Molecular Mechanism Of Growth Advantage Of Hybrid Yunlong Grouper Based On Transcriptome Analyses

The grouper is an important economic marine fish in China,with a large market demand.However,traditional fishing methods are no longer able to meet the market demand,so the grouper aquaculture industry is gradually emerging.After years of artificial breeding and cultivation,the economic traits of many groupers have severely declined,and their germplasm has severely deteriorated.It is urgent to carry out the cultivation and application of new varieties of groupers.The Yunlong grouper,which was obtained from the cross between Epinephelus moara and Epinephelus lanceolatus,is one of the important economic fishes.It has the advantages of fast growth and strong resistance to disease,so it is widely concerned.In this study,we carried out a comparative analysis of the whole transcriptome of the liver of Yunlong grouper and its maternal parent,Epinephelus moara,and identified differentially expressed mRNAs,lncRNAs and their miRNAs between the two fish to investigate the molecular mechanisms underlying the growth of Yunlong grouper.A comparative transcriptome analysis between Yunlong grouper and Epinephelus moara identified 867 differentially expressed genes,of which 640 genes were up-regulated and 227 genes were down-regulated in Yunlong grouper.GO and KEGG function enrichment analysis of differentially expressed genes showed that the functions of these genes were mainly enriched in redox process(GO:0055114),translocation,DNA mediation(GO:0006313),translocation(GO:0032196),DNA integration(GO:0015074),cell growth regulation(GO:0001558),reaction to organic substances(GO:0010033)and cell growth(GO:0016049).662 differentially expressed lncRNAs were found between Yunlong grouper and Epinephelus moara,of which 610 lncRNAs were up-regulated and 52 were down-regulated in Yunlong grouper;GO and KEGG functional enrichment analysis showed that the functions of these differential lncRNAs are mainly enriched in GO terms such as nuclear(GO:0005634),extracellular(GO:0044424),membrane bound organelle(GO:0043227),membrane bound organelle(GO:0043231),intracellular(GO:0005622),organelle(GO:0043226),and intracellular organelle(GO:0043229),and KEGG functions are significantly enriched in the adhesion and connection pathway(q-value<0.05).A total of 247 known miRNAs and 265 novel miRNA were obtained.Eleven differentially expressed miRNAs were found between Yunlong grouper and Epinephelus moara,of which 9 miRNAs were up-regulated and 2 were down-regulated in Yunlong grouper.GO and KEGG function enrichment analysis of differentially expressed miRNA showed that the candidate target genes were not significantly enriched in GO function.KEGG is mainly concentrated in Hedgehog signaling pathway,basal excision and repair,oxidative phosphorylation,steroid hormone biosynthesis,myocardial contraction,phagocyte,metabolic pathway,pyrimidine metabolism and other pathways(p-value<0.05).The number of genes in metabolic pathway is large(gene number=18);The enrichment degree is the highest in taurine and low taurine metabolic pathways(rich factor=0.111).From the above analysis,it can be seen that in the GO functional enrichment analysis of mRNA,lncRNA and miRNA,there are enrichment of biological processes such as redox process,translocation and DNA mediation.In addition,steroid hormone synthesis pathway,adhesion pathway,basal resection and repair,oxidative phosphorylation,myocardial contraction and some other pathways are significantly enriched.These results provide theoretical basis for revealing the molecular mechanism of heterosis of fish growth traits,and also provide important basic data for the development of aquaculture.In addition,further in-depth study on the specific role of these biological processes and pathways in the growth of Yunlong grouper will help us better understand the molecular mechanism and physiological and biochemical processes of fish growth.For example,redox process plays an important role in cell energy metabolism and cell signal transmission,and may be involved in the regulation of energy metabolism in the growth of Yunlong grouper.Steroid hormone synthesis pathway also plays an important role in the reproduction and growth of grouper.In addition,revealing the molecular mechanism of the formation of heterosis in fish growth traits can provide reference and enlightenment for studying the excellent traits of other economic fish.To sum up,it is of great significance to study the molecular mechanism of the growth advantage of Yunlong grouper for us to better understand the growth and development process of fish and promote the development of fish aquaculture.