| Chinese shrimp(Fenneropenaeus chinensis)is one of the important mariculture economic species in China,and from the 1980s to 1990s,Chinese shrimp made a major breakthrough in production and gradually became one of the important mariculture species in China.The shrimp aquaculture industry in China is still facing great challenges due to the danger of white spot syndrome virus(WSSV)and the uneven quality of domestic shrimp germplasm resources.To ensure the sustainable development of the shrimp industry in China,the Yellow Sea Fisheries Research Institute has been implementing the Chinese shrimp breeding program since 1996,and has produced several new shrimp species with excellent traits.In order to investigate the genomic genetic variation of Chinese shrimp under long-term artificial selection pressure,this study was conducted to understand the genetic structure and genetic diversity of the wild and artificially selected populations by analyzing the genetic differentiation,genetic diversity and allele frequency variation between populations through 2b-RAD simplified genome sequencing of four generations of selected and wild populations.The new Chinese shrimp variety "Huanghai 5" was selected for disease resistance and growth rate as the target traits,using multi-trait composite breeding technology,and was selected for six consecutive generations,and its resistance to WSSV was improved compared with the unselected Chinese shrimp.In order to screen for differences in gene expression between the WSSV-resistant and WSSV-sensitive groups of Chinese shrimp,we performed WSSV infection and transcriptome sequencing on the resistant and sensitive lines in this study,and used weighted gene co-expression network analysis(WGCNA)to screen for differences in gene expression between the WSSV-resistant and sensitive groups of Chinese shrimp.In this study,we used weighted gene co-expression network analysis(WGCNA)to screen and identify highly synergistic gene sets in the WSSV resistance network of Chinese shrimp,and then screen for WSSV-related candidate genes to provide a theoretical basis for WSSV resistance in Chinese shrimp at the molecular level.The main results of this study are as follows.1.Genetic diversity analysis and screening for differential SNP loci between selected and wild populations of Chinese shrimpA total of 83,767 SNP loci were obtained from the four-generation Chinese shrimp selection population and a wild population using 2b-RAD simplified genome sequencing technology.The highest genetic differentiation was 0.0260 between the wild population and the 2019 selection population,and the lowest genetic differentiation was 0.0190 between the 2015 selection population;the genetic differentiation coefficient(Fst)between the wild population and the selection population was less than 0.05,which was weak genetic differentiation.The results of population principal component analysis(PCA)showed that the genetic structure did not change significantly between the wild population and the selected population.The genetic diversity statistics showed that the mean values of expected heterozygosity(He)were 0.1716 and 0.1806,the mean values of observed heterozygosity(Ho)were 0.1861 and 0.1943,the mean values of polymorphism information content(PIC)were 0.1428 and 0.1515,and the mean values of nucleotide polymorphism(Pi)were 0.1732 and 0.1813 for the wild population and the selected population,respectively.0.1813,where each genetic diversity index of the selected population in 2017 and 2019 was significantly different from the wild population(P<0.05).Selection elimination analysis was performed between the selection populations of different generations and the wild population,and 92,103,166 and 117 selected SNP loci were obtained,respectively,with a total number of four loci.The number of loci with increasing allele frequencies between adjacent generations of selected populations was 7107,of which 3674 loci deviated significantly from Hardy-Weinberg equilibrium(P<0.05);the number of loci with decreasing allele frequencies was 8501,of which 4101 loci deviated significantly from Hardy-Weinberg equilibrium(P<0.05).The results indicated that Chinese shrimp still had high genetic selection potential after repeated generations of artificial selection and could continue to be used as artificial selection material.2.Candidate gene screening for WSSV resistance in Chinese shrimpWSSV infection experiments were performed on WSSV-resistant and sensitive lines of Chinese shrimp,and transcriptome sequencing was performed using two lines infected with WSSV 96 h high viral load individuals,low viral load individuals and individuals not infected with WSSV.18 sample libraries were sequenced to obtain Clean bases ranging from 11.63G～14.54G;sequencing error rate was in the range of The sequencing error rate was 0.02%～0.03%;the GC content ranged from 49.89%～54.45%,which was within the normal range;the lowest values of Q20 and Q30 were 96.5%and 92.17%,respectively.The weighted gene co-expression network analysis(WGCNA)was used to find the core genes in the gene regulatory network of WSSV resistance in Chinese shrimp.The gene co-expression network was constructed using WGCNA,and specific modules as well as genes with high connectivity in the modules were screened in combination with phenotypic traits.The MEdarkmagenta module was found to be highly correlated with WSSV viral load concentrations,and this module contained 69 genes.The results of GO and KEGG analysis of this module indicated that the y-interferon-inducible gene annotated in the Antigen processing and presentation pathway The lysosomal thiol reductase gene(GILT)was strongly associated with WSSV.To provide some theoretical basis for the subsequent disease resistance and molecular breeding of Chinese shrimp. |
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