Genome-Wide Association Study Of Important Agronomic Traits In Melon

Melon(Cucumis melo L.)is one of the top ten fruits in the world,and China is the largest melon producer in the world.The breeding for good cultivars is very important for the fast development of melon industry,while the prerequisite is dissecting the genetic basis for the formation of these important agronomic traits such as fruit villi,tumour,groove,mask,external color,flesh color,soluble solids content and so on.Due to the complex regulatory mechanism of these traits which are usually controlled by multiple genes,the identification of elite loci for these traits from nature population will be helpful for speeding up the breeding process and improving the multi-faceted quality of melon.In this study,a panel of 200 melon germplasms of world collection was selected,and the phonotypes of fruit,leaf and seed related traits in different environments were investigated.In addition,these 200 melon materials were resequenced using NGS technology,and genome-wide association analysis was carried to identify the associated SNP or genes for the important agronomic traits in melon.The main results are as follows:(1)Core germplasm selection22 SSR markers were used to analyze the genetic relationship and population structure of 242 melon germplasm.42 of them with chaos genetic background and close relationship were eliminated for further analysis,and the remaining 200 melon materials were subsequently used for phenotyping and resequencing by NGS technology.Among the 200 melon accession,88 of them belong to subsp.melo,91 of them belong to subsp.agrestis and 21 of them were wild melon.(2)Phenotyping and statistics analysisGenetic diversity analysis of 200 accessions revealed that 7 quality traits and 15 quantitative traits had a diversity index greater than 1.Furthermore,the generalized heritability analysis of 91 agronomic traits revealed that the generalized heritability of 56 traits was higher than 70%in 2017 and 2018,and the generalized heritability of three traits(small flesh,semi-texture distribution,fruit shape ovulation)is less than 50%in 2017 and 2018.(3)Genetic analysisAfter re-sequencing all the materials using Next Sequencing Technology,a total of 2,894,560 high-quality SNP were obtained,and the phylogenetic tree for these accessions was found to be mainly divided into three subgroup.Subgroup I had a total of 68 materials,including 65 subsp.melo germplasm,and 3 are subsp.agrestis germplasm.Subgroup II has a total of 99 materials,including 86 subsp.agrestis germplasm,12 subsp.melo germplasm,and 1 wild germplasm.Subgroup III has a total of 33 materials,including 20 wild,11 subsp.melo germplasm and 2 subsp.agrestis.Principal component analysis(PCA)showed that all the materials were clearly divided into three subgroups,which was consistent with the phylogenetic tree.In the linkage disequilibrium analysis,the decay distance of all materials was found to be 60 Kb.(4)Genome-wide association analysis(GWAS)By comparing different models for genome-wide association analysis,it was found that the compressed mixed linear model(CMLM)is the best for the natural population in this study.Then,a genome-wide association analysis was performed using the best linear unlicensed prediction(BLUP)value of 91 traits,and a total of 2475 significant SNP were detected for 64 traits including 62 quality traits and 2 quantitative traits.Among of these SNPs,246 of them were selected to screen for candidate genes for these traits in a 60 kb interval,and finally 1423 candidate genes were identified in the candidate regions.