Abstract
Background
A collection of 175 melon (Cucumis melo L.) accessions (including wild relatives, feral
types, landraces, breeding lines and commercial cultivars) from 50 countries was selected to
study the phenotypic variability for ripening behavior and sugar accumulation. The variability
of single nucleotide polymorphisms (SNPs) at 53 selected candidate genes involved in sugar
accumulation and fruit ripening processes was studied, as well as their association with
phenotypic variation of related traits.
Results
The collection showed a strong genetic structure, defining seven groups plus a number of
accessions that could not be associated to any of the groups (admixture), which fitted well
with the botanical classification of melon varieties. The variability in candidate genes for
ethylene, cell wall and sugar-related traits was high and similar to SNPs located in reference
genes. Variability at ripening candidate genes had an important weight on the genetic
stratification of melon germplasm, indicating that traditional farmers might have selected for
ripening traits during cultivar diversification. A strong relationship was also found between
the genetic structure and phenotypic diversity, which could hamper genetic association
studies. Accessions belonging to the ameri group are the most appropriate for association
analysis given the high phenotypic and molecular diversity within the group, and lack of
genetic structure.
The most remarkable association was found between sugar content and SNPs in LG III,
where a hotspot of sugar content QTLs has previously been defined. By studying the
differences in allelic variation of SNPs within horticultural groups with specific phenotypic
features, we also detected differential variation in sugar-related candidates located in LGIX
and LGX, and in ripening-related candidates located in LGII and X, all in regions with
previously mapped QTLs for the corresponding traits.
Conclusions
In the current study we have found an important variability at both the phenotypic and
candidate gene levels for ripening behavior and sugar accumulation in melon fruit. By
combination of differences in allelic diversity and association analysis, we have identified
several candidate genes that may be involved in the melon phenotypic diversity.