Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates. We generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing. In total, 157,878 contigs were assembled and 15,444 genes were annotated. We examined gene expression level changes among the parents and their triploid offspring. The mechanisms of dosage compensation that reduced triploid expression levels to the diploid state were determined in triploid fish. In this situation, novel gene expression and gene silencing were observed. Then, we established a model to determine the extent and direction of expression level dominance (ELD) and homoeolog expression bias (HEB) based on the relative expression level among the parents and their triploid offspring. Our results showed that the genome-wide ELD was biased toward maternal genome in triploid. Extensive alterations in homoeolog expression suggested a combination of regulatory and epigenetic interactions through the transcriptome network. Additionally, the expression patterns of growth genes provided insights into the relationship between the characteristics of growth and underlying mechanisms in triploids. Regulation patterns of triploid state suggest that various expression levels from the initial genomic merger have important roles in adaptation.

Distant hybridization can generate transgressive hybrid phenotypes that lead to the formation of new populations or species with increased genetic variation. In this study, we produced an experimental hybrid goldfish (EG) by distant crossing of red crucian carp (Carassius auratus) × common carp (Cyprinus carpio) followed by gynogenesis.

The assessment of genetic improvement was comprehensively analyzed using the mtDNA Cyt b gene and SSR markers among three farmed grass carp populations caught in May 2024. The results of an mtDNA Cyt b gene analysis in 198 individuals showed that the haplotype diversity index (H_i) and nucleotide diversity index (P_i) were 0.555 and 0.00058, respectively. The results of the analysis of SSR marker data in 196 individuals indicated that the unequal dosage amplification at the same locus was found in the CC population. Moreover, the total number of alleles (A: 338), number of alleles per locus (Na: 15.36), observed heterozygosity (Ho: 0.8391), expected heterozygosity (He: 0.8380), and polymorphic information content (PIC: 0.8191) in the KC population was relatively higher than that in the CC (A: 129; Na: 5.86; Ho: 0.0025; He: 0.6191; PIC: 0.5747) and CY (A: 293; Na: 8.77; Ho: 0.821; He: 0.7483; and PIC: 0.5747) populations. The FST and AMOVA analysis showed the existence of a significant differentiation (p < 0.001), with a high genetic differentiation between the CC and CY populations. In summary, a high genetic variability exists in the KC population, while the father (CY) and mother (CC) populations have relatively low genetic variability. This study reveals evidence of the existence of a “micro-hybrid”. Moreover, the results demonstrated that combining both gynogenesis and backcross breeding technology is vital for the genetic improvement of grass carp. Moreover, continuous research into the genetic health of these populations is required as well as support for the protection of germplasm resources and artificial breeding.

During meiosis, ataxia telangiectasia mutated (ATM) kinase senses DNA double-strand breaks (DSBs) and regulates multiple downstream processes, including DSB repair and p53-mediated apoptosis. The allotriploid crucian carp (3nAT, 3n = 150), derived from distant hybridization between female diploid red crucian carp (2nRCC) and male allotetraploid hybrids (4nAT), is sterile and exhibits extensive germ cell apoptosis associated with abnormal meiosis. Here, we used the ATM kinase inhibitor KU55933, to investigate the sterility mechanism. Following intraperitoneal treatment with KU55933 (KU-3nAT), germ cell apoptosis was markedly reduced, and a small number of morphologically abnormal gametes were produced. Meiosis- and gamete maturation-related genes were upregulated, whereas pro-apoptotic genes were downregulated, indicating that meiotic arrest was partially attenuated. However, KU-3nAT sperm exhibited abnormal structures with rounded heads, retained cytoplasm, and absent or malformed flagella. Self-crossed and hybrid embryos with 2nRCC arrested at gastrulation, while a few KU-3nAT ♀ × 4nAT ♂ embryos hatched. These results suggest that ATM/p53-associated apoptosis contributes to germ cell loss at the proposed pachytene checkpoint in 3nAT, while ATM inhibition permits limited gamete production but does not restore normal gamete function or embryonic development.