Abstract：Abstract The external characters of melon (Cucumis melo) fruit are the important agronomic characters which are closely related to the consumption habits. Discovery of the genes/loci affecting melon fruit character variation provides a basis for genetic improvement of exterior fruit quality. For this purpose, a total of 104 SSR markers distributed evenly across the melon chromosomes were used in the present study for identification the genotypes of a melon core collection, which was established using a stratified sampling method in our previous study. Five fruit characters of melon, fruit length (FL), fruit diameter (FD), fruit shape index (FS), flesh thickness (FT) and fruit fresh weight (FW) were determined during three years (from 2013 to 2015), and the genotype data of the core set was performed with genome-wide association study (GWAS). The results showed that a total of 456 alleles were detected in the melon core set, with polymorphism information index (PIC) of the markers ranged from 0.12~0.89 (mean=0.51). The core set had a high level of genetic diversity, all the Shannon's index of the five characters in the core set exceeded 2.0. Based on the Bayesian model, the melon core set could be separated into two subgroups, which were coincident with the subspecies classification of melon. This finding indicated that the melon core collection was suitable for association mapping. Totally, 42 loci (P＜0.01) associated with the five characters were detected by GWAS within three successive years, of which four loci appeared repeatedly under three environmental conditions and 21 loci appeared repeatedly under two environmental conditions. Most of the stably expressed loci were in agreement with the previous results from linkage analysis. There were 10, 5, 9, 8 and 10 loci associated with FL, FD, FS, FT and FW, respectively, with the maximum explanation of phenotypic variation (R2) loci of HNM36, HNM16, CMCCA145, HNM31 and HNM31, respectively. Ten loci were found to associate with two or more characters, indicating the existence of trait correlation or pleiotropism. The results will lay a basis for fine mapping of melon fruit character QTL, candidate gene discovery and molecular marker development.
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