A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons.

Wild progenitors of crops are important resources for breeding and for understanding domestication, but identifying them is difficult. Using an integrative approach, we discovered that a Sudanese form of melon with nonbitter whitish pulp, known as the Kordofan melon, is the closest relative of domesticated watermelons and a possible progenitor. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofan melon at the chromosome level. Our analyses imply that early farmers brought into cultivation already nonbitter watermelons, different from other domesticated Cucurbitaceae crops such as cucumber. The Kordofan melon genome is a significant new resource for watermelon breeding. 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 and other species of to search for the potential progenitor of the domesticated watermelon. A Sudanese form with nonbitter whitish pulp, known as the Kordofan melon ( subsp. ), 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 Nile Valley 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 Kordofan melon at the chromosome level, using a combination of Pacific Biosciences 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 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.

Funder

Funder name	Awards
Deutsche Forschungsgemeinschaft, Germany	DFG 603/27-1
National Institute of Food and Agriculture, United States	Specialty Crop Research Initiative (grant 2020-51181-32139)
Natural Environment Research Council, United Kingdom	Independent Research Fellowship (grant NE/S014470/1)