Ancient DNA reveals early use of melons in China's Song Dynasty

Melon (Cucumis melo L.) domestication is thought to have independently occurred once in Northeast Africa and twice in India. However, archaeobotanical seed remains suggest a possible additional domestication in China. Because Cucumis seeds are difficult to diagnose morphologically, genomic data from archaeological material are needed to test these scenarios and to infer ancient melon traits. We sequenced two Song Dynasty melon seeds from Shuomen Gugang (China), recovering 4.5x and 1.7x nuclear genome coverage. Nuclear and chloroplast analyses place both seeds within cultivated C. melo accessions from China, supporting introduction from the broader Asian domestication pool rather than an independent Chinese domestication event. To test whether Song Dynasty melon seeds carried trait associated with sweet dessert melons, we analyzed loci underlying fruit phenotypes. Both seeds lacked alleles associated with orange flesh; one carried an allele linked to yellow/orange peel coloration and the other possessed alleles associated with green flesh and reduced acidity. These results suggest that melons in Song Dynasty China were likely consumed as fresh or culinary fruits rather than as highly sweet dessert melons. Their flesh color echoes the Song-period aesthetic traditions, exemplified by the appreciation of jade-green celadon, which was often produced in melon-shaped forms. Thus, by anchoring East Asian archaeobotanical remains within modern melon genomic variation, our study provides a temporal framework for melon dispersal into China and demonstrates how ancient genomics can illuminate crop use in the past.