Nonadditive and allele-specific expression of insulin-like growth factor 1 in Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (O. aureus, ♂) hybrids

Nonadditive and allele-specific expression of ghrelin in hybrid tilapia

Background

Interspecies hybridization is an important breeding method to generate fishes with heterosis in aquaculture. Using this method, hybrid Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (Oreochromis aureus, ♂) has been produced and widely farmed due to its growth and appetite superiorities. However, the genetic mechanism of these advanced traits is still not well understood. Ghrelin is a crucial gene that regulates growth and appetite in fishes. In the present study, we focused on the expression characteristics and its regulation of ghrelin in the hybrid.

Results

The tissue distribution analysis showed that ghrelin was predominantly expressed in the stomach in the hybrid. Ghrelin was more highly expressed in the stomach in the hybrid and Nile tilapia, compared to blue tilapia, showing a nonadditive pattern. Two single-nucleotide polymorphism (SNP) sites were identified including T/C and C/G from the second exon in the ghrelin gene from Nile tilapia and blue tilapia. By pyrosequencing based on the SNP sites, the allele-specific expression (ASE) of ghrelin in the hybrid was assayed. The result indicated that ghrelin in the hybrid showed higher maternal allelic transcript ratios. Fasting significantly increased ghrelin overall expression at 4, 8, 12, 24, and 48 h. In addition, higher maternal allelic transcript ratios were not changed in the fasting hybrids at 48 h. The cis and trans effects were determined by evaluating the overall expression and ASE values in the hybrid. The expression of ghrelin was mediated by compensating cis and trans effects in hybrid.

Conclusion

In summary, the present lines of evidence showed the nonadditive expression of ghrelin in the hybrid tilapia and its regulation by subgenomes, offering new insight into gene expression characteristics in hybrids.

Master-Key Regulators of Sex Determination in Fish and Other Vertebrates-A Review

In vertebrates, mainly single genes with an allele ratio of 1:1 trigger sex-determination (SD), leading to initial equal sex-ratios. Such genes are designated master-key regulators (MKRs) and are frequently associated with DNA structural variations, such as copy-number variation and null-alleles. Most MKR knowledge comes from fish, especially cichlids, which serve as a genetic model for SD. We list 14 MKRs, of which dmrt1 has been identified in taxonomically distant species such as birds and fish. The identification of MKRs with known involvement in SD, such as amh and fshr, indicates that a common network drives SD. We illustrate a network that affects estrogen/androgen equilibrium, suggesting that structural variation may exert over-expression of the gene and thus form an MKR. However, the reason why certain factors constitute MKRs, whereas others do not is unclear. The limited number of conserved MKRs suggests that their heterologous sequences could be used as targets in future searches for MKRs of additional species. Sex-specific mortality, sex reversal, the role of temperature in SD, and multigenic SD are examined, claiming that these phenomena are often consequences of artificial hybridization. We discuss the essentiality of taxonomic authentication of species to validate purebred origin before MKR searches.

Infection by the Parasite Myxobolus bejeranoi (Cnidaria: Myxozoa) Suppresses the Immune System of Hybrid Tilapia

Myxozoa (Cnidaria) is a large group of microscopic obligate endoparasites that can cause emerging diseases, affecting wild fish populations and fisheries. Recently, the myxozoan Myxobolus bejeranoi was found to infect the gills of hybrid tilapia (Nile tilapia (Oreochromis niloticus) × Jordan/blue tilapia (O. aureus)), causing high morbidity and mortality. Here, we used comparative transcriptomics to elucidate the molecular processes occurring in the fish host following infection by M. bejeranoi. Fish were exposed to pond water containing actinospores for 24 h and the effects of minor, intermediate, and severe infections on the sporulation site, the gills, and on the hematopoietic organs, head kidney and spleen, were compared. Enrichment analysis for GO and KEGG pathways indicated immune system activation in gills at severe infection, whereas in the head kidney a broad immune suppression included deactivation of cytokines and GATA3 transcription factor responsible for T helper cell differentiation. In the spleen, the cytotoxic effector proteins perforin and granzyme B were downregulated and insulin, which may function as an immunomodulatory hormone inducing systemic immune suppression, was upregulated. These findings suggest that M. bejeranoi is a highly efficient parasite that disables the defense mechanisms of its fish host hybrid tilapia.

Insulin-like growth factor 1 injection changes gene expression related to amino acid transporting, complement and coagulation cascades in the stomach of tilapia revealed by RNA-seq

Insulin-like growth factor 1 (IGF-1) is a key hormone that regulates fish growth. It acts on a variety of organs and regulates multiple signaling pathways. In order to explore the specific effects of IGF-1 on fish nutrient absorption, immune system, and other functions, the present study investigated the transcriptional changes of stomachs in tilapia by IGF injection. The tilapias were divided into two groups which were injected with saline (C group) and IGF-1 (2 μg/g body weight) (I group), respectively. After three times injections, the stomachs from the tested tilapias were collected 7 days post the first injection and the transcriptomes were sequenced by Illumina HiSeqTM 2000 platform. The results showed that a total of 155 DEGs were identified between C and I groups. By gene ontology (GO) enrichment analysis, two GO terms related to absorption function were enriched including organic acid transport, and amino acid transport which contained 6 functional DEGs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that Staphylococcus aureus infection, as well as complement and coagulation cascades pathways were enriched and contained 6 DEGs. Taken together, the present study indicated that IGF-1 injection altered gene expression related to amino acid transporting, complement and coagulation cascades which provides a promise immunopotentiation therapy by IGF-1 in digestive tract of tilapia.

Integration of mRNA and miRNA Profiling Reveals Heterosis in Oreochromis niloticus × O. aureus Hybrid Tilapia

Heterosis is a widespread biological phenomenon in fishes, in which hybrids have superior traits to parents. However, the underlying molecular basis for heterosis remains uncertain. Heterosis in growth and survival rates is apparent in hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂). Comparisons of growth and hematological biochemical characteristics and mRNA and miRNA transcriptional analyses were performed in hybrid and parents tilapia stocks to investigate the underlying molecular basis for heterosis. Growth characteristics and hematological glucose and cholesterol parameters were significantly improved in hybrids. Of 3097 differentially expressed genes (DEGs) and 120 differentially expressed miRNAs (DEMs) identified among three stocks (O. niloticus, O. aureus, and hybrids), 1598 DEGs and 62 DEMs were non-additively expressed in hybrids. Both expression level dominance and overdominance patterns occurred for DEGs and DEMs, indicating that dominance and overdominance models are widespread in the transcriptional and post-transcriptional regulation of genes involved in growth, metabolism, immunity, and antioxidant capacity in hybrid tilapia. Moreover, potential negative regulation networks between DEMs and predicted target DEGs revealed that most DEGs from miRNA-mRNA pairs are up-regulated. Dominance and overdominance models in levels of transcriptome and miRNAome facilitate the integration of advantageous parental alleles into hybrids, contributing to heterosis of growth and improved survival. The present study provides new insights into molecular heterosis in hybrid tilapia, advancing our understanding of the complex mechanisms involved in this phenomenon in aquatic animals.

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

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.

Localization of RNA Pol II CTD (S5) and Transcriptome Analysis of Testis in Diploid and Tetraploid Hybrids of Red Crucian Carp (♀) × Common Carp (♂)

Polyploidy occurs naturally in fish; however, the appearance of these species is an occasional and gradual process, which makes it difficult to trace the changes in phenotypes, genotypes, and regulation of gene expression. The allotetraploid hybrids (4nAT) of red crucian carp (RCC; ♀) × common carp (CC; ♂) generated from interspecies crossing are a good model to investigate the initial changes after allopolyploidization. In the present study, we focused on the changes in the active sites of the testicular transcriptome of the allotetraploid by localization of RNA Pol II CTD YSPTSPS (phospho S5) using immunofluorescence and RNA-seq data via bioinformatic analysis. The results showed that there was no significant difference in signal counts of the RNA Pol II CTD (S5) between the different types of fish at the same stages, including RCC, CC, 2nF₁, and 4nAT, which means that the number of transcriptionally active sites on germ cell chromosomes was not affected by the increase in chromosome number. Similarly, RNA-seq analysis indicated that in the levels of chromosomes and 10-kb regions in the genome, there were no significant changes in the highly active sites in RCC, 2nF₁, and 4nAT. These findings suggest that at the beginning of tetraploid origin, the active transcriptome site of 4nAT in the testis was conserved in the regions of the genome compared to that in RCC and 2nF₁. In conclusion, 4nAT shared a similar gene expression model in the regions of the genome with RCC and 2nF₁ with significantly different expression levels.