source, and synthesis of muscle and rapid compensatory growth occurred, which resulted in increased weight (He et al, 2015). As the normal synthesis and growth of muscle, muscle contraction was no longer inhibited and expression levels returned to normal (Figure 7, Troponin).…”