Rapid genomic DNA variation in newly hybridized carp lineages derived from Cyprinus carpio (♀) × Megalobrama amblycephala (♂)

Abstract

Background: Distant hybridization can generate changes in phenotypes and genotypes that lead to the formation of new hybrid lineages with genetic variation. In this study, based on the establishment of two bisexual fertile carp lineages, including the improved diploid common carp (IDC) lineage and the improved diploid scattered mirror carp (IDMC) lineage, from the interspecific hybridization of common carp (Cyprinus carpio, 2n = 100) (♀) × blunt snout bream (Megalobrama amblycephala, 2n = 48) (♂), provided a good platform to investigate the relationship of genetic and variation between the parents and their hybrid progenies. Result: In this study, we investigated the genetic variation of 12 Hox genes in the two types of carp lineages derived from common carp (♀) × blunt snout bream (♂). Hox gene clusters were abundant in the first generation of IDC, but most were not stably inherited in the second generation. In contrast, we did not find obvious mutations in Hox genes in the first generation of IDMC, and almost all the Hox gene clusters were stably inherited from the first generation to the second generation of IDMC. Interestingly, we found obvious recombinant clusters of Hox genes in both carp lineages, and partially recombinant clusters of Hox genes were stably inherited from the first generation to the second generation in both types of carp lineages. On the other hand, some Hox genes were gradually becoming pseudogenes, and some genes were completely pseudogenised in IDC or IDMC. Conclusions: Our results provided important evidence that distant hybridization produces rapid genomic DNA changes that may or may not be stably inherited, providing novel insights into the function of hybridization in the establishment of improved lineages used as new fish resources for aquaculture.

Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus

“…The mixed model was chosen for the Sox genes as no substitution model could be decided according the aa sequence. MrBayes was run for 10 million generations with two runs and four chains in parallel and a burn-in of 25%, and the analysis was terminated after the average standard deviation of the split frequencies fell under 0.01 ( Luo et al, 2019 ). The final trees were visualized in FIGTREE (V1.4.4) software.…”

Research advances and future perspectives of genomics and genetic improvement in allotetraploid common carp

“…These observations could to some degree reflect the increased difficulty of allopolyploidization in vertebrates relative to plants and suggest that common carp can serve as a model species for investigating vertebrate polyploidization. Other researchers established two bisexual fertile carp lineages from the hybridization of common carp (♀) and blunt snout bream (♂), providing insights into the role of hybridization in improving strains in aquaculture 62 . Alternatively, hybridization can decrease diversity and lead to genetic pollution in parental species or extinction of pure taxa in the wild if hybrids escape into natural waters 57,63,64 ; thus, hybrids require proper management.…”