The hidden, ancient history of summer’s favorite fruit

“Watermelons are just fascinating,” biologist Susanne S. Renner earnestly tells Inverse.

She should know. Currently an honorary professor of biology at the University of Washington, Renner is the lead author of a new study published this week in the journal Proceedings of the National Academy of Sciences that rewrites the origin story of everyone’s favorite summer fruit.

Renner and her colleagues’ findings reveal how the watermelon got its evolutionary groove and became the sweet, sticky, brilliant superstar of the summer barbecue.

“[Watermelons] have long played a huge role, culturally and biologically,” Renner says. Yet as invested as we may be in these fruits today, their past speaks to another, seedier aspect of America’s culinary history.

What’s new — In the new study, Renner and her team reveal that modern-day watermelons likely originate from the Sudanese Kordofan melon (C. lanatus), which is the closest known relative of domesticated watermelons.

The findings rewrite the history of this sweet summer treat, which it appears came to modern tables by way of northeast Africa. Yet when Renner began her research, scientists believed watermelons had entirely different genetic roots.

“At the time [in] 2015, everybody thought that[...] the sweet watermelon that we eat today came from South Africa,” Renner says.

In 2015, Renner was working on a “side project” at the University of Munich, where she was previously based, related to the family relationships among Citrullus — the genus that includes watermelons.

Her co-author on the study, Guillaume Chomicki, began sequencing DNA from Citrullus specimens coming in from Africa — and the picture they had had in their mind’s eye started to fragment.

“It turned out there were more species than previously thought, and that plants from South Africa were not genetically close to today’s domesticated watermelon,” she says.

How they did it — The researchers mapped out the genome of the Kordofan melon, which, unlike the ruby-red watermelon, has a white, waxy pulp. Interestingly, yet the Kordofan melon is much like domesticated watermelons in one key respect: It is sweet to the taste — a clue to their shared genesis.

The scientists analyzed the Kordofan melon’s genome on a chromosome level and traced its genetic evolution across 400 related Citrullus plants, enabling them to identify which traits it shared — and which it did not — with today’s domesticated watermelons.

The researchers identified 15,824 structural variants — gene differences — which have evolved between the Kordofan melon and a common modern watermelon varietal known by the catchy moniker “97103.”

How the watermelon got its groove — The findings offer two important insights into how modern watermelons came to be:

1. Kordofan melons carry a genetic trait for “bitterness loss” — in other words, the two melon species share a similar sweet taste.
2. The coral red color of the watermelon’s flesh is unique to domesticated watermelons — it cannot be found in Kordofan melons.

Based on the findings, the researchers suggest that “fruit sweetness has gradually increased over the course of watermelon domestication.”

The researchers suspect that selective breeding by farmers led to the signature, sweet, red pulp that we cannot help but associate with watermelons.

Where watermelons come from — The findings give rise to two possible theories on the evolution of the watermelons — and how the fruit became a global phenomenon.

1. One theory states that the crop may have been cultivated by the Nubian people in East Africa and then spread further north to Egypt and other regions.

From there, it would have been traded between ancient kingdoms and ultimately, would have proliferated across continents.

1. The second theory argues the watermelons originated in West Africa and spread north to Libya, where ancient Citrullus seeds have been found in the Sahara.

Egyptologists will also appreciate the study’s findings, as the work lends biological credence to depictions of what looks like watermelons in paintings on the walls of Ancient Egyptian tombs. These drawings indicate that Ancient Egyptians likely consumed these melons as a dessert more than four thousand years ago.

As Renner explains:

“There are at least two wall paintings[...] that show what we think are watermelons — large oval fruits with darker stripes, exactly like watermelons — and in both cases served on a tray, hence probably eaten raw, not cooked,” she says.

“There’s an Ancient Egyptian saying, which, translated from the hieroglyphs, goes, ‘Fill your stomach with a watermelon,’” she says. The saying appears to have been synonymous with the modern phrase “don’t worry, be happy,” she adds.

Why it matters — Beyond uncovering the ancient origins of this popular food, there’s another reason why scientists care about the genetic origins of watermelons — and this has more to do with their future.

Renner worked with researchers Zhangjun Fei and Shan Wu at the Boyce Thompson Institute to together uncover the genetic potential of Kordofan melons, which appear to be less vulnerable to disease than modern watermelons. This is important if we want to increase watermelons’ resilience to disease.

“By comparing genomes of highly domesticated watermelons with the Kordofan genome, Zhangjun and his postdoc Shan Wu found variation in disease resistance genes that appear to have changed during domestication,” Renner says.

The ancestral melons still exist in the Darfur region of Africa, and the U.S. Department of Agriculture also has a few Kordofan melon seeds, although they’re not actively breeding them. Yet these results suggest perhaps they could be cross-bred to boost watermelons’ hardiness.

What’s next — Armed with this new information on the genetic links between the Kordofan melon and the modern watermelon, Renner and her colleagues hope farmers can breed disease-resistant melons that can withstand changing environmental conditions during the era of the climate crisis.

“Farmers in Sudan are growing the Kordofan melon as it is and are exchanging seeds locally, and Sudanese colleagues told us that it is well-adapted to local soil and rainfall conditions,” Renner says.

For now, we may tuck into our watermelon slices at summer barbecues with greater appreciation for their extensive history. When you next bite into that flesh, consider that these fruits once graced Ancient Egyptian dining tables thousands of years before they made it to Western dinner plates.

Abstract: Wild relatives or progenitors of crops are important resources for breeding and for understanding domestication. Identifying them, however, is difficult because of extinction, hybridization, and the challenge of distinguishing them from feral forms. Here, we use collection-based systematics, iconography, and resequenced accessions of Citrullus Lantus and other species of Citrullus to search for the potential progenitor of the domesticated watermelon. A Sudanese form with non-bitter whitish pulp, known as the Kordofan melon (C. lanatus subs p.cordophanus), appears to be the closest relative of domesticated watermelons and a possible progenitor, consistent with newly interpreted Egyptian tomb paintings that suggest that the watermelon may have been consumed in the NileValley as a dessert by 4360 BP. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofanmelon at the chromosome level, using a combination of Pacific Bio-sciences and Illumina sequencing as well as Hi-C mapping technologies. The genetic signature of bitterness loss is present in the Kordofan melon genome, but the red fruit flesh color only became fixed in the domesticated watermelon. We detected 15,824 genome structural variants (SVs) between the Kordofan melon and a typical modern cultivar, “97103,” and mapping the SVs in over 400 Citrullus accessions revealed shifts in allelic frequencies, suggesting that fruit sweetness has gradually increased over the course of watermelon domestication. That a likely progenitor of the watermelon still exists in Sudan has implications for targeted modern breeding efforts.