Genetic Diversity Analysis Of 7 Populations Of Meretrix Meretrix

In this study,RNA sequencing was used to sequence the transcription of Meretrix meretrix,through the statistics and analysis of different types of microsatellites in the transcriptome of Meretrix meretrix,the distribution frequency and number of microsatellites were understood.Because of its high mutation rate and abundant polymorphic loci,microsatellite has become a kind of popular molecular marker.Studying the microsatellite characteristics of Meretrix meretrix is conducive to the application of individual identification,germplasm resource identification,biological genetic mapping,genetic diversity analysis and other aspects of research.The microsatellite sequences（simple sequence repeats,SSR）and codon bias in the RNA-sequencing of Meretrix meretrix were analyzed and compared using the method of bio-informatics.The results showed that after searching the SSR loci of Meretrix meretrix,8856 complete SSR loci were found.The total length of SSR was 162416bp,with an average length of 18.34bp,accounting for about 0.15%of the total sequence size.There were 3001 single base repeats,2254 three base repeats,2200 four base repeats,1052two base repeats,332 five base repeats,and 13 six base repeats in the Meretrix meretrxi.The SSR of Meretrix meretrix RNA-sequencing contains 26 repeats,among which the most dominant is 2809 single base repeats A/T,the second is 907 triple base repeats AAC/TTG,the fourth base repeats AAAC/TTTG and AT/TA 588 and 561 double base repeats respectively,which indicates that the distribution of microsatellites in the RNA-sequencing of Meretrix meretrix has a preference for A/T.The average length of SSR（integrity）of Meretrix meretrix is 18.34bp,and the main length of microsatellite is 12-20bp,accounting for 41%.The results of this study will provide theoretical basis for the development of microsatellite markers,population genetic diversity,genetic linkage map,germplasm resource identification and molecular genetic breeding of Meretrix and other shellfish.It has an important reference value for further research on genetic marker assisted breeding and population genetics by using microsatellite marker technology.In order to understand the changes of genetic diversity of Jiangsu red shell population breeding generations of Meretrix meretrix,to observe the effect of continuous population breeding on the genetic structure of Meretrix meretrix population and the long-term sustainability of the follow-up breeding program.Fifteen microsatellite markers were used to analyze seven populations of Meretrix meretrix,including SY,SR and SRF₁～SR⁵F₅.The results showed that a total of 765 alleles were detected in 15 pairs of primers,with 18 alleles per locus,with an average of 51 alleles per locus.N_a declined from the increase in breeding generations.The average range of H₀ was 0.4422-0.5022,and the H_e ranges was 0.6424-0.6798.Among the 105 population-locus combinations,38population-locus combinations significantly deviated from equilibrium,indicating that there was a certain degree of heterozygosity loss at each point,the average value of Shannon genetic diversity index was 1.3000-1.4649,and PIC at each locus was 0.5750-0.6298,Indicating that the population had high locus polymorphism.The Fisk value of the inbreeding coefficient within the population ranges from-0.0157-0.7409,with an average of 0.2777,Indicating that there is a certain level of inbreeding in the population.The F_stis 0.0455 which indicates that about 4.55%of the variation in Meretrix meretrix population is caused by the genetic differences in different populations,and 95.45%of the variation comes from the gene flow of each population is 0.9002-18.9478,and the average gene flow is 8.8065.There is strong gene communication between each population.UPMGA clusters analysis showed that the（SY）of Meretrix meretrix and its selected populations were clustered into one branch.The results showed that although the genetic diversity index of the selected population of Meretrix meretrix was slightly lower than that of the basic population（SY and SR）after 5 generations of artificial breeding,it did not lead to a significant change in genetic diversity and still had high genetic diversity.In order to explore the relationship between the single nucleotide polymorphism（SNP）of cyclin dependent kinases 1（cdk1）gene and growth traits of Meretrix meretrix,7 populations including the initial brood stocks with red shell color from Jiangsu and its off springs were choose as study subjects,the SNP loci in exon region of cdk1 gene of all individuals were screened by direct sequencing,and correlation analysis were conducted between the selected SNP loci and different growth traits（shell length,shell width,shell height,body weight）.The results showed that there were 15 SNP loci in the exons of cdk1gene,which found 6 SNP loci were significantly correlated with growth traits.Among the6 SNP loci,1 SNP loci were synonymous mutations（443T>A;）and 5 SNP loci were non-synonymous mutations（356G>A;713G>A;1121C>G;1201G>A 1229A>T）,the amino acids（Cys119Tyr;Arg238His;Thr374Arg;Gly401Ser;Asn410Arg）were induced respectively.Linkage disequilibrium analysis of 6 SNP loci significantly correlated with growth traits of Meretrix meretrix.The genetic parameters of 6 SNP loci with significant correlation between cdk1 gene and growth traits were analyzed by Popgen32 software in7 populations.The results showed that the H_e was lower than the H₀,PIC was 0.2339-0.3040,all showed moderate polymorphism,and the genetic differentiation index among populations was 0.0046-0.0274,indicating that the genetic differentiation among populations was low.There was a significant correlation between cdk1 gene and growth traits.The frequency of 6 SNP loci in the breeding population showed an increasing trend,reflecting that the breeding line of Meretrix meretrix in Jiangsu Province had accumulated some genetic variation in growth traits.The results showed that six SNP loci and haplotypes of cdk1 gene were significantly associated with growth traits,and there was no significant change in genetic structure of breeding population of Meretrix meretrix in Jiangsu province and the construction of haplotypes provided some reference materials for the breeding of Meretrix meretrix.