A thousand melon genomes: understanding the past to improve the future

One of the many melon varieties that has been sequenced in the study, growing in the greenhouses of Torre Marimon

In 2012, the Melonomics project, a public-private consortium led by researchers from the Centre for Research in Agricultural Genomics (CRAG) published the first complete genome sequence of melon. Seven years later, and based in data from the Melonomics project, a Chinese research team has sequenced the genome of 1,175 melon varieties, which practically represent the extant diversity of the Cucumis melo species. The CRAG team led by Jordi Garcia-Mas has participated in this analysis, and the results are published this week in the journal Nature Genetics.

"The study of all of these melon varieties has allowed the understanding of how melon domestication happened 4.000 years ago," explains Jordi Garcia-Mas, IRTA researcher at CRAG and one of the leading scientists of the study that is published this week.

The research suggests that melon was domesticated three times independently, once in Africa and twice in India.

“This new genomic information contributes to the knowledge on the domestication of this plant species and represents a valuable information that can be applied to melon breeding to obtain new varieties faster and more precisely,” adds Garcia-Mas.

In a "News & Views" article in the same issue of Nature Genetics, German scientists suggest that genome editing tools as CRISPR/Cas9 could be added to melon breeding tools. This technology is already under development at the laboratory of Dr. Garcia-Mas.

What we know about melon domestication

According to data from the Food and Agriculture Organization of the United Nations (FAO), more than 30 million tones of melon were produced worldwide in 2017, half of them in China. Spain is the main melon producer in the EU, and the first world exporter. The consumed melon varieties are grouped in two subspecies, melo and agrestis. The former is cultivated worldwide, and contains the most appreciated melon varieties for consumers as types "Piel de Sapo", "Yellow Canary", "Cantalup" or "Galia". The subspecies agrestis, is cultivated only in East Asia and contains varieties and accessions that produce bitter melons with less flesh content.

In the study published in Nature Genetics, varieties belonging to both melon subspecies have been sequenced, including wild accessions that are not consumed. The results suggest that each of these subspecies was domesticated independently in Asia from wild varieties of melo and agrestis subespecies.

Using association studies, authors have successfully identified 208 regions of the melon genome that control interesting fruit agronomic traits as external colour, flesh colour, acidity, aroma or the presence of sutures in the skin. All these data represents a valuable tool for breeding this important crop, with the ultimate goal of obtaining melon varieties that can be cultivated in a sustainable manner and that produce fruits of excellent quality.

Reference article:
Zhao, G., Lian, Q., Zhang, Z. et al. A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nature Genetics 51, 1607–1615 (2019) doi:10.1038/s41588-019-0522-8