Genetic Diversity And Genetic Structure Of Different Geographical Populations Of Black Carp Based On Mitochondrial And Nuclear Genome

Black carp(Mylopharyngodon piceus)is one of the four major fishes in China.It mainly feeds on mollusks such as snails,clams and mussels in the water.Because of its delicious meat,fast growth rate,rich protein content and high nutritional value,it has high potential market value ability and market demand,and plays a very positive and important role in ensuring the supply of high-quality and healthy aquatic products in China in the future.It is very important to systematically investigate the genetic diversity of black carp germplasm resources and deeply explore the current situation of black carp germplasm resources.Therefore,in this study,we selected the method of splicing the complete mitogenome of black carp through first-generation sequencing,and using high-throughput sequencing to obtain high-quality SNP sites of black carp nuclear genome.We specifically studied the genetic evolution index,variation sources,historical dynamics,phylogeny,degree of differentiation and genetic structure of different geographical populations of black carp in China,The purpose is to fully understand the current genetic background of black carp resources in China.The specific research results are as follows:1.Genetic evolution analysis of different geographical populations of black carp based on the complete mitogenomeThe study on the genetic diversity of black carp populations is the prerequisite for the protection of black carp germplasm resources.In order to explore the germplasm resources and genetic background of black carp,we used the complete mitogenome for the first time to study the genetic diversity and genetic differentiation of black carp.The results showed that the length of complete mitogenome of 90 black carp ranged from16598 bp to 16614 bp.the average content of A + T of complete mitogenome was 56.6%,the average content of G + C of complete mitogenome was 43.4%,and the content of A + T was significantly higher than that of G + C in black carp complete mitogenome.A total of 245 mutation sites and 247 nucleotide mutations were detected in black carp complete mitogenome,which include 74 singleton mutation sites and 171 parsimony informative sites.The number of mutation sites of the wild populations were between73 to 130,the number of nucleotide diversity was between 0.0018 to 0.0024,and the number of average nucleotide difference was between 30.5 to 40.2.The number of mutation sites of farmed populations were between 66 to 99,the number of nucleotide diversity was between 0.0010 to 0.0023,and the number of average nucleotide difference was between 17.4 to 33.9.The genetic diversity of cultured black carp was lower than that of wild black carp,and there was a phenomenon of germplasm degradation.The genetic differentiation of black carp populations was between 0.08 to0.55,and the gene flow was between 0.20 to 3.45.AMOVA analysis revealed that the mutation mainly occurred within the black carp populations.The neutral test suggested that the wild black carp has experienced a bottleneck effect in history,and then a rapid population expansion process.The NJ evolutionary tree based on genetic distance showed that Suzhou farmed population,Yulin farmed population,Foshan farmed population,Yangzhou wild population and Jiaxing wild population were clustered into one branch,Shishou wild population,Ruichang wild population,Changsha wild population were clustered into another branch.2.Genetic evolution analysis of different geographical populations of black carp based on nuclear genomeMaintaining the level of genetic diversity within aquatic animals is conducive to improving the adaptability of aquatic animals to different environments.It is the basis for the sustainable development of fish germplasm resources.In order to explore the germplasm status,differentiation degree and genetic background of black carp populations in China,this study selected the nuclear genome SNPs of black carp for the first time for analysis.A total of 139 black carp samples were collected from 9 different populations,and a number of 53,322 high-quality SNPs were reserved after GBS sequencing and filtering.The study found that the average values of observed heterozygosity,expected heterozygosity and nucleotide diversity of wild black carp populations were 0.284,0.260,and 0.175,respectively.The average values of observed heterozygosity,expected heterozygosity and nucleotide diversity of wild black carp populations were 0.284,0.258,and 0.173,respectively.The genetic diversity of cultured black carp was lower than that of wild black carp,and there was a phenomenon of germplasm degradation.AMOVA molecular analysis of variance suggested that genetic mutation mainly occurred within the black carp populations.The genetic differentiation of each population was between 0.003 to 0.133,and the genetic distance was between 0.037 to 0.143.The phylogenetic tree revealed that there was an obvious relationship between the clustering of wild populations of black carp and their geographical distance.Wild populations in the middle reaches of the Yangtze River gathered together and Wild populations in the lower reaches of the Yangtze River gathered together.There was a certain species quality hybrid phenomenon in Suzhou cultured population,Weinan wild population and Ruichang wild population.