Genomic and epigenetic alterations in diploid gynogenetic hybrid fish

Abstract Gynogenesis, as an effective technology to manipulate genome, is used fairly widely in aquaculture-related research. However, the knowledge regarding gynogenesis in allodiploid hybrid fish with the hybrid genome producing haploid gametes is sparse. This study focused on the analyses on the genomic and epigenetic alterations of the gynogenetic hybrids with improved trait. The mature eggs of the fourth generation (BTF4, 2n = 48) of allodiploid hybrid fish of blunt snout bream (BSB, 2n = 48, Megalobrama amblycephala, ♀) × topmouth culter (TC, 2n = 48, Culter alburnus, ♂) were activated by UV-irradiated sperm from koi carp (Koi, 2n = 100, Cyprinus carpio haematopterus, ♂) and doubled by cold shock. The analyses of the DNA content and morphological observation confirmed that all of the progenies were gynogenetic diploids (GBTF4, 2n = 48), suggesting that the eggs of BTF4 possessed the hybrid genome. A genomic survey resulted from microsatellite indicated that 87.72% of the GBTF4 genome was the same as that of BTF4, 12.25% of the GBTF4 genome exhibited polymorphism compared with that of BTF4, and 0.03% of the GBTF4 genome was inherited from Koi. On the other hand, the results of methylation sensitive amplification polymorphism (MSAP) showed that the DNA methylation level (38.61%) in the GBTF4 genome was lower than that (40.99%) in the BTF4 genome. In addition, MSAP profiling also showed 30.1% methylation pattern changes in GBTF4 compared with BTF4 at 588 randomly selected CCGG sites. These results enriched our knowledge regarding the combination of hybridization and gynogenesis and the genomic and epigenetic alterations in allodiploid hybrid fish following process of gynogenesis, providing new insights into fish genetic breeding.