About

John Bamberg is a professor affiliated with the USDA Vegetable Crops Research Unit and is involved in the Plant Breeding and Plant Genetics Program. His research focuses on plant breeding, with a particular emphasis on vegetable crops and genetic resources. He is associated with the U.S. Potato Gene Bank and conducts research at the Plant Sciences Building/Moore Hall in Madison, WI. His work contributes to the development and preservation of plant genetic resources, supporting advancements in vegetable crop production and breeding.

Research topics

• Biology
• Agronomy
• Horticulture
• Veterinary medicine
• Genetics
• Medicine
• Biotechnology
• Environmental science
• Environmental resource management
• Botany
• Evolutionary biology
• Ecology
• Microbiology

Selected publications

• Ancient use and long-distance transport of the Four Corners Potato (Solanum jamesii) across the Colorado Plateau: Implications for early stages of domestication

  PLoS ONE · 2026-01-21

  articleOpen access

  Despite its long history, utilitarian value, and cultural significance to several Indigenous Tribes in the Southwest USA, the extent to which the Four Corners potato (Solanum jamesii Torr.) has been domesticated requires circumscription. Establishing the temporal and spatial dimensions of intentional cultivation would provide an essential component of the domestication argument. This project tests the hypothesis that S. jamesii tubers were processed with ground stone tools from archaeological sites located beyond the natural range of the species, especially where genetic evidence has previously indicated human transport and establishment in gardens. Microbotanical evidence, in the form of starch granules from 401 ground stone tools at 14 archaeological sites, is examined. More than 6,600 starch granules were recovered from the tools; 163 of which were assigned to S. jamesii. Four sites (North Creek Shelter, Long House/Mesa Verde, Pueblo Bonito/Chaco Canyon, and Point of Pines) show consistent use of S. jamesii (ubiquity >18%), as early as 10,900 cal BP, and well into Puebloan times. Three of these sites are located far north of the species' center of distribution in the Mogollon region, across hundreds of kilometers of the Colorado Plateau, and still support an extant population nearby. This suggests an anthropogenic distribution of S. jamesii across the Four Corners region and a unique cultural identity around the use of this native potato. These findings, combined with ethnographic interviews and nutritional data, provide clear evidence of use in relation to natural and anthropogenic distributions, thereby allowing an assessment of the degree to which these energy-rich, nutritious, and compact tubers were purposely used and transported.

  PublisherDOI

• An Optimized Core Sample of the Wild Potato Solanum fendleri in the USA

  American Journal of Potato Research · 2025-09-03

  article1st authorCorresponding
  PublisherDOI

• A chromosome-level genome assembly of Solanum brevicaule (PI 473011) Y1-5, a wild potato relative with robust resistance to potato cyst nematodes

  2025-10-10

  articleOpen access

  Potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are globally recognized quarantine pests that can cause severe yield losses in potatoes if left uncontrolled. Deploying host resistance remains the most effective, economical, and environmentally sustainable strategy for PCN control. The U.S. Potato Genebank (USPG) maintains a rich collection of wild potato species, providing a valuable resource for discovering novel resistance to PCN. In this study, we identified a Solanum brevicaule clone (PI 473011; designated Y1-5) from the USPG that exhibits robust resistance to both PCN species. We sequenced the whole genome of Y1-5 using PacBio high-fidelity (HiFi) sequencing technology and generated a haplotype-resolved assembly, with genome sizes of 763.49 Mb and 764.93 Mb for haplotypes 1 and 2, respectively. Repeat elements accounted for approximately 65% of the genome, while gene prediction identified 80,021 protein-coding genes, over 96% of which were functionally annotated. A comprehensive set of genes encoding nucleotide-binding and leucine-rich repeat (NLR) proteins‒intracellular receptors that mediate disease resistance‒was identified in the annotated genome. NLR genes were particularly enriched on chromosomes 4, 6, and 11. Importantly, Y1-5 was found to encode more coiled-coil-type NLRs (CNLs) than several previously sequenced wild Solanum clones. These findings suggest that Y1-5 may serve as a promising new source of resistance to potato diseases. Development of this genomic resource is valuable for understanding the mechanisms of PCN resistance and for supporting potato breeding efforts to develop varieties with durable nematode resistance.

  PublisherOA PDFDOI

• Assigning Species Names to Ambiguous Populations in the US Potato Genebank

  American Journal of Potato Research · 2025-02-13

  articleSenior author
  PublisherDOI

• Genotyping wild Potato (Solanum) Seedlots Improves with High-Read Bulks

  American Journal of Potato Research · 2025-07-18

  article1st authorCorresponding
  PublisherDOI

• On the association scheme of perfect matchings and their designs

  ArXiv.org · 2025-07-01

  preprintOpen access1st authorCorresponding

  We investigate generalisations of 1-factorisations and hyperfactorisations of the complete graph $K_{2n}$. We show that they are special subsets of the association scheme obtained from the Gelfand pair $(S_{2n},S_2 \wr S_n)$. This unifies and extends results by Cameron (1976) and gives rise to new existence and non-existence results. Our methods involve working in the group algebra $\mathbb{C}[S_{2n}]$ and using the representation theory of $S_{2n}$.

  PublisherOA PDFDOI

• Field Screening of Solanum demissum Confirms its late Blight Resistance in the Toluca Valley, Mexico

  American Journal of Potato Research · 2024-03-12 · 3 citations

  article
  PublisherDOI

• Tuber Calcium Accumulation in the Wild Potato Solanum Microdontum

  American Journal of Potato Research · 2024-09-23

  article1st authorCorresponding
  PublisherDOI

• Evidence for human‐caused founder effect in populations of <i>Solanum jamesii</i> at archaeological sites: II. Genetic sequencing establishes ancient transport across the Southwest USA

  American Journal of Botany · 2024-07-01 · 2 citations

  articleOpen access

  PREMISE: The domestication of wild plant species can begin with gathering and transport of propagules by Indigenous peoples. The effect on genomic composition, especially in clonal, self-incompatible perennials would be instantaneous and drastic with respect to new, anthropogenic populations subsequently established. Reductions in genetic diversity and mating capability would be symptomatic and the presence of unique alleles and genetic sequences would reveal the origins and ancestry of populations associated with archaeological sites. The current distribution of the Four Corners potato, Solanum jamesii Torr. in the Southwestern USA, may thus reflect the early stages of a domestication process that began with tuber transport. METHODS: Herein genetic sequencing (GBS) data are used to further examine the hypothesis of domestication in this culturally significant species by sampling 25 archaeological and non-archaeological populations. RESULTS: Archaeological populations from Utah, Colorado and northern Arizona have lower levels of polymorphic loci, unique alleles, and heterozygosity than non-archaeological populations from the Mogollon region of central Arizona and New Mexico. Principle components analysis, Fst values, and structure analysis revealed that genetic relationships among archaeological populations did not correspond to geographic proximity. Populations in Escalante, Utah were related to those on the Mogollon Rim (400 km south) and had multiple origins and significant disjunctions with those populations in Bears Ears, Chaco Canyon, and Mesa Verde sites. CONCLUSIONS: Movement of tubers from the Mogollon region may have occurred many times and in multiple directions during the past, resulting in the complex genetic patterns seen in populations from across the Four Corners region.

  PublisherOA PDFDOI

• Morphometric analysis of wild potato leaves

  Genetic Resources and Crop Evolution · 2024-03-06 · 5 citations

  articleOpen accessCorresponding

  Abstract To catalog and promote the conservation and use of crop wild relatives, comprehensive phenotypic and genotypic information must be available. Plant genotyping has the power to resolve the phylogenetic relationships between crop wild relatives, quantify genetic diversity, and identify marker-trait associations for expedited molecular breeding. However, access to cost-effective genotyping strategies is often limited in underutilized crops and crop wild relatives. Potato landraces and wild species, distributed throughout Central and South America, exhibit remarkable phenotypic diversity and are an invaluable source of resistance to pests and pathogens. Unfortunately, very limited information is available for these germplasm resources, particularly regarding phenotypic diversity and potential use as trait donors. In this work, more than 150 accessions corresponding to 12 species of wild and cultivated potatoes, collected from different sites across the American continent, were analyzed using computer vision and morphometric methods to evaluate leaf size and shape. In total, more than 1100 leaves and leaflets were processed and analyzed for nine traits related to size, shape, and color. The results produced in this study provided a visual depiction of the extensive variability among potato wild species and enabled a precise quantification of leaf phenotypic differences, including shape, color, area, perimeter, length, width, aspect ratio, convexity, and circularity. We also discussed the application and utility of inexpensive but comprehensive morphometric approaches to catalog and study the diversity of crop wild relatives. Finally, this study provided insights for further experimental research looking into the potential role of leaf size and shape variation in plant–insect interactions, agronomic productivity, and adaptation.

  PublisherOA PDFDOI

Frequent coauthors

• Alfonso del Río

  University of Wisconsin–Madison

  66 shared

• Jiwan P. Palta

  47 shared

• Sandra E. Vega

  University of Wisconsin–Madison

  28 shared

• David M. Spooner

  University of Georgia

  25 shared

• Jiming Jiang

  Michigan State University

  21 shared

• Fusheng Wei

  First Affiliated Hospital of Jiangxi Medical College

  20 shared

• Uwe Wirtz

  AbbVie (United States)

  20 shared

• Hanhui Kuang

  First People’s Hospital of Zunyi

  20 shared

Education

• Ph.D., Mathematics

  University of California, Berkeley

  1982

• B.S., Mathematics

  University of California, Berkeley

  1977