For years, pumpkin breeding relied on a fragmented genome assembled with short-read sequencing technology, which left thousands of gaps and missed large stretches of repetitive DNA. That made it nearly impossible to pinpoint genes controlling important traits like fruit shape, sugar accumulation, and flesh thickness—hindering efforts to develop better varieties through molecular breeding. Based on these challenges, there is an urgent need for a complete, accurate reference genome and a systematic dissection of the genetic architecture underlying pumpkin fruit traits.
Now, a team from the Guangdong Academy of Agricultural Sciences and Huazhong Agricultural University has delivered exactly that. Their findings were published (DOI: 10.1093/hr/uhag141) on April 16, 2026, in Horticulture Research. Using a combination of PacBio HiFi, ultra-long Oxford Nanopore, Illumina, and Hi-C sequencing technologies, the researchers assembled a 289.6-megabase telomere-to-telomere (T2T) genome for the pumpkin inbred line YGX2019—a major leap forward from the previous draft genome.
The new genome includes all 40 telomeres across 20 chromosomes, with only eight gaps remaining—down from more than 10,000 in the old version. Half of the chromosomes are now single, gap-free contigs, and the assembly contains 29,901 protein-coding genes with a BUSCO completeness score of 97.9%. The team also built a high-density genetic map using 200 F₂ offspring from two parent lines with contrasting fruit shapes—one flat and lantern-like, the other long and olive-shaped. The map contains 7,213 markers spanning 2,538 centimorgans. Screening 20 fruit traits—including weight, diameter, flesh thickness, sugar, starch, pectin, fiber, and pigment content—they identified 165 quantitative trait loci (QTLs). Among them, a major QTL on chromosome 14 explained over 31% of the variation in the transverse-to-longitudinal diameter ratio, a key measure of fruit shape. Within that interval, the team pinpointed a β-tubulin gene (Mos_14HG000790) whose expression was significantly higher in flat-shaped varieties than in long-shaped ones. Promoter variations between the two parents suggest this gene helps determine whether a pumpkin grows wide or elongated. For longitudinal flesh thickness, another major QTL on chromosome 12 was fine-mapped to an 82-kilobase interval containing an auxin-responsive IAA9 gene (Mos_12HG001420)—a close relative of a tomato gene known to repress cell elongation and control fruit size.
“For the first time, we can see the pumpkin genome end to end—every telomere, every gap closed,” the authors said. “That completeness is what made it possible to find the actual genes behind fruit shape and flesh thickness, not just rough estimates of where they might be. And the fact that we found candidate genes with clear expression patterns and promoter differences between varieties tells us we’re on the right track toward understanding the molecular switches that control pumpkin development.”
The implications for breeding are substantial. The two candidate genes—β-tubulin and IAA9—are now promising targets for marker-assisted selection (MAS) and gene editing. Breeders could use the tightly linked molecular markers developed in this study to screen seedlings for desirable fruit traits long before harvest, saving years of field trials. Beyond fruit morphology, the 165 QTLs identified include regions controlling sugar, starch, and carotenoid content—offering a roadmap for improving both yield and nutritional quality. The complete genome also provides a solid reference for studying other economically important traits, such as disease resistance and stress tolerance, and lays the groundwork for a pumpkin pan-genome that captures the full genetic diversity of the species.
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References
DOI
10.1093/hr/uhag141
Original Source URL
https://doi.org/10.1093/hr/uhag141
Funding information
This work was supported by the Science and Technology Innovation Strategy Project (R2023PY-JX006), the Project of Guangdong Provincial Department of Agriculture and Rural Affairs (NYQN2024019), the Modern Seed Industry Innovation Capability Enhancement Project of Guangdong Academy of Agricultural Sciences (2025ZYTS), the Special Fund for Scientific Innovation Strategy–Construction of High Level Academy of Agriculture Science (R2022YJ-YB1001), the National Bulk Vegetable Industry Technology System Guangzhou Comprehensive Experimental Station (CARS-23-G50), the Major Science and Technology Special Project of Xinjiang Uygur Autonomous Region (2024A02007-1), and the Hainan Province Major Science and Technology Plan Project (ZDYF2025XDNY089).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.