| Arachis hypogaea L.is the fourth largest oil crop in the world,based on its important economic and nutritional value.In recent years,with the increasing emphasis on oil production and the continuous enhancement of people's living standard,peanut production is increasing in China.Henan is the largest peanut producer in China,accounts for 22%and 27%of the national total plantation area and production,respectively.Peanut varieties with high yield,sound quality,good resistance against disease and pests as well as harboring ideal plant growth type have always been the breeding objects for peanuts.Understanding the molecular mechanism of important agronomic traits and the genetic background of peanut germplasms besides cultivated varieties are necessary for genetic improvement either by tranditional breeding or by molecular design.In this study,high quality single nuclotide polymorphism(SNP)data obtained by tunable genotyping by sequencing(tGBS)technology was used to characterize the genetic diversity of 320 peanut germplasms and to conducted genome-wide association mapping(GWAS)of peanut agronomic,quality,growth period and yield related traits.The SNP markers related to the important traits provide valuable information for gene cloning and molecular marker assisted breeding.Furthermore,molecular markers and coefficient of parentage(COP)values were used to analyze the genetic relationship of 106 registered peanut varieties released in Henan province,providing guidance for parent selection in future peanut breeding.The main research results are as follows:1.A total of 37,128 high quality SNPs detected by tGBS were used to constructed the phylogenetic tree of 320 peanut accessions.Results indicated that the tested accessions were grouped into three clusters.Almost all of the peanut accessions in cluster C1 were from the sub-spiceses called var.fastigiata.Meanwhile,clusters C2 and C3 mainly consisted of var.vulgaris and subsp.hypogaea,respectively.The results of principal component analysis were consistent with relationships indicated in the phylogenetic tree.Population structure analysis revealed that var.fastigiata and var.vulgaris were not separated when K=2(subgroup number),whereas they were clearly separated when K=3.The fixation index(FST)value confirmed that fastigiata was closely related to var.vulgaris(FST=0.2838),while var.hypogaea was clearly distinct from the other two subgroups of botanical types(FST>0.4).Moreover,the nucleotide diversity(?)value implied that var.vulgaris exhibited the highest genetic diversity(0.048),followed by var.fastigiata(0.035)and var.hypogaea(0.012).This conclusion provides a theoretical basis for the application of peanut germplasms in breeding program,and helps to improve the genetic diversity of breeding varieties.2.Using software TASSEL 5.2.13 with mixed linear model(MLM),a subset of 10,004 SNP loci with minor allele frequency(MAF)above 0.05 were used to conduct genome-wide association analysis for peanuts agronomic,quality,growth period and yield related traits.At the significance level of 0.05(threshold value is 5.3),119 SNPs were found to be correlated significantly with peanut traits.A set of 19 SNPs were detected to be associated with agronomic traits such as main stem height,lateral branch length,the total number of branches,the number of fruit branches/the total number of branches,with phenotypic contribution rate of 7.95%?18.53%.One SNP located on chromosome B06 associated with the main stem height was detected in two environments,while the rest SNPs were only detected in one environment.Fifty SNPs were associated with quality traits such as sucrose,oleic acid and linoleic acid content and the ratio between oleic acid and linoleic acid,with phenotypic contribution rate of 8.78%?23.17%.Among them,nine SNPs were associated with the ratio between oleic acid and linoleic acid and could be detected in two or three environments,while the rest were only detected in one environment.A total of 33 loci were found to be significantly correlated with the flowering time,with phenotype contribution rate of 8.45%?18.80%,of which 8 loci were detected in two environments.Altogether,there were 26 loci associated with yield traits such as hundred pods weight,hundred kernal weight,surface area,perimeter,diameter,length,width and the ratio between length and width of pod and seed,the phenotypic contribution rate were 7.61%?16.90%.Among them,21 loci have pleiotropic effects controling two or more traits,and 14 loci can be detected in two or more environments.Particularly,3 loci named SARAIP.B05?29253753,SARAIP.B06?72952240,SARAIP.B06?97561085 not only controled multiple traits but also can be detected in all four tested environments.The results provided valueable resources for peanut gene cloning and molecular marker assisted breeding.3.The genetic relationships of 106 peanut varieties released in Hennan Province between 1982 and 2016 were analyzed by molecular markers and their known pedigree information.Pedigree analysis showed that the most majority of the released varieties could be traced back to the same ancestor namely Fuhuasheng,and about 92%of the released varieties shared parental relationship.The coefficient of parentage(COP)values ranged from 0 to 0.773 with the average of 0.149.Cluster analysis indicated that 106 peanut varieties were gathered into 9 and 10 groups respectively according to molecular markers and the coefficient of parentage.Some of the groups from two clustering results correspond to each other and the var.vulgaris were clearly distinct from var.hypogaea.Population structure analyzed by molecular markers demonstrated that the 106 varieties could be divided into three subgroups in accordance with the classification according to botanical and pod characteristics,which was consistent with the results of molecular markers cluster analysis.The obtained results from this study show that the genetic background of the peanut varieties in Henan province is very narrow and the genetic diversity is insufficient,thus,the utilization of new germplasm resources should be paid more attention in the future peanut breeding. |
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