| In recent years,aquaculture industry has made great achievements in China.However,the inbreeding of cultured population,reverse reservation of parents and other factors results in germplasm degradation and frequent shrimp diseases of aquatic animals,which seriously affects the healthy and sustainable development of aquaculture.It is necessary to conduct research on genetic diversity of aquatic animals for speeding up the cultivation of fine varieties of aquatic animals.Single Nucleotide Polymorphism(SNPs),the third generation of molecular marker,has achieved incessant growth and improvement in detection and analysis technology and attracted extensive attention from researchers in various countries.SNPs could be adopted to study Aquatic animals germplasm by determining the DNA sequence level,analyzing investigate genetic structureand genetic differentiation among different populations of Aquatic animals.It is conducive to more accurately evaluating genetic characteristics of germplasm sand the relationships among them,and providing theoretical basis for future seed breeding.The specific research contents are as follows:(1)Screening of SNP markers of M.rosenbergii and analysis of genetic diversity of different populations.SNPs were mined in transcriptome sequencing reports from muscle tissue of M.rosenbergii combined with NCBI.Polymorphism of 60 SNPs candidate loci from transcriptome sequencing of M.rosenbergii was detected in Malaysian wild population(MW)by direct sequencing technology.A total of 25 primers(41.7%)had a biallelic gene and could be used for genetic diversity analysis.(2)Genetic diversity analysis of different populations M.rosenbergii based on SNP markers.Then 25(41.7%)SNPs were selected because they can be genotyped ideally in 150 individuals of M.rosenbergii Shanghai(SH),Zhejiang(ZJ),Malaysia(MF)three cultured populations and growth products breeding group(BG)and Malaysia wild populations(MW).Among these,the distribution range of observed heterozygosity(Ho)was 0.18～0.30 and expected heterozygos(He)was 0.28～0.37.And the average polymorphic information content of the four populations were 0.293,0.241,0.210,0.271,respectively,which were characterized by medium and low polymorphism.At the level,the HW balance of each group has different degrees of deviation.Among them,the Malaysian cultured population has the largest number of deviations.Those makers can be used for genetic diversity analysis of M.rosenbergii in the absence of linkage disequilibrium.At the level,the HW balance of each group has different deviation,however,the Malaysian cultured population has the largest number of deviations.F-test was performed on 25 SNP markers in five populations,and the inbreeding coefficient was between 0.151 and 0.342.The average inbreeding coefficient of the three cultured populations was higher than that of the wild population,which is caused by a serious inbreeding.The genetic similarity coefficient and genetic distance between the five populations ranged from 0.659 to 0.968 and 0.032 to 0.417,respectively.The MF population and BG population had the smallest genetic similarity coefficient but largest genetic distance.In contrast,the SH and ZJ population had the largest genetic similarity coefficient but the smallest genetic distance.The range of genetic differentiation index and gene flow were 0.045～0.363 and 0.440～5.293,respectively.The highest value appeared between MF population and MW population.The lowest value appeared between SH population and ZJ population,which was 0.045 resulting in almost no genetic differentiation.The SH population and the ZJ population have the highest gene flow and that of the MF and MW population were the lowest.AMOVA estimated the variation of 26.33% between groups and 73.67% among individuals within the population.At 9 out of the 25 SNP loci in five populations,the genotype analysis of the BG population is contrary to the other four populations.What’s more,at 14 out of 25 SNPs,the number of heterozygous individuals is generally decreased in three cultured populations compared with the MW population.The study is beneficial to the futher research in population genetics and genetic breeding analysis of M.rosenbergii.(3)Genetic diversity analysis of different generations of growth and breeding lines of M.rosenbergii based on SNP markers.The genetic diversity of four generations of F1～F4 in the growth and breeding line of M.rosenbergii was analyzed by using 25 SNP markers.The results showed that the average observed heterozygosity Ho of the 25 SNP loci in the four generations was0.2615 ～0.3326,the average expected heterozygosity He ranged from 0.2829 to 0.3839,and the average polymorphic information content values ??of the four generations were: 0.311,0.296,0.263,and 0.214,except for the F4 group,which showed low polymorphism levels,Moderate polymorphism levels,And the polymorphism levels are reduced from generation to generation.The Hardy-Weinberg equilibrium of each generation has different degrees of deviation,and the F4 population has the largest number of deviations.The genetic similarity coefficient between F1 and each offspring decreased from generation to generation,and the genetic differentiation index increased from generation to generation.Four consecutive generations of artificial breeding,the gene is gradually purified,and the genetic stability is getting better and better.(4)Correlation analysis between growth traits and SNP markers of M.rosenbergiiIn order to investigate the correlation between SNP markers and growth traits of M.rosenbergii,the direct sequencing technique was used to detect the polymorphism of the extreme populations of M.rosenbergii growth traits using 25 SNP markers developed,using genotypes.Percentage screening showed that 6 markers were potentially correlated with the growth traits of M.rosenbergii in extreme populations,and further verified the correlation between these SNP markers and growth traits in large populations,using a general linear model for SNP markers and the growth of M.rosenbergii The correlation between the width of the head and chest,the width of the first abdominal section,the height of the first abdominal section,and the weight trait were examined.The results showed that the average observed heterozygosity(Ho)of the six SNP markers in the Zhejiang population of M.rosenbergii was 0.3944,the average expected heterozygosity(He)was 0.4342,and the average polymorphic information content(PIC)was 0.336.Polymorphism indicates that the Zhejiang population of M.rosenbergii has rich genetic diversity.Correlation analysis showed that4 of the 6 SNP loci were significantly associated with growth traits(P < 0.05),and the genotype GG of locus SNP6 was significantly correlated with body length,head thorax width and body weight.(P<0.05);genotype AA of locus SNP7 was significantly correlated with five growth traits(P<0.05);GG genotypes at site SNP16 were more relative to the growth traits of the other two genotypes.It is small and significantly different from the AG genotype;the CG genotypes of the three genotypes of the SNP24 locus are significantly different from the GG genotype in the first high abdominal trait.It is concluded that the GG genotype of SNP6 locus,the AA genotype of SNP7 locus and the SNP24 CG genotype may be the dominant genotypes of these loci,and the GG genotype of SNP16 locus may be the inferior genotype of this locus. |
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