Genetic Diversity Analysis Of Tomato (Solanum Lycopersicum L.) Germplasm Resources Based On Morphological And SNP Markers

Tomato(Solanum Lycopersicum L.)is one of the most important vegetable crops in the world.This research studied genetic diversity analysis of tomato germplasm collection based on morphological and SNP.Firstly,the diversity evaluation of 29 phenotypic traits in 322 tomato were collection.Variation coefficients,Shannon-Wiener information index cluster analysis,principle component analysis,correlation and regression analysis were comprehensively used to evaluate the relationship of characteristics and select important characteristics.Then,Based on the clustering results of phenotypic traits,46 tomato genomic DNA covering different taxa were selected for primer selection,and it was determined that SNP markers with high polymorphism and good genotyping could be amplified for subsequent studies,and use 120 SNP covering the whole chromosome of tomato were selected by the 374 SNP,Based on KASP typing,185 tomato germplasm resources were genotyped using 120 highly polymorphic SNP.The major results showed as follows:1.The genetic diversity of phenotypic traits was rich in these tomato germplasms,the leaf type is mainly the common leaf;the abscission layer is mainly the layer.A total of 40 mutation types were detected in 13 quality traits.In qualitative traits,the highest Shannon-Wiener diversity index was growth vigor(1.52).In quantitative traits,the highest genetic diversity indexes were leaf length(2.08)and leaf width(2.07),and the highest coefficient variation(CV)was the fruit cracking rate(70.93%).The coefficient of variation CV of 16 quantitative traits ranged from 11.71%to 70.93%,and the genetic diversity index(H')varied from 1.49 to 2.08.There was a complex relationship among these traits.The cumulative contribution rate of the first 9 principal components was 64.58%,which contains most of the information of all indicators.2.Comprehensive evaluation analysis of phenotypic traits showed that:The highest D value(0.585)was No.65,its best overall performance.The correlation analysis between the phenotypic traits and D value showed that the phenotypic traits except flesh thickness,style length than stamens,leaf shape,leaf color were significantly correlated with the D value.20 phenotypic traits were selected out as evaluation indexes by stepwise regression analysis.The 322 tomato resources were divided into 6 groups at the genetic distance of 17.5 by means of systematic clustering and inter group aggregation.The group V contained 133 resources mainly characterized by round fruit shape and limited growth habit.Group VI contained 175 resources mainly characterized by small single fruit weight and unlimited growth habit.3.46 tomato germplasm was genotyped using 374 SNPs distributed throughout the genome.75 SNPs were not polymorphic and could not distinguish between the genotypes of the samples;116 SNPs with non-specific amplification that did not distinguish samples well;A total of 185 SNPs(49.4%)were polymorphic in the entire collection.Can be used for subsequent genetic diversity analysis.4.Genotype data were analysed by Powermarker V3.25.The results showed that a total of 348 alleles were detected in 120 SNP markers with 2.892 alleles per locus.The average major allele frequency was 0.674,ranging from 0.429 to 0.962.The heterozygosity ranging from 0 to 0.557 with an average of 0.032.Variable levels of Polymorphic information content(PIC),ranging from 0.071 to 0.571,were detected with average value of 0.325.The indicating that the SNP markers used in this study were reasonably informative.The average coefficient of genetic distance between any 2 germplasm resources ranged from 0.002 to 1.141 with a mean of 0.528.The largest distance was 1.141,between R96 and R106,while the least was 0.002(R137 vs R139).185 germplasm resources could be grouped into four clusters at the genetic distance of 0.25.A11 resources were divided into three cluster based on genetic structure analysis.The above results that the analysis of genetic diversity and genetic relationship of tomato,could provide data for utilization and developing new varieties in breeding program.