Grass carp (Ctenopharyngodon idellus) is an important aquaculture species in China that is affected by serious diseases, especially hemorrhagic disease caused by grass carp reovirus (GCRV). Grass carp have previously shown age-dependent susceptibility to GCRV, however, the mechanism by which this occurs remains poorly understood. Therefore, we performed transcriptome and metabolome sequencing on five-month-old (FMO) and three-year-old (TYO) grass carp to identify the potential mechanism. Viral challenge experiments showed that FMO fish were susceptible, whereas TYO fish were resistant to GCRV. RNA-seq showed that the genes involved in immune response, antigen presentation, and phagocytosis were significantly upregulated in TYO fish before the GCRV infection and at the early stage of infection. Metabolome sequencing showed that most metabolites were upregulated in TYO fish and downregulated in FMO fish after virus infection. Intragroup analysis showed that arachidonic acid metabolism was the most significantly upregulated pathway in TYO fish, whereas choline metabolism in cancer and glycerophospholispid metabolism were significantly downregulated in FMO fish after virus infection. Intergroup comparison revealed that metabolites from carbohydrate, amino acid, glycerophospholipid, and nucleotide metabolism were upregulated in TYO fish when compared with FMO fish. Moreover, the significantly differentially expressed metabolites showed antiviral effects both in vivo and in vitro. Based on these results, we concluded that the immune system and host biosynthesis and metabolism, can explain the age-dependent viral susceptibility in grass carp.

The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method. In total, we identified five Y-linked scaffolds (totaling 347 Kb) and six Y-specific sequences that could be used as sex-specific markers, demonstrating the suitability of NGS-based re-sequencing of pooled DNAs for the identification of sex markers in fish. Moreover, 14 putative Y-linked genes were described for the first time. All the genes, except for un-y1, un-y2, and ubq-y, showed high similarity to their female homologs. RT-PCR revealed that ubq-y was only expressed in the male hypothalamus and pituitary. These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.

The grass carp (Ctenopharyngodon idellus) is an important species in freshwater aquaculture both in China and on a global scale. Variety degeneration and frequent diseases have limited the further development of grass carp aquaculture. Thus, new and improved varieties are required. Here, we identified and assessed the body weight and disease resistance in a random mating population of 19 ♀ × 22 ♂ grass carp, which were derived from different water systems. In both the growth experimental group of 10,245 fish and grass carp reovirus (GCRV)-infected group with 10,000 fish, 78 full-sib families were statistically analyzed for body weight and GCRV resistance. The findings showed that body weight traits had low heritability (0.11 ± 0.04, 0.10 ± 0.03 and 0.12 ± 0.05), GCRV resistance traits had high heritability (0.63 ± 0.11); body weight was higher in 3 families, whereas GCRV resistance was significantly greater in 11 families. Our results confirmed that the natural germplasm resources of wild grass carp were genetically diverse. Breeding of GCRV resistant varieties of grass carp have better genetic basis. This study provides the basis for constructing basal populations for grass carp selective breeding, quantitative trait loci (QTL) and genome-wide association studies (GWAS) analysis.