Transcriptomic profiling reveals the mechanism of fast growth of an allodiploid hybrid fish

Abstract

Distant hybridization is an important technique and widely used in fish genetic breeding. In previous research, we obtained the allodiploid hybrid (BR, 2n = 49) derived from the inter-subfamily hybridization of female blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48) and male rare gudgeon (Gobiocypris rarus, RG, 2n = 50), which had obvious growth advantages over the male parent RG. However, less is known about the potential mechanisms of fast growth in BR. In this study, the liver transcriptomes of BR and parents were analyzed by RNA-seq technology. A total of 4.73 × 10⁸ clean reads and 11,040 co-expressed unigenes were obtained. The results showed that the differentially expressed genes in BR were asymmetric compared with those in both parents. Interestingly, the genome-wide expression level dominance (ELD) was biased toward the BSB genome in BR, even if BR inherited one more chromosome from RG than that from BSB. The KEGG analysis of ELD genes showed that most metabolism pathways were enriched in ELD-BSB, such as biosynthesis of unsaturated fatty acids, fatty acid elongation, pyruvate metabolism, and so on. Furthermore, the growth genes of BR were most enriched in the ELD-BSB (34.38 %) than in other categories. The expression levels of some key hormone genes (ghra, ghrb, igf1, igfals, igf2bp2, and grb2) were upregulated in BR compared with those in RG. This study provided an insight into the potential molecular mechanism of the fast growth in BR, which will be of great significance in fish genetic breeding.