Genetic and genomic enhancement of the aquaculture production of hybrid catfish

Abstract

Channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus) are two important freshwater aquaculture species in the United States. Interspecific hybridization is an efficient strategy to enhance production traits. The hybridization between these two species has resulted in the production of a superior hybrid catfish (Ictalurus punctatus ♀ × Ictalurus furcatus ♂), which has proven to be highly advantageous in pond farming and accounted for over 50% of the total catfish production in the United States. However, this heterosis phenomenon in hybrid catfish is conditional, and can be affected by cultured the environment. The parental species, channel catfish, have a dominant growth advantage in the tank rearing environment compared to blue catfish and hybrid catfish. The molecular mechanism of the environment-dependent heterosis is of interest and still poorly understood. To confirm the robustness of environment-dependent heterosis in catfish and pave the way for investigation of genetic basis, a catfish farming experiment was designed in two rearing environments and performed for a period exceeding two years. Here, we characterized fitness in growth and survival in a longitudinal study and revealed environment-dependent heterosis in catfish. In earthen ponds, F1 hybrids outgrow both parental species due to a 4-month rapid growth phase in the second year. A bimodal accelerated growth pattern is unique to F1 hybrids in pond culture environment only. In sharp contrast, the same genetic types cultured in tanks display outbreeding depression, in which hybrids perform the worst and channel catfish are superior in growth across development. To the best of our knowledge, our findings represent the first example of opposite fitness shifts in response to environmental changes in interspecific vertebrate hybrids, suggesting a broader fitness landscape of F1 hybrids. Future genomic studies based on this experiment will help to understand the genome-environment interaction in shaping the F1 progeny fitness in the scenario of environment-dependent heterosis and outbreeding depression. As one of the parental species for hybrid catfish, the genetic information of blue catfish is also essential for genomic study. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. Thus, we sequenced the blue catfish using whole-genome sequencing (WGS). The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA-seq evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species SNP density is 0.32% between the most agriculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered a significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing, and genome engineering, as well as reproductive enhancement of the blue catfish and hybrid catfish. Although differences were observed between the two parental species for the economic trait such as growth rate and disease resistance, the divergence of the transcriptome across multiple tissues between these two species is still largely unknown. Using high-throughput RNA sequencing, we generated transcriptomic resources for the heart, liver, intestine, mucus, and muscle of these two species. The number of expressed genes across tissues ranged from over 20,000 in the mucus to 5036 in the muscle. Gene Ontology analysis demonstrated the functional specificity of the differentially expressed genes (DEGs) in respective tissue. Overall, three major biological process categories were enriched, which are involved in the metabolism pathway, immune activity, and response to stress. Eight interesting tissue-specific genes were identified, including lrrc10, fabp2, myog, pth1a, hspa9, cyp21a2, agt, and ngtb. This transcriptome resource will facilitate future studies assessing the molecular mechanism of environment-dependent heterosis and pave the way for genetic breeding in catfish. The gene expression in hybrids exhibited greater variability compared to their purebred parents, which are manifested as transgressive genes and may explain increased phenotypic variability. Here, phenotypic characterization and transcriptomic analyses were performed for this study in the channel catfish and blue catfish parents and reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate 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, the 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 1,140 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 in vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.