Sugar content is an important component of fruit quality. Although sugar transporters are known to be crucial for sugar accumulation, the role of genes encoding SWEET sugar transporters in fruit sugar accumulation remains elusive. Here we report the effect of the SWEET genes on fruit sugar accumulation in apple. A total of 25 MdSWEET genes were identified in the apple genome, and 9 were highly expressed throughout fruit development. Molecular markers of these 9 MdSWEET genes were developed and used for genotyping of 188 apple cultivars. The association of polymorphic MdSWEET genes with soluble sugar content in mature fruit was analyzed. Three genes, MdSWEET2e, MdSWEET9b, and MdSWEET15a, were significantly associated with fruit sugar content, with MdSWEET15a and MdSWEET9b accounting for a relatively large proportion of phenotypic variation in sugar content. Moreover, both MdSWEET9b and MdSWEET15a are located on chromosomal regions harboring QTLs for sugar content. Hence, MdSWEET9b and MdSWEET15a are likely candidates regulating fruit sugar accumulation in apple. Our study not only presents an efficient way of implementing gene functional study but also provides molecular tools for genetic improvement of fruit quality in apple-breeding programs.

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