Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Growth Superiority in a Novel Gymnocypris Hybrid, Gymnocypris przewalskii ♀ × Gymnocypris eckloni ♂

Abstract

Artificial hybrid breeding can optimize parental traits to cultivate excellent hybrids with enhanced economic value. In this study, we investigated the growth performance and transcriptomes of Gymnocypris przewalskii (♀) and Gymnocypris eckloni (♂) and their F1 hybrid fishes. Hatched individuals of G. przewalskii (GP) and G. eckloni (GE) of the same size and their F1 hybrids (GH) were separately cultured for eight months in three cement tanks (n = 3). The growth indexes were measured, which showed that the growth rate of the groups was GE > GH > GP, while the survival rate was GH > GE > GP. The RNA-Seq data analysis of the muscles from the three Gymnocypris fish strains revealed that gene transcription has a significant impact on F1 hybrid fish and its parents. The differentially expressed genes (DEGs) in GH show less differences with GP, but more with GE. qRT-PCR was used to confirm the expression profiles of the chosen DEGs, and the results showed positive correlations with the RNA-seq data. KEGG enrichment results indicated that the DEGs were related to a variety of molecular functions, such as glycolysis/gluconeogenesis, arachidonic acid formation, citrate cycle, and the MAPK, PI3K-Akt, or mTOR signal pathways. Subsequent analysis indicated that there may be a significant correlation between the differential expression of IGF2 and a difference in the growth of GE and GP.

Keywords: Gymnocypris przewalskii; Gymnocypris eckloni; growth performance; hybrid F1; transcriptome.

Figure 1

(a) The principal component analysis (PCA) plot shows the distribution of samples in different groups samples. (b) Bar graph shows the DEGs in GH vs. GP and GH vs. GE.

Figure 2

Volcano plots and a Venn diagram depicting differentially expressed genes (DEGs) in the hybrid F1 and its parents: (a) DEGs in GH vs. GE, (b) DEGs in GH vs. GP, and (c) Venn diagram illustrating up- and down-regulated genes in GH vs. GP and GH vs. GE. The grey dot of (a,b) means the expressed genes has no significant difference.

Figure 3

Hierarchical cluster analysis of DEGs of three groups (GP, GH and GE). Different colors represent different relative abundance of genes, where red represents higher intensity and blue represents lower intensity.

Figure 4

Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs in muscles in the GH vs. the GE.

Figure 5

Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs in muscles in the GH vs. the GP.

Figure 6

The enrichment analysis of DEGs in KEGG pathways (top 20) in the GH vs. GE. The horizontal axis in the figure is the enrichment score; the larger the bubble, the higher the number of genes enriched in the pathway; as the bubble color changes from blue to yellow to red, the enrichment p-value decreases and the significance increases.

Figure 7

The enrichment analysis of DEGs in KEGG pathways (top 20) in the GH vs. GP. The horizontal axis in the figure is the enrichment score; the larger the bubble, the higher the number of genes enriched in the pathway; as the bubble color changes from blue to yellow to red, the enrichment p-value decreases and the significance increases.

Figure 8

The data comparison validating DEGs determined via RT-PCR and RNA-seq. (a) The data comparison validating DEGs determined via RT-PCR and RNA-seq in GH vs. GE. (b) The data comparison validating DEGs determined via RT-PCR and RNA-seq in GH vs. GP. PGK1, proto-oncogene c-Fos; Co6a6, collagen alpha-6 (VI) chain; EGFR, epidermal growth factor receptor; GHR, growth hormone-binding protein; FOS, phosphoglycerate kinase 1;MK13, mitogen-activated protein kinase 1; IGF2, insulin-like growth factor II; G3P, glyceraldehyde 3-phosphate dehydrogenase; GLNA, glutamine synthetase QtsA; VGFAA, vascular endothelial growth factor A-A; G6PC, glucose-6-phosphatase. The pink-colored bar represents the expression levels of DEGs determined via RNA-seq in GH vs. GP and GH vs. GE, and the green-colored bar indicates the expression levels of DEGs determined via quantitative real-time PCR in GH vs. GP and GH vs. GE. Blue line indicates FC = 1 (p = 0.05); above the line means up-regulation (p < 0.05), and below the line means down-regulation (p < 0.05).