Revealing chromosomal loci and compositional variations in different ploidy lineages of common carp (♀) × blunt snout bream (♂) via in situ hybridization

Distant hybridization enhances interspecific gene flow, facilitating emergence of novel species and polyploid lineages. However, investigating the genetic evolutionary relationships between distantly hybridized vertebrate offspring of different ploidy and their parental species remains challenging. Here, we conduct a comprehensive investigation of chromosomal composition and variation in the homodiploid crucian carp-like (NCRC) lineage and the autotetraploid carp (4nNC) lineage formed by distant hybridization of female common carp ( Cyprinus carpio , COC) × male blunt snout bream ( Megalobrama amblycephala , BSB), elucidating these genetic evolutionary relationships. Through fluorescence in situ hybridization (FISH), we demonstrate that both the NCRC and 4nNC lineages exhibit characteristics of red crucian carp ( Carassius auratus red var., RCC), with these traits becoming increasingly pronounced with successive generations, indicating that distant hybridization leads to unstable chromosomal composition and rapid variation in early generations. Furthermore, using genomic in situ hybridization (GISH), we find that the NCRC lineage undergoes extensive chromosomal translocation and its genomic genetic composition is more closely related to RCC than to its original parents (COC and BSB). The 4nNC lineage also exhibits widespread chromosomal translocations, and its genome undergoes a rapid diploidization process to maintain genomic stability. Based on GISH-COC and GISH-RCC karyotype analysis, we hypothesize that the chromosome set of the 4nNC lineage comprises four carp chromosome sets, two of which have been reorganized into a crucian carp-like composition. This study elucidates the genomic genetic configuration of female COC × male BSB hybrid lineages, offering a theoretical foundation for genetic variation and evolution in homoploid and polyploid vertebrates. • Common carp (♀) × blunt snout bream (♂) hybrid genomes develop crucian carp characteristics. • Chromosomal evidence reveals the potential evolutionary pathway of crucian carp. • Homodiploids exceed autotetraploids in chromosomal variation under hybrid stress. • The autotetraploid karyotype is newly proposed, revealing its diploidization outcome.