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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Emerging Pests and Pathogens Research » Research » Publications at this Location » Publication #426849
Research Project: Biology and Management of Invasive Plant Pathogens Affecting Potato and Soybean

Location: Emerging Pests and Pathogens Research

Title: A chromosome-level genome assembly of Solanum brevicaule (PI 473011), a wild potato relative with robust resistance to potato cyst nematodes

Author
item SHANMUGAVEL, SENTHILKUMAR - Oregon State University
item CHEN, SHIYAN - Cornell University
item Yang, Huijun
item Bamberg, John
item Wang, Xiaohong
item SATHUVALLI, VIDYASAGAR - Cornell University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2026
Publication Date: 6/12/2026
Citation: Shanmugavel, S., Chen, S., Yang, H., Bamberg, J.B., Wang, X., Sathuvalli, V. 2026. A chromosome-level genome assembly of Solanum brevicaule (PI 473011), a wild potato relative with robust resistance to potato cyst nematodes. The Plant Genome. 19, e70265. https://doi.org/10.1002/tpg2.70265.
DOI: https://doi.org/10.1002/tpg2.70265

Interpretive Summary: Potato cyst nematodes (PCN; golden nematode and pale cyst nematode) are quarantine pests that pose a serious threat to the U.S. potato industry. The availability of resistant potato cultivars is critical for the effective control and containment of these devastating potato pests. We screened wild potato clones from the U.S. Potato Genebank collection and identified a clone (named Y1-5) that exhibits robust resistance to PCN. We then obtained a high-quality whole-genome sequence of the Y1-5 clone using long-read sequencing technology and analyzed its repertoire of candidate resistance genes. The identified Y1-5 clone is valuable not only for advancing our understanding of nematode resistance mechanisms but also for developing potato cultivars with novel and durable resistance to potato cyst nematodes.

Technical Abstract: Potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are globally recognized quarantine pests that can cause significant yield losses in potatoes if left uncontrolled. The deployment of host resistance remains the most effective, economical, and environmentally friendly strategy for combating these devastating pathogens. The U.S. Potato Genebank (USPG) maintains a rich collection of wild potato species, representing a valuable source for discovering novel resistance to PCN. In this study, we identified a Solanum brevicaule (PI 473011) clone (named Y1-5) from the USPG that exhibits robust resistance to both PCN species. We sequenced the whole genome of Y1-5 using PacBio HiFi technology. Genome assembly and scaffolding resulted in a haplotype-resolved assembly, with genome sizes of 763.49 Mb and 764.93 Mb for haplotypes 1 and 2, respectively. Repeat elements were found to constitute approximately 65% of the genome. Gene prediction and functional annotation identified 26,953 gene models and 29,423 proteins in haplotype 1, and 28,287 gene models and 30,549 proteins in haplotype 2, with over 96% of the predicted genes being functionally annotated. In silico prediction of resistance (R) gene identified 886 and 861 putative R gene loci, in haplotype 1 and haplotype 2, respectively, with chromosomes 4, 6, and 11 showing high enrichment of R genes. The identification of the S. brevicaule clone Y1-5 and the availability of its high-quality genome are valuable for understanding the mechanisms of PCN resistance and for supporting potato breeding efforts to develop varieties with durable nematode resistance.