Abstract Cucurbita moschata, commonly known as pumpkin, is highly valued for its nutritional content, stress tolerance, fruit phenotypic diversity, excellent characteristics of easy-planting and transportation, and long shelf-life, which makes it recommended as an essential crop for the mitigation of food and nutritional challenges. However, the absence of a high-quality reference genome hinders genetic improvement studies on pumpkins. Here, we successfully assembled the first telomere-to-telomere (T2T) genome of Cucurbita moschata L. (2n = 40) with a total size of 289.6 Mb (Contig N50 = 11.2 Mb). It comprises all 40 telomeres, 8 gaps, and 29 901 protein-coding genes (BUSCO = 97.9%), and half of the chromosomes are composed of a single contig. Additionally, to investigate the genetic basis of fruit traits in pumpkin, we developed an F2 genetic population consisting of 200 individuals and constructed a high-density genetic linkage map using the assembled genome as the reference. Quantitative trait locus (QTL) mapping of 20 fruit traits was applied. An AUX/IAA gene and a β-tubulin gene were identified as candidate genes regulating longitudinal flesh thickness and transverse/longitudinal diameter ratio, respectively. In summary, the genome assembly for C. moschata and QTL mapping results provide valuable resources for molecular breeding and functional genomics studies in the pumpkin.
Lu et al. (Tue,) studied this question.