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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #427876
Research Project: Characterization of Host Resistance and Biology of Diseases and Nematodes in Vegetable Crops

Location: Vegetable Research

Title: Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Author
item SUN, HONGHE - Cornell University
item ZHANG, JIE - National Engineering Center For Vegetables
item LIAO, SHENGJIN - National Engineering Center For Vegetables
item GUO, SHAOGUI - National Engineering Center For Vegetables
item ZHOU, ZHE - Cornell University
item ZHAO, XUEBO - Cornell University
item WU, SHAN - Cornell University
item ZHAO, JIANTAO - Cornell University
item GONG, GUOYI - National Engineering Center For Vegetables
item WANG, JINFANG - National Engineering Center For Vegetables
item LI, MAOYING - National Engineering Center For Vegetables
item YU, YONGTAO - National Engineering Center For Vegetables
item REN, YI - National Engineering Center For Vegetables
item TIAN, SHOUWEI - National Engineering Center For Vegetables
item LI, SHAOFANG - National Engineering Center For Vegetables
item ZHANG, HAIYING - National Engineering Center For Vegetables
item HAMMAR, SUE - Michigan State University
item MCGREGOR, CECILIA - University Of Georgia
item Jarret, Robert
item WECHTER, PATRICK - Clemson University
item BRANHAM, SANDRA - Clemson University
item Kousik, Chandrasekar
item Levi, Amnon
item GRUMET, REBECCA - Michigan State University
item XU2, YONG - National Engineering Center For Vegetables
item FEI, ZHANGJUN - Cornell University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/9/2026
Publication Date: 5/5/2026
Citation: Sun, H., Zhang, J., Liao, S., Guo, S., Zhou, Z., Zhao, X., Wu, S., Zhao, J., Gong, G., Wang, J., Li, M., Yu, Y., Ren, Y., Tian, S., Li, S., Zhang, H., Hammar, S.A., Mcgregor, C., Jarret, R.L., Wechter, P., Branham, S.E., Kousik, C.S., Levi, A., Grumet, R., Xu2, Y., Fei, Z. 2026. Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon. Nature. https://doi.org/10.1101/2025.07.25.666869.
DOI: https://doi.org/10.1101/2025.07.25.666869

Interpretive Summary: Watermelon is an important vegetable crop grown in 44 states in the U.S.A. and across the world. There are many species of watermelon including wild ones that posses many useful traits for breeding pest and disease resistance and better quality watermelons. USDA ARS scientists in Charleston and Griffin in collaboration with researchers from Universities and research labs across the world have developed an extensively detailed map of the all the watermelon species genomes (called Super-Pangenome) to help in precision breeding of watermelon cultivars with improved traits. This information will be useful to public and private plant breeders, seed company researchers, USDA scientists and other researchers across the world and. This information will help breed better quality watermelon with pest and disease resistance that will ultimately the watermelon farmers and improve rural economy.

Technical Abstract: Pangenomes are increasingly critical for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here, we report a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated near-gapless genomes representing all seven watermelon species. The super-pangenome captures approximately one million structural variants (SVs), enabling accurate variant genotyping across ~900 watermelon accessions and substantially expanding variant discovery both across and within species. Broader sampling within the pangenome provides insights into genome evolution among watermelon species and sheds light on the origin of cultivated watermelon. SV-inclusive genome-wide association studies enhance trait mapping resolution and identify a copy number variation upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, our findings and genomic resources establish a foundational framework for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crop species.