| In order to better understand the genetic diversity of tomato germplasm resources,solve the problems of high repetition rate of genetic variation,low utilization efficiency and high difficulty in breeding excellent varieties of tomato germplasm resources in Ningxia.In this study,the genetic diversity,cluster analysis,principal component analysis and population structure analysis of 504 tomato germplasm resources were conducted by using KASP technology and 60 pairs of HIGHLY polymorphic SNP primers screened and distributed on 12 chromosomes.Based on the typing results of 504 tomato samples with 60 pairs of SNP primers,four sampling ratios(20%,15%,10%and 5%)were set up,and core germplasm was constructed by Corehunter software.T test was used to compare the differences of genetic parameters(number of alleles,Shannon’s information index,polymorphism information value,gene diversity)between the core germplasm constructed with different sampling ratios and the original germplasm,and determine the optimal sampling ratio.GeneAIEx software was used to conduct principal component analysis of tomato core germplasm and original germplasm based on genetic distance to judge the representativeness and rationality of core germplasm constructed by optimal sampling ratio.The core germplasm constructed by the optimal sampling ratio was used to identify the resistance to powdery mildew at seedling stage in laboratory.The genome-wide association analysis was performed using the mixed linear model MLM(Q+K)combined with 60 SNP molecular markers covering the whole genome of tomato.The main results are as follows:1.Genetic diversity analysis of Tomato germplasm resources based on SNP markers:A total of 181 alleles were detected by 60 SNP markers,with an average of 3 alleles per locus.The average frequency of the main alleles was 0.659 with a range of 0.375 to 0.905,among which NDP7560 was the highest and NDP7781 the lowest.Gene diversity ranged from 0.178 to 0.658,with an average of 0.45.The polymorphism information value(PIC)ranged from 0.171 to 0.583,with an average value of 0.381.NDP7723(0.554),NDP7589(0.501),NDP7529(0.551),NDP7710(0.508),DNP7625(0.577),NDP7596(0.569),DNP7661(0.537),NDP7368(0.512),DNP7781(0.583)had 9 highly polymorphic SNP markers;The average genetic distance between different materials was 0.62.At the genetic distance of 0.36,504 tomato materials were divided into 7 groups,including 2 materials in category i,120 materials in category ii,8 materials in category iii,72 materials in category iv,2 materials in categories v and vi,and 298 materials in category vii.Principal component analysis divided the population into three groups.According to population structure analysis,504 tomato germplasm resources were divided into 3 groups at K=3,with 79 in the first group,302 in the second group and 123 in the third group.2.According to the calculation,the retention ratio of alleles at the four sampling ratios of 20%,15%,10%and 5%was 94%,96%,100%and 92%respectively.The average polymorphism information value(PIC)(20%sampling ratio),Shannon’s information index(15%sampling ratio),the number of alleles(5%sampling ratio)were significantly different from the original germplasm(α=0.05).The gene diversity,allele number,Shannon’s information index and allele retention rate of 50 core germplasm were 45.5,181,1.23 and 100%,respectively,which were not significantly different from those of the original germplasm at the level of 0.05.The optimal sampling ratio of 10%was determined.The best sampling build core germplasm and original species of tomato,principal coordinates analysis results show that the core germplasm is uniformly distributed in the whole tomato germplasm resources,cluster analysis could be divided into five types,50 core germplasm 1 class 1 materials,2 class 18 material,class 3 7 materials,class 4 November materials,5 class has 13 material,The results showed that the 50 tomato core germplasm constructed in this study were representative and could replace the genetic information of the original germplasm when the optimal sampling ratio was 10%.3.To the building of tomato indoor seedling powdery mildew disease resistance identification of core germplasm,among them there are 9 show the resistance of materials,as there are 33 disease material,sense of eight copies of materials,no immunity and disease-resistant material,combined with early screening of 60 SNP marker GWAS analysis,to detect a SNP loci associated with tomato powdery mildew,Of phenotypic contribution rate of 32.89%,found via the SGN,predicted genes SL2.50 Ch02.Path1.Gene2036,located in the downstream associated markup.The results for the next step of ningxia tomato genetic breeding and germplasm resources of core germplasm collection,excavation and construction to provide theoretical and material basis,and further illustrates the SNP markers can be used as tomato germplasm resources related effective tools and guiding parents selection,through genome-wide association analysis of tomato powdery mildew,It can lay a good foundation for accurate phenotypic identification and gene function verification and development of powdery mildew. |
PDF Full Text Request