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Researchers Conduct Resequencing to Unravel Melon Diversity


NEW YORK (GenomeWeb) – A study appearing online last night in Molecular Biology and Evolution suggests much of the phenotypic variability found within the melon species Cucumis melo may be traced back to structural changes and transposon insertions that diversify the plants' genomes.

Researchers from Spain and Italy did genome sequencing on wild and domesticated melons from seven diverse varieties, identifying millions of SNPs, thousands of transposable element insertions, and hundreds of genes apparently impacted by structural variants.

The team has already started to tap this collection of diverse genetic variants in search of contributors to key melon features and growth characteristics in the hope of finding clues for future melon plant improvements.

Co-corresponding author Josep Casacuberta, with Spain's Centre for Research in Agricultural Genomics, said the study "reveals the high plasticity of the melon genome, and paves the way for future analyses to address melon breeding goals, such as increasing the quality of the fruit, or resistance against pests and diseases."

The C. melo species encompasses a wide range of edible and wild plants that fall into botanical groups within the melo and agrestis sub-species, the researchers noted. To get a better look at the genomic variation behind this diversity, they used the Illumina Genome Analyzer IIx to resequence the genomes of three C. melo accessions from the melo sub-species and four accessions representing the agrestis sub-species with DNA isolated from young leaf samples.

When the team started analyzing and comparing these sequences, it uncovered almost 4.4 million SNPs. Meanwhile, the available paired-end reads and coverage-depth data helped to track down 902 genes affected by structural variations in at least one of the melons.

The researchers suspect that transposons may play an important part in features that distinguish different melon varieties as well, since up to 60 percent of the more than 2,700 polymorphic transposable elements they identified turned up in just one of the varieties considered.

Genomic variants differed with genome location, clustering at sites near the centers of chromosomes and waning at chromosome ends.

The genetic diversity was typically higher amongst the wild lines, the team found, followed by the cultivated landrace varieties. The improved or 'elite' varieties had lower levels of both transposable element and nucleotide diversity overall, particularly across large swaths of sequence on chromosomes 1 and 6.

Nevertheless, the researchers saw spikes of diversity punctuating the genome sequences in these plants, highlighting sites that may have undergone strong selection during the development of these improved lines. 

Through comparisons with the cucumber genome, the team teased apart melon relationships with one another and within the Cucurbitaceae family. It also used comparative approaches to start searching for genes believed to influence the sugar content, color, and smell of melons, along with dozens of genes implicated in disease resistance, providing a jumping off point for future studies aimed at augmenting specific melon traits.