Transcriptome analysis reveals the involvement of ubiquitin-proteasome pathway in the regulation of muscle growth of rice flower carp

Growth mechanism of economically important aquaculture species has aroused widespread interest among scholars. Rice flower carp (Cyprinus carpio), commonly cultured in rice-fish farming systems, shows wide variation in body mass at the same age, which limits the development of commercial aquaculture. In this study, muscle tissues from 20-month-old fish of different sizes were used for transcriptome analysis and muscle histological studies. The muscle histological analysis showed the muscle growth in rice flower carp main depends on the hypertrophic growth of muscle fibers. A total of 30,590 unigenes were generated by muscle trancriptome analysis, including 403 differentially expressed genes (DEGs). Of these, 157 DEGs were upregulated and 246 DEGs were downregulated. Nine unigenes related to the ubiquitin-proteasome pathway were identified using differential expression analysis. This study initially revealed that the differences in growth of rice flower carp could be due to hypertrophic growth of muscle fibers caused by higher protein deposition, and the ubiquitin-proteasome pathway was an important factor affecting the growth rate of rice flower carp. E3 ubiquitin-protein ligase ari7, g2e3, Neurl1 and rnf144ab were upregulated in the slow-growing fish, indicating the binding of ubiquitin to target protein was enhanced. Foxo3 was upregulated in the slow-growing fish, which could promote the muscle loss. Eif4a2 was upregulated in the fast-growing fish, increasing protein translation efficiency. Some genes related to active muscle contraction such as actb, actg, camk2a, and camk2b were upregulated in the fast-growing rice flower carp muscle. In summary, these results provide valuable information about the key genes for use as biomarkers of growth in selective breeding programs for rice flower carp and provide novel insights into the regulatory mechanisms of muscle growth.