| Melon is one of the most important vegetable fruit crops with significant economic value.Melon fruit is belived to be rich in nutrition for containing proteins,carbohydrates,carotene,vitamin B1,vitamin B2,niacin,calcium,phosphorus,iron and other nutrients,which could be good for human body.In a hot summer,melon are favored by people for its effect of soared,except vexed enfold,diuretic.China is one of the secondary center of origin of thick-skin melon,and is considered as a primary and secondary origin center of thin-skin melon.Melon germplasm resources are rich and the the degree of variation of fruit characters is great,which provides basic material to the genetic improvement of melon on some traits such as melon yield,quality and flavour.In the previous study,a core collection of 189 melon was constructed,which was a good group of genetic research since that the phenotypic and molecular level of genetic diversity was very rich.A natural population constituded by the core germplasm constructed and some extra complement germplasm was used for material in this study.The genetic diversity,population structure,relative kinship,the linkage disequilibrium(LD)and fruit phenotypic variation in the natural population was analyzed by 98 SSR markers that were well-distributed on melon's chromosomes.The association analysis between markers and fruit traits of multi environmental conditions were subsequently performed using GLM(general linear model)and MLM(mixed linear model)programs.This study explore loci and excellent alleles significantly associated with fruit traits,and explore the feasibility of using Genome-wide association studies(GWAS)method to analyze the genetic basis of fruit trait variation in melon.At the same time,the results of this study also provides the marker and genetic information and excellent carrier materials for the high yield and high quality breeding of melon.The main results are listed:Analysis on the variation of fruit characters of melon:The results of variation analysis of fruit traits in 192 core and expand germplasm showed that:in the 18 fruit phenotypic traits of melon,the average genetic diversity(H')of qualitative characters(fruit shape,ground color of fruit skin,vein shape,vein color,fruit net,distribution of net,thickness of net,density of net,flesh color,flesh texture,pulp color,flesh juiciness,aroma)was 1.22 and the average genetic diversity(H')of quantitative characters(flesh thinckness,fruit length,fruit width,weight of single fruit,total soluble solid content)was 2.02.In total,the fruit phenotypic traits of the melon selected had substantial variance.The qualitative characters owned much richer genetic variance than quantitative characters.Genetic diversity analysis of melon by SSR:Multiple sequence alignment was used to develop 42 SSR markers in melon EST,and 56 SSR markers are selected from papers published.These single-locus markers were well-distributed on 24 chromosomes of melon and markers in each pair of chromosomes were ranged from 5 to 15.A total of 380 alleles were identified in the natural population using 98 polymorphic SSR markers.Every marker detected 2?11 alleles with an average of 3.88 alleles per locus.The range of He,Ho,I and PIC were 0.04?0.83,0,00?0.11,0.12?1.85 and 0.04?0.81,and the average were 0.54,0.03,0.94,0.54.The proportion of rare alleles proportion was 2%.Above all showed that the melon core collection and expand germplasm have a significant excess of variations in DNA.The clustering analysis of 192 melon germplasm by molecular primers data showed that the total germplasm is grouped into 4.However the materials of each group come from wide origin areas and their phenotypic traits are different.It illustrated the genetic background of these germplasm is more complicated.Analysis of population structure and relative kinship:The natural population was divided into two groups P1 and P2 according to structure analysis based on bayesian algorithm.P1 group contained 71 melon lines(36.98%),and 121 melon lines(63.02%)are distributed into group P2,Group P1 could also be futher divied into two sub-groups,G1 and G2,of which melons are mainly belong to thin-skin subspecies from China.Group P2 could be further departed into two sub-groups,G3 and G4.The melon lines in G3 and G4 are mainly thick-skin melon from abroad countries and the north-west of China.In the association panel,almost 69.80%kinship between any two lines is below 0.05.These results indicate that 192 melon germplasm slected to be used in association analysis has the weak relationship,so there is no need to remove any germplasm.Linkage disequilibrium:There were 3551 loci pairs detected in the linkage disequilibrium.A certain degree of linkage disequilibrium between two loci of collinear chromosomes and noncollinear chromosomes can be detected by LD analysis.We found that r2 value declined rapidly with the genetic distance increased by calculating the r2 value of pair wise markers in the same chromosome to simulate the trend lines of LD.When the cut off value of r2 was setted to 0.2,it was found that the decay of the average LD in genome is about 6 cM.Association mapping of fruit traits in melon:In GLM and MLM model,56 and 49 loci were detected significantly associated with 5 traits of fruit 26 associated markers detected in two models were HNM16,HNM31,CMCTTN175,DM0767,TJ204,HNM20,CMCAN90,DM0035,CM46,CM38,CMBR150,CMCTTN166,CMTC47,DE1557,CM38,HNM12,HNM13,HNM22,HNM31,HNM36,HNM37,HNM38,CMCTTN166,CMCTTN175,CMGA128,HNM18,A total of 37 makers could be detected at least in 2 years,and they were HNM37,DM0035,HNM36,CM38,HNM13,DM0804,DE1218,CMBR150,HNM20,HNM38,CMCTTN175,CM46,HNM33,HNM16,HNM23,CMCAN90,TJ204,HNM31,DM0767,CMCTTN166,MU44460.Comparing the results in GLM model and MLM model,we found that MLM model can control the false positive caused by population structure and relative kinship more efficiently than the GLM model.Exploration of elite alleles about the fruit traits and typical material:Consistently 14 loci were detected in two models and different experiment years analysis.The phenotype of allelic variation in 12 loci are significantly different.The allele HNM31-262,FHNM37-210 and CMCTTN175-135,were demonstrated that they are benefit to increase the potential efficiency of weight of single fruit;and the corresponding accessions were Hetaodonggua,Baidonggua and 92004.The alleles significantly increasing the flesh thickness were HNM31-265 and TJ204-216;and the corresponding accessions were both PMR-45.The alleles significantly increasing the fruit length were HNM20-162,CMCAN90-136 and DM0035-131;and the corresponding accessions were PI-165508,PI-165508 and PIM 36192.The alleles significantly increasing the fruit width was HNM18-163;and the corresponding accessions was PI-164409.The allele CMBR150-214,CMCTTN166-151 and CM38-133 had the greatest positive effect on the soluble solid content traits;and the corresponding accessions were PI-145594,Jiangxiligua and Jiangxiligua. |
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