Environment-Dependent Heterosis and Transgressive Gene Expression in Reciprocal Hybrids between the Channel Catfish Ictalurus punctatus and the Blue Catfish Ictalurus furcatus

Abstract

The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F₁s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F₁s than the parental species). A total of 1140 transgressive genes were identified in F₁ hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F₁s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent heterosis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.

Keywords: RNA-Seq; aquaculture; environment; heterobeltiosis; heterosis; transcriptomics; transgressive genes.

Figure 1

Morphometric measurements of channel catfish (C), Ictalurus punctatus, blue catfish (B), I. furcatus, and their reciprocal F1 hybrids raised in the tank environment. (A) Schematic illustration of four genetic cross types: channel catfish (C) parental cross (PC), blue catfish (B) parental cross (PB), blue catfish female × channel catfish male hybrids (F₁BC), and channel catfish female × blue catfish male hybrids (F₁CB) (B); Morphometric traits measured in this study: body weight (C); total length (D); body length (E); head length (F); head width (G); head depth (H) caudal depth (I); and body depth (J). Statistical significance was assessed by nonparametric Mann-Whitney U test (*, p < 0.05; **, p < 0.01;). The different colors representing the four genetic types were used consistently in this and subsequent figures.

Figure 2

Plasma biochemical and immunological measurements in channel catfish (C), Ictalurus punctatus, blue catfish (B), I. furcatus, and their reciprocal F₁ hybrids raised in the tank environment. Plasma lysozyme activity (A); alternative complement pathway hemolytic activity (B); plasma glucose level (C); and plasma lactate level (D) were measured in channel catfish parental cross (PC), blue catfish parental cross (PB), blue catfish female × channel catfish male hybrids (F₁BC), and channel catfish female × blue catfish male hybrids (F₁CB). Statistical significance was assessed by non-parametric Mann–Whitney U test (*, p < 0.05; **, p < 0.01).The different colors representing the four genetic types were used consistently in this and subsequent figures.

Figure 3

Transcriptome-wide gene expression correlation and differentially expressed genes in the liver among channel catfish (C), Ictalurus punctatus, blue catfish (B), I. furcatus, and their reciprocal F₁ hybrids raised in the tank environment (diagonal panels). Bottom-left panels: volcano plots of six pairwise comparisons among the four genetic types from channel catfish parental cross (PC), blue catfish parental cross (PB), blue catfish female × channel catfish male hybrids (F₁BC), and channel catfish female × blue catfish male hybrids (F₁CB). Differentially expressed genes (DEGs) are highlighted (FDR < 0.05). The x-axis stands for log₂ fold changes, and the y-axis represents −log₁₀(p-value). The vertical lines indicate |log₂FoldChange| = 1.5. Upper-right panels: scatterplots of the log₂ (RKPM) values for six pairwise comparisons among the four genetic types. Spearman’s rank correlation coefficient ρ and the corresponding p-values are labeled.

Figure 4

Pathway enrichment analysis of liver Differentially Expressed Genes (DEGs) between channel catfish Ictalurus punctatus parental cross (PC) and three other genetic types (PB: blue catfish I. furcatus parental cross, blue catfish female × channel catfish male hybrids (F₁BC), and channel catfish female × blue catfish male hybrids (F₁CB). (A) Hierarchical clustering of significant gene ontology terms shared in at least two of the three comparisons (PC vs. PB, PC vs. F₁BC, and PC vs. F₁CB); (B) A circular plot of shared DEGs in the three comparisons; (C,D) Enriched functional categories for upregulated genes in PC compared to PB (C) and downregulated genes in PC compared to PB (D); Enrichment scores measured by −log₁₀(p-value) were shown on the x-axis; (E) A plot of enriched term network for upregulated genes in PC. GO terms were represented by the same color dots as in (C), and the interconnectivity was represented by the edges.

Figure 5

Identification and functional enrichment analysis of liver transgressive genes in the reciprocal hybrids of channel catfish, Ictalurus punctatus, and blue catfish, I. furcatus. (A) Definition of different classes of transgressive genes based on the gene expression levels in channel catfish parental cross (PC), blue catfish parental cross (PB), blue catfish female × channel catfish male hybrids (F₁BC), and channel catfish female × blue catfish male hybrids (F₁CB). The y-axis represents relative gene expression levels. The gene counts were labeled for each class; (B) Piechart of transgressive gene distributions in hybrid catfish; (C) Venn diagram of transgressive genes in F₁BC and F₁CB hybrids; (D) Enriched functional categories for concordant and discordant transgressive genes; (E) Enriched functional categories for upregulated transgressive genes in F₁BC and F₁CB hybrids. Enrichment scores measured by −log₁₀(p-value) were shown on the x-axis.

Figure 6

Quantitative reverse transcription PCR validation of differentially expressed genes and transgressive genes. PC: channel catfish Ictalurus punctatus parental cross; PB: blue catfish I. furcatus parental cross; F₁BC: blue catfish female × channel catfish male hybrids; F₁CB: channel catfish female × blue catfish male hybrids. Barplots of qRT-PCR relative quantification and RNA-seq RPKM values (Reads Per Kilobase of transcript per Million mapped reads) for non-transgressive genes cyp2k1 (A) and fgf1 (B), concordant transgressive genes hmox (C) and irf7 (D), and discordant transgressive genes tm4sf4 (E) and creg1 (F). Mann–Whitney U test was used to assess the statistical significance (*, p < 0.05; **, p < 0.01; ***, p < 0.001).