| Litopenaeus vannamei is one of the most important marine aquaculture species in the world,and the breeding of its fine varieties is the cornerstone of industrial development.Since its introduction to my country at the end of the 20 th century,after nearly 30 years of breeding and improvement,the genetic improvement of L.vannamei in important economic traits such as growth,survival and disease resistance has achieved remarkable results.However,genetic improvement projects based on traditional selection methods face problems such as long selection cycles,high costs,and low selection accuracy.Therefore,the use of new methods and technologies to accurately measure genetic parameters,rationally formulate breeding programs and breeding goals is of great significance for shortening the breeding cycle,reducing breeding costs,and improving selection accuracy.In this paper,the genetic parameters of important economic traits of L.vannamei were evaluated based on microsatellite molecular markers and resequencing SNPs,and genome-wide association analysis(GWAS)was used to perform association analysis on important economic traits to further analyze the importance from a molecular perspective.The genetic mechanism of economic traits is expected to provide important technical support for genetic improvement of L.vannamei.The main results of this research are as follows:1.Evaluation of genetic parameters of body length,body weight and WSSV resistance of L.vannamei based on microsatellite markers8 microsatellite loci were used to genotype mother and offspring of 69 families of L.vannamei,and the pedigree reconstruction and the calculation of the molecular relationship correlation were carried out by using the genotyping information.The reconstructed pedigree,the molecular affinity and the physical pedigree were used to construct the additive genetic correlation matrix.Then,the genetic parameters of body length,body weight and WSSV resistance were evaluated.Finally,through the cross validation method,the prediction ability and accuracy of genetic parameter evaluation were compared.The results of genotyping showed that 166 alleles were detected in 8microsatellite loci,the number of alleles in each locus was 12-45,the average number of alleles in each locus in parent and offspring population was 9.50 and 18.13,the average observed heterozygosity was 0.618 and 0.709,the average expected heterozygosity was 0.749 and 0.775,the average polymorphism information content was 0.711 and 0.750,respectively,all of loci showed high polymorphism.The heritability of reconstructed pedigree,molecular affinity and physical pedigree analysis showed that the heritability of body length was 0.119 ± 0.031,0.120 ± 0.032,0.132 ±0.030,the heritability of body weight was 0.176 ± 0.039,0.182 ± 0.040,0.172 ± 0.034,and the heritability of resistance to WSSV was 0.135 ± 0.033,0.134 ± 0.033 and 0.098± 0.031,respectively.In the heritability of body length,body weight and resistance to WSSV,the standard deviation of molecular affinity was smaller than that of reconstructed pedigree and physical pedigree.Through cross validation,the prediction ability and accuracy of the three genetic parameters evaluation from high to low are molecular affinity,reconstructed pedigree and physical pedigree.The results showed that it was more accurate to evaluate the body length,body weight and WSSV resistance of L.vannamei by using microsatellite molecular markers than using physical pedigree.In the method of evaluating heritability by using microsatellite molecular markers,it was more effective to directly use the genetic correlation of offspring.This study provides a more accurate method for the evaluation of genetic parameters of L.vannamei and a reference for further breeding.2.Evaluation of genetic parameters of important economic traits in L.vannamei based on re-sequencing SNPsThe phenotypic values of body weight,full length,body length,tail length and survival time after infection were collected by growth test and artificial infection WSSV test.The genotypic data of 300 individuals were obtained by whole genome re sequencing.Combined with the phenotypic values and genotypic data,p BLUP,GBLUP and ss GBLUP models were established to compare and analyze the resistance of different methods to WSSV traits and growth.The influence of genetic parameters on the evaluation of the morphological traits.The results showed that,compared with p BLUP model,the accuracy of g BLUP model in predicting body weight,total length,body length,tail length and survival time after infection increased by 4.77%,21.93%,19.73%,19.34% and 63.44%,respectively,while the accuracy of ss GBLUP model increased by 10.07%,25.44%,25.72%,19.34% and 122.58%,respectively.Among them,WSSV resistance was the most improved in g BLUP and ss GBLUP methods The prediction accuracy of ss GBLUP model was higher than that of g BLUP model.The results of genetic correlation and phenotypic correlation showed that the models had little influence on the evaluation of genetic correlation and phenotypic correlation.The genetic correlation of growth traits evaluated by different models was 0.767-0.999,the phenotypic correlation was 0.548-0.991,which was a medium high positive correlation.The genetic correlation between growth traits and WSSV resistance traits was(-0.198)-(-0.019),and the phenotypic correlation was(-0.443)-(-0.115),all of which were negative correlation.In conclusion,compared with the traditional p BLUP model,g BLUP model and ss GBLUP model can improve the prediction accuracy of genetic parameters of growth traits and WSSV resistance traits of L.vannamei,and reduce the prediction bias.ss GBLUP model has higher prediction accuracy and lower bias.This study provides a new method and idea for the evaluation of genetic parameters of growth traits and WSSV resistance traits of L.vannamei,and provides an experimental basis for the further development of breeding programs and breeding new varieties.3.Genome wide association analysis of important economic traits of L.vannamei based on re-sequencingUsing genome-wide re-sequencing data and phenotypic values of body weight,full length,body length,tail length and WSSV resistance traits,combined with g BLUP and ss GBLUP models,the effects of adding significant fixed effect factors and Hmatrix in genome-wide association analysis model on association analysis were compared,and the growth traits and growth and WSSV resistance traits were analyzed by using multi trait mixed linear model,By analyzing the distribution of significant loci,the explanation rate of phenotypic variation and the function of related genes,the correlation between growth traits and growth and WSSV resistance traits was further explored.The evaluation results of different models showed that when the significant fixed effect factor(model II)and H matrix(model III)were added to the model,the logarithm of likelihood value,AIC value,BIC value,the number of associated loci and P value were better than those of the original model(model I).When-7)2)> 7 and8 were used as the significance criteria for growth traits and WSSV resistance traits.175 significant loci were screened for growth traits and 156 genes were annotated,with the explanation rate of phenotypic variation ranging from 24.79% to 54.43%;90significant loci were screened for WSSV resistance traits and 49 related genes were annotated,with the explanation rate of phenotypic variation ranging from 56.20% to56.63% All of them were controlled by microgenes.The results of gene function annotation and multi trait analysis showed that the gene expression products related to growth traits were important components of nucleus,mainly involved in cell division and protein binding,while the gene expression products related to WSSV resistance traits were important components of cytoplasmic mitochondria,mainly involved in glycolysis and gluconeogenesis.The genetic correlation between growth traits and WSSV resistance traits ranged from-0.003 to-0.002,and the SNP effect of highly significant loci in WSSV resistance traits was positive,while weight and full length traits were negative.The results showed that there might be weak negative correlation or no correlation between growth traits and WSSV resistance traits.Based on the method of genome-wide association analysis,the genetic mechanism and relationship of growth and WSSV resistance traits were deeply analyzed in this paper,which is of great value to guide the collaborative improvement of multiple traits in breeding and lay the experimental foundation for further breeding of new varieties. |
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