A team of genetic researchers from Italy and Spain has completed the first comprehensive analysis of the genomes of seven melon varieties.

The scientists proved that highly cultivated and bred lines show the least diversity, with wild melons being the most diverse.

Their study, published online in the journal Molecular Biology and Evolution, describes more than 4.3 million single sequence DNA variants, together with an important number of structural variants including deletions, inversions, duplications, and mobile element movements.

“This 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,” said study senior author Dr Josep Maria Casacuberta from the Center for Research in Agricultural Genomics in Barcelona, Spain.

“On a more general perspective, studies such as this one will be needed to breed new plant varieties allowing to respond to the challenges in agriculture, including a growing human population, land and water scarcity, and the future impact of climate change.”

Overall, Dr Casacuberta and co-authors found 902 genes that may be affected by DNA structural variations, with 53 genes putatively involved in disease resistance (29), cell-wall metabolism (10), aroma volatiles metabolism (9), sugar metabolism (4) and carotenoid biosynthesis (1).

The mobile elements, gene-hopping structures called transposons, have been very active during recent melon evolution, and the study reports on a number of transposon insertions that may be linked to the variability of important agronomic traits, even between two closely related elite lines.

“The variability found among 7 melon varieties representing the species diversity and including wild accessions and highly-breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed non-uniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding,” the scientists said.

“We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly-selected candidate regions.”

“Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.”

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Walter Sanseverino et al. Transposon insertion, structural variations and SNPs contribute to the evolution of the melon genome. Mol Biol Evol, published online July 14, 2015; doi: 10.1093/molbev/msv152