Study On Construction Of SNP Database And Genetic Diversity Of Different Populations In Chinese Shrimp(Fenneropenaeus Chinensis)

Chinese shrimp?Fenneropenaeus chinensis?is an important marine aquaculture shrimp in China.However,the Chinese shrimp industry has been challenged by many problems,especially the large-scale outbreak of the white spot syndrome virus?WSSV?epidemic in 1993,which has dealt a heavy blow to the shrimp industry.Under this background,Chinese scholars have carried out the breeding of new varieties of F.chinensis,and have obtained four new breeding varieties,which have effectively promoted the healthy and sustainable development of the shrimp breeding industry.In order to explore the genetic diversity of the artificially selected populations,the present study analysed three continuously selected populations of“Huanghai No.2”from 2015to 2017(G₉-G₁₁1 generation),and the unselected,captured population from the west coast of the Korean Peninsula.The four populations were sequenced by 2b-RAD reduced-representation genome sequencing technology for high-throughput SNP development.Further analysis of the genetic diversity parameters,genetic differentiation,genetic distance and the genetic structure of the breeding population and the wild population were conducted,in order to provide scientific data support for further breeding of Chinese shrimp.The main results are as follows:1.Construction of SNP Database of Chinese shrimp F.chinensisIn order to establish a universal and high quality Chinese shrimp SNP database,SNP markers using two sets of reference sequences?Ref?were developed based on shrimp individuals of different sources and different years,one is the F-Ref of two parents of F.chinensis for constructing high-density linkage map,and the P-Ref of four randomly selected individuals from the breeding population.The results of genotyping indicated that 66,985 and 66,304 SNPs were obtained according to F-Ref and P-Ref respectively in the breeding population,and 65,088 and 66,009 SNPs were obtained according to F-Ref and P-Ref,respectively.There was no significant difference in the number of SNPs,genome coverage and representativeness obtained by the two sets of Ref.In this paper,we finally determined to construct the Chinese shrimp SNP marker database using F-Ref,which included 90,775 SNPs total.2.Evaluation of genetic diversity of F.chinensis breeding population in genome levelParameters of genetic structure and genetic diversity of G₉-G₁₁1 were analysed and showed that the average nucleotide diversity?Pi?was 0.1439,0.1587 and 0.1674 in G₉-G₁₁,the average observed heterozygosity?Ho?were 0.1388,0.1515 and 0.1609,and the polymorphic information content?PIC?was 0.1241,0.1360 and 0.1430,respectively.Genetic diversity parameters of the G₉-G₁₁ parent population showed an upward trend,but there's no significant difference.F-test showed that the total Fst value of three generations was 0.0061,and the degree of genetic differentiation between each adjacent generations was weak(G₉-G₁₀ 0.0029,G₁₀-G₁₁ 0.0026).The genetic distances of adjacent generations decreased slightly,which were 0.0029 and 0.0026 in G₉-G₁₀and G₁₀-G₁₁,respectively.The gene flow was 62.91-94.63 in all generations,which indicated that the gene exchange was sufficient.The statistical data show that the artificial breeding has not reduced the genetic diversity of F.chinensis,and the genetic communication between the generations is sufficient and the genetic differentiation is small.3.Analysis of differences in genome level between F.chinensis breeding populations and wild populationThe population genetic diversity,genetic structure and selection elimination analysis of the F.chinensis"Huanghai 2"G₉-G₁₁ generation samples and the unselected wild Chinese shrimp population were analyzed.The average observed heterozygosity?Ho=0.1504?and polymorphism information content?PIC=0.1343?of the three breeding populations of"Huanghai No.2"and the observed heterozygosity?Ho=0.1428?and the wild Chinese shrimp in the west coast of Korean Peninsula?Ho=0.1428?There was no significant difference in the polymorphism information content?PIC=0.1269?.The genetic differentiation coefficient Fst between the breeding population and the wild population was 0.0220-0.0234,indicating that the genetic differentiation between"Huanghai No.2"breeding population and the wild population was weak.The gene communication between the two groups was sufficient,and the gene flow was 10.43-11.12.The G₉-G₁₁ breeding generation and the wild population were selected and eliminated,and a total of 246 commonly selected differential SNP loci were screened.These markers provide the basis for further SNP site association analysis and functional verification.