Strategies for crop improvements require an in-depth understanding of plant domestication history. Two studies in Nature Genetics provide high-resolution maps of genetic variation across melon and watermelon species, respectively, and identify candidate loci linked to fruit quality traits through genome-wide association studies (GWAS) and population genomic analyses.

Credit: Dorling Kindersley Ltd/Alamy

Zhao et al. re-sequenced the genomes of 1,175 diverse accessions of melon (Cucumis melo L.), including 134 wild and 1,041 cultivated accessions, to characterize the fruit’s population structure and domestication history, which hitherto had been inferred predominantly from molecular marker analyses as well as archaeological and historical data. A phylogenetic tree, built on the basis of a subset of 17,055 single-nucleotide polymorphisms (SNPs) at fourfold degenerate sites, indicated the existence of three distinct clades with separate botanical characteristics. The authors speculate that three independent domestication events occurred, one in Africa and two in India. Focusing on the clades from India, the team identified independent domestication events for the two major melon subspecies, C. melo ssp. melo and C. melo ssp. agrestis, with distinct domestication mechanisms for fruit mass, flesh bitterness and acidity. A GWAS for 16 agronomic traits (for example, flesh and peel colour) using 1,067 diverse accessions identified 208 significant association signals in the melon genome.

Guo et al. focused on another Cucurbitaceae family member, the watermelon (Citrullus lanatus), which was known to originate in Africa. First, the authors improved the watermelon cultivar ‘97103’ reference genome, assembling a de novo genome from PacBio long reads, BioNano optical maps and Hi-C chromatin interaction maps. Next, they re-sequenced 414 Citrullus accessions, representing all 7 extant species and various geographical locations, and inferred phylogenetic relationships using 89,914 SNPs at fourfold degenerate sites. A GWAS for 7 fruit quality traits, including sugar content and fruit shape, identified 43 association signals, of which 8 overlapped previously identified loci.

useful genomic resources for further analysis

These studies provide useful genomic resources for further analysis. Knowledge of the genes linked to domestication and agronomic traits will be valuable for breeding these important fruit crops.