Transcriptome Profiling Revealed Basis for Growth Heterosis in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂)

Jinglin Zhu,Dayu Li,Jie Yu,Binglin Chen,Liangyi Xue,Zhiying Zou,Wei Xiao,Hong Yang

doi:10.3390/fishes7010043

Abstract

Hybrid tilapia were produced from hybridization of Nile tilapia (Oreochromis niloticus) and blue tilapia (O. aureus). Comparative transcriptome analysis was carried out on the liver of hybrid tilapia and their parents by RNA sequencing. A total of 2319 differentially expressed genes (DEGs) were identified. Trend co-expression analysis showed that non-additive gene expression accounted for 67.1% of all DEGs. Gene Ontology and KEGG enrichment analyses classified the respective DEGs. Gene functional enrichment analysis indicated that most up-regulated genes, such as FASN, ACSL1, ACSL3, ACSL6, ACACA, ELOVL6, G6PD, ENO1, GATM, and ME3, were involved in metabolism, including fatty acid biosynthesis, unsaturated fatty acid biosynthesis, glycolysis, pentose phosphate pathway, amino acid metabolism, pyruvate metabolism, and the tricarboxylic acid cycle. The expression levels of a gene related to ribosomal biosynthesis in eukaryotes, GSH-Px, and those associated with heat shock proteins (HSPs), such as HSPA5 and HSP70, were significantly down-regulated compared with the parent tilapia lineages. The results revealed that the metabolic pathway in hybrid tilapia was up-regulated, with significantly improved fatty acid metabolism and carbon metabolism, whereas ribosome biosynthesis in eukaryotes and basal defense response were significantly down-regulated. These findings provide new insights into our understanding of growth heterosis in hybrid tilapia.

Highlights

Heterosis, or hybrid vigor, refers to the superior performance of F1 progeny compared with their homozygous parents [1]
Identification of Differentially Expressed Genes A total of 2319 differentially expressed genes (DEGs) were identified, of which 956, 1119, and 1411 DEGs were found between O. niloticus and hybrid tilapia (N vs. NA), O. aureus and hybrid tilapia (A vs. NA), O. niloticus and O. aureus (N vs. A), respectively
DEGs Related to Fatty Acid Metabolism We found that five genes related to fatty acid biosynthesis, including fatty acid synthase (FASN), long-chain fatty acid-CoA ligase (ACSL1, ACSL3, ACSL6), and acetyl coenzyme A carboxylase (ACACA) of NA had higher FPKMs value than both N and A, and so were long-chain fatty acid elongase (ELOVL5 and ELOVL6) and fatty acid desaturase (FADS2), involved in unsaturated fatty acid biosynthesis

Summary

Introduction

Hybrid vigor, refers to the superior performance of F1 progeny compared with their homozygous parents [1]. The differentially expressed genes (DEGs) and pathways related to heterosis have been identified through the transcriptome profiles analysis in aquatic species, such as hybrid grouper (Epinephelus fuscogutatus ♀× E. lanceolatus ♂) [10,11], hybrid pufferfish (Takifugu obscurus ♀× T. rubripes ♂) [12], hybrid tambacu (Colossoma macropomum ♀× Piaractus mesopotamicus ♂) [13], hybrid tilapia (Oreochromis niloticus ♀× O. aureus ♂) [14,15], hybrid carp (Hypophthalmichthys nobilis ♀× H. molitrix ♂) [16], hybrid seabream (Acanthopagrus schlegelii ♂× Pagrus major ♀) [17], hybrid cypriniformes [Megalobrama amblycephala ♀× (M. amblycephala ♀× Culter alburnus ♂) ♂] [18], hybrid Chinese soft-shelled turtle (Pelodiscus sinensis Japanese strain ♀× P.sinensis Qingxi black turtle ♂) [19], sea cucumber (Chinese Apostichopus japonicus ♀× Russian A. japonicus ♂) [20], and hybrid abalone (Haliotis gigantea ♀× H. discus hannai ♂) [21] These works could help us to further understand the molecular mechanism of the heterosis in various aquatic species

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Conclusion