Grass carp (Ctenopharyngodon idellus, GC), as the highest-output fish in China, is economically important. The production of gynogenetic grass carp (GGC) will provide important germplasm resource for producing improved GC. At present, knowledge regarding the heterologous sperm DNA in gynogenetic offspring is little. Thus, revealing paternal DNA in GGC at the molecular level would be highly significant for fish genetic breeding. In this study, ultraviolet-treated sperm of koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100), was used to activate the eggs of GC (2n = 48). Afterwards, cold shock (0–4 °C) was administered for 12 min to double the chromosomes, resulting in GGC. No significant difference (p > 0.05) was found between GGC and GC in appearance, erythrocytes size and chromosome numbers. However, at the molecular level, a specific microsatellite DNA fragment (MFW1-gynogenetic grass carp, MFW1-G) derived from the paternal parent KOC was found to be transmitted into GGC. For the first time, this study provided an evidence at the molecular level that the DNA fragment derived from the paternal parent occurred in GGC. This finding is of great significance for fish genetic breeding.

Culter alburnus (topmouth culter, TC) is extensively distributed in various rivers and lakes in China. As a widely adaptive fish species, they have significant economic value and special ecological roles. Intergeneric hybridization is a pivotal strategy for generating novel hybrid lineages and species. In a previous study, we obtained an improved bisexual hybrid culter, BTBTF₁, derived from the hybrid lineage of Megalobrama amblycephala (blunt snout bream, BSB, 2n = 48, ♀) × Culter alburnus (2n = 48, ♂). In this study, we established an improved hybrid culter lineage by the self-crossing of BTBTF₁ and evaluated the biological characteristics regarding cytology, morphology, and genetics. DNA content and chromosome analyses confirmed that BTBTF₁-F₂ was a diploid lineage (2n = 48), with morphological traits exhibiting intermediate values between parental species, except for significantly TC-biased full-length-to-body length (FL/BL) and body length-to-head length (BL/HL) ratios (p < 0.05). ITS sequencing analysis revealed that BTBTF₁-F₂ inherited ITS1 sequences from BSB and TC. The global methylation level in BTBTF₁-F₂ was substantially reduced compared to progenitors, characterized by elevated full and diminished hemimethylation states. Transcriptomic analysis identified 7877 differentially expressed genes (DEGs), displaying 9.05%/8.30% maternal (BSB)-dominant and 17.01%/18.95% paternal (TC)-dominant expression patterns in BTBTF₁ and F₂. Remarkable intergenerational similarity in phenotypic and molecular profiles, coupled with bidirectional inheritance of progenitor characteristics, confirmed BTBTF₁-F₂ as a genetically stable allodiploid lineage. Remarkably, methylation patterns, and DEG expression collectively demonstrated significant TC-oriented bias (p < 0.05). This study reports a novel stabilized allodiploid culter lineage after a comprehensive assessment at cytology, morphology, and genetic levels, and provides new insights into genetic bias in hybrid progeny.

The genomes of newly formed natural or artificial polyploids may experience rapid gene loss and genome restructuring. In this study, we obtained tetraploid hybrids (4n=148, 4nJB) and triploid hybrids (3n=124, 3nJB) derived from the hybridization of two different subfamily species Carassius cuvieri (♀, 2n = 100, JCC) and Megalobrama amblycephala (♂, 2n = 48, BSB). Some significant morphological and physiological differences were detected in the polyploidy hybrids compared with their parents. To reveal the molecular traits of the polyploids, we compared the liver transcriptomes of 4nJB, 3nJB and their parents. The results indicated high proportion chimeric genes (31 > %) and mutated orthologous genes (17 > %) both in 4nJB and 3nJB. We classified 10 gene patterns within three categories in 4nJB and 3nJB orthologous gene, and characterized 30 randomly chosen genes using genomic DNA to confirm the chimera or mutant. Moreover, we mapped chimeric genes involved pathways and discussed that the phenotypic novelty of the hybrids may relate to some chimeric genes. For example, we found there is an intragenic insertion in the K+ channel kcnk5b , which may be related to the novel presence of the barbels in 4nJB. Our results indicated that the genomes of newly formed polyploids experienced rapid restructuring post-polyploidization, which may results in the phenotypic and phenotypic changes among the polyploidy hybrid offspring. The formation of the 4nJB and 3nJB provided new insights into the genotypic and phenotypic diversity of hybrid fish resulting from distant hybridization between subfamilies.