Genetic Analysis Of Population Structure And Growth And Parapodia Of Apostichopus Japonicus Based On Genome Resequencing And GWAS

Apostichopus japonicas is an important economic species with high nutritional value.However,our knowledge of the genetic diversity of Chinese A.japonicas and the genetic changes that occur during domestication or trait selection is very limited.In this study,we used the Illumina Hi Seq2500sequencing platform to re-sequence the whole genes of 254 samples from six populations of S.japonicus,including the new variety"Anyuan 1"（AY-1）and the main breeding areas in China,revealing the population structure and genetic diversity characteristics of Chinese cultured s.japonicus.The artificially selected regions and candidate genes of"Anyuan 1"were identified,which were associated with four candidate genes related to economic traits,providing important information for germplasm resource protection and genetic breeding of A.japonicas.The main research contents of this paper are as follows:1.254 individuals of A.japonicus were re-sequenced,including"Anyuan 1"and 5 major breeding populations in northern China,and 1.49Tb of original data were obtained.Reads between the sequencing data and the unique location of the reference genome ranged from 92.57%-93.80%,with an average sequencing depth of 10.58x.SNPs were distributed unevenly across the genome,with 53.74%in the intergene region,25.51%in the intron,and 3.51%in exon,which were filtered（MAF 0.05,max-missing 0.8）obtained 11,736,971 high-quality SNPs for subsequent analysis.2.Population structure,phylogenetic tree,and PCA divided the population into two subgroups,namely"Anyuan 1"subgroup（AY-1）and the Northern China subgroup（CN）.The genetic background of the two subpopulations was differentiated,and phenotypic analysis showed that the two subpopulations were differentiated in the number of parapodia.3.The analysis of nucleotide diversity and linkage imbalance showed that the genetic diversity of S.Chinensis was higher overall,but the genetic diversity of the AY-1 population was relatively lower,and the allelic linkage degree was higher,and it was subjected to more positive selection.4.Population genetic analysis(Tajima’s D analysis,F_STanalysis,and ROD analysis)obtained selected intervals and genes of the AY-1 population,among which some candidate intervals were related to the economic trait of breeding target the number of warts.GO analysis of candidate genes showed that the two subpopulations were different in immune function,temperature stimulation response,signal transduction,protein synthesis,decomposition,and transport.5.Genome-wide association analysis（GWAS）was used to identify 39 candidate genes for 4economic traits of A.japonicus,and the genes with non-synonymous SNPs were verified.BSL78＿00022 and BSL78＿00023 were found to be the key genes for the number of A.japonicus.The gene BSL78＿00022 encodes a protein related to cell differentiation and proliferation,and three non-synonymous substitutions（Ser-Phe,Glu-asp,and Ala-Val）of this gene were presumed to be related to the changes in the number of A.japonicus.The pleiotropic gene BSL78＿04631,which is related to body weight and body wall weight,promotes protein synthesis and cell growth,and non-synonymous substitution（Ile-Val）of this gene is presumed to be the reason for the difference in body weight and body wall weight of A.japonicus.