Sequencing the Watermelon Genome Reveals Flaw in Breeding

Today’s juicy, sweet, giant watermelons were bred at a cost: They lost much of their disease resistance. That’s one key insight revealed by an international consortium of more than 60 scientists who recently published the genomic sequence of watermelon (Citrullus lanatus).

It turns out that the watermelon genome is not that complex, relatively speaking. It’s composed of about 475 million base pairs, only about half of what’s found in the tomato genome and about the same as rice.

By comparing the genomes of 20 different watermelons, including three varying subspecies, the researchers were able to create a first-generation genetic map that pinpoints the genomic regions that have been involved in selection for watermelon breeding, such as size, yield, and taste.

But, while selecting for some of those desirable characteristics, watermelon breeders neglected disease resistance, said Zhangjun Fei, PhD, a scientist at the Boyce Thompson Institute for Plant Research at Cornell University in Ithaca, N.Y., and one of the project’s leaders. Domesticated watermelons are susceptible to a number of maladies, including gummy stem blight, bacterial rind necrosis, and downy mildew.

The international consortium is now working to identify disease resistance-related genes from non-domesticated watermelons—a family of genes known as NBS-LRR genes. “With this knowledge, we can develop markers to breed more specifically disease-resistant fruit,” he said. Doing so without sacrificing the desirable traits that have been bred in, such as sweeter and bigger fruit, won’t be easy. “It’s probably a five- or six-year process,” said Dr. Fei. “We are trying to create more disease-resistant watermelon while also improving fruit quality.”

The research appeared in the Nov. 25 online version of the journal Nature Genetics.

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