Differential gene expression and SNP association between fast- and slow-growing turbot (Scophthalmus maximus)

Abstract

Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates.

Co-expression Analysis of Sirtuins and Related Metabolic Biomarkers in Juveniles of Gilthead Sea Bream (Sparus aurata) With Differences in Growth Performance

“…Notably, the muscle of fast-growing fish exhibited high expression levels of pgc1 α, a well-recognized marker of increased mitochondrial activity and thereby aerobic oxidative capacity (Austin and St-Pierre, 2012 ; Wenz, 2013 ). This finding is in contrast to the observations of Robledo et al ( 2017 ) in turbot indicating the up-regulation of the glycolytic pathway in the muscle of selected fast-growing fish, which could reflect changes in energy demand as well as in swimming and feeding behavior. While the increased pgc1 α expression in fast-growing fish did not occur along with changes in OXPHOS gene expression, it is known that PGC1α-mediated enhance of oxidative capacity may result from an increase in the number of mitochondria (Srivastava et al, 2009 ) or from the effects of PGC1α on the activity of the enzymes (Austin and St-Pierre, 2012 ) without altering OXPHOS gene expression.…”

Integrating Genomic and Morphological Approaches in Fish Pathology Research: The Case of Turbot (Scophthalmus maximus) Enteromyxosis

“…This strategy can be combined with the search of single nucleotide polymorphisms (SNPs) associated with disease resistance, either on identified candidate genes or detected through genome-wide association analysis (GWAS) using high throughput genotyping approaches (genotyping-by-sequencing or SNP arrays). The investigation of SNP variants has been recently applied in turbot in combination with RNA-Seq to another main target trait for aquaculture production, growth rate (Robledo et al, 2017c).…”

Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

“…In the present study, RNA-seq was used to analyze the phenotypes of growth performance because ESTs may directly influence organism performance and also built the cornerstone of the database for other economical traits [ 66 , 67 , 68 , 69 , 70 , 71 ]. For example, considerable research using RNA-seq has been performed on the economically important aquaculture species of Atlantic salmon, rainbow trout, turbot, gilthead seabream, and Pacific white shrimp, which helps comprehension of the variation of transcripts between cells, tissues, ontogenetic, food nutrition, and environmental conditions and facilitates analysis if those traits or performance indicators are correlated with the polymorphic markers [ 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 ]. The common economic aquaculture grouper species—orange-spotted grouper, giant grouper, and hybrid grouper ( E. fuscoguttatus × E. lanceolatus )—have been evaluated for growth trait performance, virus resistance, dietary supplementation, and temperature challenge, and the results have revealed some underlying molecular mechanisms [ 80 , 81 , 82 , 83 ].…”