Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid (Epinephelus fuscogutatus♀ × E. lanceolatus♂)

Abstract

Background: Groupers (Epinephelus spp.) have been widely cultivated in China and South-East Asian countries. As a novel hybrid offspring crossed between E. fuscogutatus♀ and E. lanceolatus♂, Hulong grouper exhibits significant growth superiority over its female parent, which made it a promising farmed species in grouper aquaculture industry in China. Hulong grouper present a good combination of beneficial traits from both parent species, but the molecular mechanisms of its heterosis still remain poorly understood.

Results: Based on RNA sequencing and gene expression profiling, we conducted comparative transcriptome analyses between Hulong grouper and its parents E. fuscoguttatus & E. lanceolatus. Six hundred sixty-two and 5239 differentially expressed genes (DEGs) were identified in the brains and livers, respectively. GO enrichment analysis of these DEGs revealed that metabolic process and catalytic activity were the most enriched GO terms. Further analysis showed the expressions of GnRH1 and GnRH3 in the brain, and GH/IGF axis related genes such as IGF-1, IGF-2b, IGFBP-1, IGFBP-2, IGFBP-4 and IGFBP-5a in the liver of the hybrid F1 were significantly up-regulated, which is in accordance with the growth superiority of hybrid grouper. Meanwhile, expressions of genes related to the protein and glycogen synthesis pathway, such as PI3KC, PI3KR, Raptor, EIF4E3, and PP1 were up-regulated, while PYG expression was down-regulated. These changes might contribute to increased protein and glycogen synthesis in the hybrid grouper.

Conclusions: We identified a number of differentially expressed genes such as GnRH1 and GnRH3, and genes involved in GH/IGF axis and its downstream signaling pathways for protein and glycogen synthesis in Hulong Grouper. These findings provided molecular basis underlying growth superiority of hybrid grouper, and comprehensive insights into better understanding the molecular mechanisms and regulative pathways regulating heterosis in fish.

Fig. 1

DEGs and the overlaps of DEGs among parental E. fuscoguttatus (Efu), E. lanceolatus (Ela) and their hybrid offsprings (Hyb). Different numbers of DEGs in brains (a) and livers (b) were identified. The overlaps of DGEs in the brain (c) and the liver (d) were also determined

Fig. 2

GO enrichment of DEGs in brains and livers of three fish species. a and b. GO biological process categories enrichment of DEGs in livers of three fish species. c and d. GO enrichment of DEGs in brains of three fish species. Compared with that in livers (c and d), the number of enriched GO terms in brain is less (a and b)

Fig. 3

Hierarchical cluster analysis of DEGs involved in the GH/IGF and downstream pathways. The color key represents RPKM normalized log₂ transformed counts in brains (a) and livers (b) of three fish species. Efu, Ela, and Hyb denote E. fuscoguttatus, E. lanceolatus and their hybrid F1, respectively

Fig. 4

Validation of differentially expressed genes by Real-time PCR. β-actin was used as an internal control and each value represents average of three separate biological replicates. Real-time PCR validates the DEGs a between the Hyb and maternal Efu and b between the Hyb and paternal Ela. GH was detected in the brains, while other genes were examined in the livers

Fig. 5

The predicted map of DEGs involved in the GH/IGF and downstream pathways regulated growth superiority. Blue arrows denote the genes with differential expression between the hybrid F1 and paternal E. lanceolatus. Red arrows denote the genes with differential expression between the hybrid F1 and maternal E. fuscoguttatus. Up or down arrows stand for up- or down-regulated in the hybrid compared with its parent(s)