Population genetic characteristics of hybrid and wild crucian carps in China based on joint sequences of mitochondrial COI gene and D-loop region

【Objective】To analyze the genetic characteristics of hybrid crucian carp derived from Carassius cuvieri(♀)×C. cuvieri red var.(♂) (HFJ),new homodiploid crucian carp-like species derived from Cyprinus carpio L.(♀)×Megalobrama amblycephala(♂) (NCRC),laboratory red crucian carp(RCC) and wild crucian carp population strains,to reveal current situation of hybrid and wild population germplasm resources,thus providing scientific evidence for crucian carp breeding.【Method】With 2 hybrid strains(HFJ and NCRC),1 laboratory strain(RCC),and 3 wild populations(collected from Wangcheng District,Changsha County,Changsha City and Changde City of Hunan Province) as research objects,mitochondrial COI gene and D-loop region of these 6 populations were amplified with PCR. DnaSP 6.12 was used to analyze the genetic diversity;MEGA 7.0.26 was used to calculate the genetic distance within and between populations;TCS Network algorithm was used to plot haplotype network and Structure 2.3.4 was used to predict the population genetic structure. Arlequin 3.5.2.2 was used to calculate genetic differentiation coefficient(F_ST) and the phylogenetic trees were constructed by Neighbor-joining method(NJ),Maximum likelihood method(ML) and Bayesian inference method(BI). Demographic history of the populations were evaluated by Tajima's D and Fu's Fs neutrality test combined with nucleotide mismatch distribution analysis.【Result】Based on joint sequences of mitochondrial DNA COI gene and D-loop,a total of 25 haplotypes(Hap1-Hap25) were identified from the 6 populations;haplotype diversity(h,0.582-0.877) and nucleotide diversity(π,0.00227-0.00532) of the 3 wild populations were significantly higher than those of2 hybrid strains and RCC strain. Haplotype network structure chart and phylogenetic tree showed that HFJ strain,which could form an independent branch,clustered with Japanese white crucian carp. Meanwhile,the genetic distance(0.0539-0.0628) and genetic differentiation coefficient(F_ST,0.95147-0.98331) between HFJ strain and other populations were the largest,followed by NCRC and RCC,indicating an obvious genetic differentiation between cultured and wild populations. AMOVA analysis based on Structure clustering analysis showed that the 6 populations were divided into 4 groups:HFJ,NCRC,RCC,and wild crucian carp,with between-group genetic variation accounted for the most(90.14%). Demographic history test of the populations showed that Neutrality tests and mismatch distribution analysis indicated that all of the 6 crucian carp populations remained stable in near history without any obvious expansion.【Conclusion】The results indicated that obvious genetic differentiation has been seen among HFJ,NCRC,and RCC strains,with problems such as declining genetic diversity. Therefore,in subsequent breeding,the number of breeding parents should be properly increased to avoid inbreeding and bottleneck effect,and more attention should be paid to protect genetic diversity of germplasm resources of cultured populations.