Assessment of the current infraspecific classification scheme in melon (Cucumis melo L.) based on genome-wide single nucleotide polymorphisms

Current nomenclature for the taxonomic classification of melon cultivars (Cucumis melo L.) at the horticultural group level relies on morphological variation in certain key characters. However, the reliability of current infraspecific classification scheme in considering horticultural groups as botanical taxa was not fully understood. In the present study, the information of horticultural group classification in melon was assessed at the molecular level using genome-wide single nucleotide polymorphisms (SNPs). A total of 143 melon accessions of 15 horticultural groups in two subspecies, subsp. melo and subsp. agresti were collected and genotyped by using Genotyping-By-Sequencing (GBS). From the filtering of resultant sequence variants, 10,949 SNPs were selected and used for downstream genetic analysis including population structure, principle component analysis, and hierarchical clustering of 143 melon accessions. Our genetic analyses indicated that the distribution of accessions at the molecular level generally matched the subspecies classification and no substantial contradictions existed between the division of accessions based on horticultural group information and genetic relatedness revealed by the GBS. However, the distinction between horticultural groups was not clear-cut, implying the limitation of considering horticultural groups as botanical taxa. To improve the resolution of horticultural group classification in melon, our SNP data may be useful as supporting information in conjunction with morphological characters.