Researchers have now taken a comprehensive look at the genomes of all seven species. They then created a resource that could help plant breeders find wild watermelon genes with improved characteristics. 

Introducing these genes into cultivated watermelon could yield high-quality sweet watermelons. These could potentially grow in more diverse climates, which will be especially important as climate change increasingly challenges farmers.

Zhangjun Fei, a faculty member at Boyce Thompson Institute and co-leader of the international effort, said: "As humans domesticated watermelon over the past 4,000 years, they selected fruit that were red, sweet and less bitter."

"Unfortunately, as people made watermelons sweeter and redder, the fruit lost some abilities to resist diseases and other types of stresses," said Fei, who is also an Adjunct Professor in Cornell University's School of Integrative Plant Science.

Improved version of a reference genome for watermelons

The researchers made these insights using a two-step process. First, they created an improved version of a "reference genome". This is used by plant scientists and breeders to find new and interesting versions of genes from their specimens.

Fei co-led the creation of the first watermelon reference genome using an East Asian cultivated variety, published in 2013.

"That first reference genome was made using older short-read sequencing technologies," Fei said. "Using current long-read sequencing technologies, we were able to create a much higher quality genome that will be a much better reference for the watermelon community."

The group then sequenced the genomes of 414 different watermelons representing all seven species. By comparing these genomes both to the new reference genome and to each other, the researchers were able to determine the evolutionary relationship of the different watermelon species.

"One major discovery from our analysis is that one wild species that is widely used in current breeding programs, C. amarus, is a sister species and not an ancestor as was widely believed," Fei said.

Wide genetic diversity among the wild species

The researchers found that cultivated watermelon was domesticated by breeding out the bitterness and increasing sweetness, fruit size and flesh color. Modern varieties have been further improved in the past few hundred years by increasing sweetness, flavor and crispy texture

The researchers also uncovered regions of the watermelon genome that could be mined to continue improving fruit quality, such as by making them bigger, sweeter and crispier.

In the past 20 to 30 years, plant breeders have crossed cultivated watermelon with other species to make the dessert watermelon more resistant to nematode pests, drought, and diseases like Fusarium wilt and powdery mildew.

These types of improvements using wild relatives is what excites Amnon Levi, a research geneticist and watermelon breeder at the USDA's Agricultural Research Service in Charleston, South Carolina. 

"The sweet watermelon has a very narrow genetic base," says Levi. "But there is wide genetic diversity among the wild species, which gives them great potential to contain genes that provide them tolerance to pests and environmental stresses."

Levi hopes to find wild genes that could improve the dessert watermelon, especially for disease resistance.

"Watermelon is susceptible to many tropical diseases and pests, whose ranges are expected to continue to expand along with climate change," says Levi. "We want to see if we can bring back some of these wild disease resistance genes that were lost during domestication."