Resequencing of 297 melon accessions reveals the genomic history of improvement and loci related to fruit traits in melon

Domestication and improvement are two important stages in crop evolution. Melon (Cucumis meloL.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, especially fruit size, flesh thickness and aroma, which are likely the results of long-term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high-quality SNPs. Population structure and genetic diversity analyses revealed independent and two-step selections in two subspecies of melon: ssp.meloand ssp.agrestisduring melon breeding. We detected 233 (similar to 18.35 Mbp) and 159 (similar to 17.71 Mbp) novel potential selective signals during the improvement stage in ssp.agrestisand spp.melo, respectively. Twoalcohol acyltransferasegenes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp.agrestisfor the characteristic aroma as compared with other cucurbits. Genome-wide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thin-skinned ssp.agrestis, thick-skinned ssp.melohas undergone a stronger selection for thicker flesh. In most melon accessions,CmCLV3has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding.