Allele-Specific Expression in Interspecific Catfish Hybrids

Interspecific hybridization results in a vast reservoir of allelic variations, which provides a good model for the analysis of allelic expression. Analysis of allele-specific expression (ASE) with interspecific hybrids provides insights for understanding the mechanisms underlying heterosis as well as specific phenotypes such as paternal predominance. In this study, we analyzed allelic expression at the transcriptome level by using RNA-Seq datasets that were generated from the liver and gill tissues of F₁ hybrid catfish (female channel catfish, Ictalurus punctatus, crossed with male blue catfish, I. furcatus). Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 2,946 (4.4%) and 4,260 (2.4%) SNPs were identified as significant ASE-SNPs, respectively. With these SNPs, a total of 501 and 674 ASE-genes were identified. Gene Ontology analysis revealed that genes encoding for cytoplasmic ribosomal proteins were highly enriched among ASE genes. Parent-origins of imbalanced alleles were determined for 26 and 16 ASE ribosomal protein genes in liver and gill, respectively. Of the 26 ASE ribosomal protein genes in the liver, 16 were of channel catfish origin and 10 were of blue catfish origin. Similarly, of the 16 ASE ribosomal protein genes in the gill, 7 were of channel catfish origin, while 9 were of blue catfish origin. Therefore, it appeared that ASE was not related selected expression of a set of ribosomal protein genes from a specific parent. However, each ribosomal protein gene appeared to be almost exclusively expressed from only one parent, indicating that ribosomes in the hybrid catfish were in “hybrid” forms, i.e., ribosomes are composed ribosomal proteins from both species, with some from channel catfish and others from blue catfish. It’s also observed that the expression percentage of ribosomal protein genes out of total genes in gill was smaller in hybrid catfish (19.75%) than channel catfish (25.31%), indicating that hybrid ribosomes probably worked more efficiently than their homozygous counterparts. This study provided new insights into heterosis at the transcriptional and translational levels. Experiments are underway to determine the molecular mechanisms of allele-specific expression including differential methylation at the promoter regions of the differentially expressed alleles.