Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus)

Abstract

Feed efficiency is an economically crucial trait for cultured animals, however, progress has been scarcely made in the genetic analyses of feed conversion efficiency (FCE) in fish because of the difficulties in measurement of trait phenotypes. In the present investigation, we present the first application of RNA sequencing (RNA-Seq) combined with differentially expressed genes (DEGs) analysis for identification of functional determinants related to FCE at the gene level in an aquaculture fish, crucian carp (Carassius auratus). Brain tissues of six crucian carp with extreme FCE performances were subjected to transcriptome analysis. A total of 544,612 unigenes with a mean size of 644.38 bp were obtained from Low- and High-FCE groups, and 246 DEGs that may be involved in FCE traits were identified in these two groups. qPCR confirmed that genes previously identified as up- or down-regulated by RNA-Seq were effectively up- or down-regulated under the studied conditions. Thirteen key genes, whose functions are associated with metabolism (Dgkk, Mgst3 and Guk1b), signal transduction (Vdnccsa1b, Tgfα, Nr4a1 and Tacr2) and growth (Endog, Crebrtc2, Myh7, Myh1, Myh14 and Igfbp7) were identified according to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations. Our novel findings provide useful pathway information and candidate genes for future studies of genetic mechanisms underlying FCE in crucian carp.

Identifying Candidate Genes Involved in the Regulation of Early Growth Using Full-Length Transcriptome and RNA-Seq Analyses of Frontal and Parietal Bones and Vertebral Bones in Bighead Carp (Hypophthalmichthys nobilis)

“…Most of these metabolic pathways are also found in reports of growth-related transcriptomes in fish, such as the PPAR signaling pathway ( Lu et al, 2019 ), carbon-metabolizing pathways ( Lu et al, 2020 ), and oxidative phosphorylation pathway ( Fu J. et al, 2019 ). The eight other aforementioned pathways also play an important role in growth, by regulating the actin cytoskeleton, cell adhesion molecules, and FoxO signaling pathway ( Pang et al, 2018 ; Lu et al, 2019 ).…”

A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio)

“…Up to now, QTL studies in common carp have covered a wide range of traits including growth, cold tolerance, meat quality, muscle fiber-related, sex determination, etc ( Sun and Liang, 2004 ; Zhang et al, 2011 ; Laghari et al, 2013 ; Peng et al, 2016 ; Zheng et al, 2016 ). Compared to other economic traits, QTL analyses for FCE traits in aquaculture fish are rarely reported due to the difficulty to measure the phenotypes for these traits ( Lu et al, 2017 ; Pang et al, 2017 ; Pang et al, 2018 ). So, it is expected that more genetics studies on FCE traits will be considered so that molecular breeding strategies for these traits would be developed.…”

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens

“…RNA sequencing (RNA-seq) has been used widely and successfully to examine economically important traits in many cultured species such as carp [ 18 ], sheep [ 19 ], cows [ 20 ], and chickens [ 21 ]. Many studies have been conducted on poultry feed efficiency using RNA-seq.…”