About

Jennifer A Kimball is an Assistant Professor in the Department of Agronomy and Plant Genetics at the University of Minnesota. She received her bachelor's degree from Ithaca College in 2005, worked as a research assistant in Dr. Susan McCouch's white rice genetics program at Cornell University, and earned her Master's and PhD in Crop Science at North Carolina State University in 2011 and 2015, respectively, under the guidance of Dr. Susana Milla-Lewis. She conducted a postdoctoral research in Dr. Peter Balint-Kurti's lab in the Department of Plant Pathology at North Carolina State University before joining the University of Minnesota in 2017. Her research focuses on wild rice (Zizania palustris) breeding, genetics, and conservation, with particular attention to characterizing the genetic and physiological bases of quantitative traits in wild rice, evaluating and monitoring the genetic diversity and environmental changes in natural wild rice stands in Minnesota, and investigating seed physiology characteristics such as recalcitrance and dormancy. Her breeding program aims to enhance the sustainability and growth of the Minnesota cultivated wild rice industry by developing improved varieties, with current efforts directed toward improving shattering tolerance and disease resistance.

Research topics

• Biology
• Agronomy
• Botany
• Genetics
• Medicine

Selected publications

• Seed shattering in a North American Oryzeae grain: Developmental and genomic signatures of early domestication

  The Plant Genome · 2026-02-12

  articleOpen accessSenior authorCorresponding

  Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic grain endemic to North America and a member of the Oryzeae tribe. As an outcrossing crop with a short breeding history, domestication progress in cultivated NWR (cNWR) is ongoing, and seed shattering remains a major barrier to yield stability. In this study, we investigated the developmental and genetic mechanisms underlying seed retention by integrating phenotypic, anatomical, and molecular analyses across wild and cultivated populations. Time-course phenotyping using four methods revealed a ∼90% reduction and 2-week delay in shattering in cNWR relative to wild populations. Histological analysis indicated differential anatomical reorganization of the abscission layer in cNWR compared to the wild type. Comparative genomic analyses identified multiple NWR homologs of key Oryza sativa shattering genes, revealing lineage-specific gene duplication, pseudogenization, and divergence from Zizania latifolia. Expression profiling of candidate genes via reverse transcription quantitative polymerase chain reaction across floret developmental stages identified the gene ZpSh5c as a potential regulator of seed shattering. Together, these findings provide new insights into the anatomical and molecular basis of seed shattering in NWR and demonstrate the utility of comparative frameworks for accelerating trait improvement in emerging, non-model crops.

  PublisherOA PDFDOI

• Transcriptional architecture underlying development, adaptation, and domestication in Northern Wild Rice ( <i>Zizania palustris</i> L.)

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-01 · 1 citations

  articleOpen accessSenior author

  A bstract Zizania palustris (Northern Wild Rice) is an aquatic grass native to North America and a crop wild relative of Oryza sativa with ecological, cultural, and agricultural significance. Here, we present a transcriptomic atlas spanning 20 tissues across six major developmental stages. Seed tissues showed shifts in abscisic acid, gibberellin, and ethylene pathways that define the hormonal basis of deep dormancy in this recalcitrant species and its release. Leaf development showed stage-specific reprogramming, from hypoxia-responsive programs in submerged tissues to cell wall remodeling and redox regulation during aquatic–aerial transitions, with photosynthesis and carbohydrate metabolism defining flag leaves and SRG1 divergence emerging as a defining feature of leaf development in Z. palustris . Reproductive tissues expressed duplicated homologs of well-recognized shattering genes with divergent regulation, consistent with subfunctionalization after whole-genome duplication. These findings provide new insight into traits underlying ecological adaptation and domestication in Z. palustris and related grasses. CORE IDEAS A first transcriptomic atlas for Northern Wild Rice maps gene expression across 20 tissues and six developmental stages, providing a foundational functional genomics resource for Zizania palustris . Seed dormancy and release are driven by coordinated hormone reprogramming, with shifts in ABA, GA, and ethylene pathways across whole seed, embryo, and endosperm. Leaf development is defined by aquatic-to-aerial transcriptional transitions, moving from hypoxia-responsive programs in submerged tissues to cell wall remodeling, redox regulation, and photosynthesis/metabolism in aerial and flag leaves. Whole-genome duplication underlies regulatory divergence in domestication traits, as duplicated homologs of canonical seed shattering genes show paralog- and tissue-specific expression consistent with subfunctionalization. The atlas identifies tissue-specific modules and stable housekeeping candidates, enabling improved experimental design (e.g., expression normalization) and accelerating candidate prioritization for breeding, GWAS/eQTL, and trait discovery. PLAIN LANGUAGE SUMMARY Northern Wild Rice ( Zizania palustris ) is an aquatic grass native to North America that is important for ecosystems, agriculture, and Indigenous cultures. In this study, we created a detailed gene expression map across 20 different tissues and six stages of plant development. We found that seeds strongly regulate plant hormones that control dormancy, helping explain why Northern Wild Rice seeds remain dormant for long periods and how they eventually germinate. Leaves showed clear changes in gene activity as plants moved from underwater growth to above-water growth, shifting from low-oxygen stress responses to processes that support photosynthesis and structural strength. In flowers, we identified duplicated genes involved in seed shattering that are regulated differently, likely due to past genome duplication events. Together, these results improve our understanding of how Northern Wild Rice is adapted to aquatic environments and how key traits relevant to domestication have evolved.

  PublisherDOI

• Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice ( <i>Zizania palustris</i> L.)

  Ecology and Evolution · 2025-03-01 · 1 citations

  articleOpen accessSenior authorCorresponding

  ABSTRACT Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping‐by‐sequencing (GBS) and obtained 5955 single‐nucleotide polymorphisms (SNPs). This collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and a Zizania aquatica outgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi‐domesticated crop and its wild counterparts. The first genome‐wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

  PublisherOA PDFDOI

• Seed Shattering in a North American Oryzeae grain: Developmental and Genomic Signatures of Early Domestication

  Research Square · 2025-07-14 · 1 citations

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• First Report of <i>Bipolaris zeicola</i> Causing Leaf Spot on Northern Wild Rice (<i>Zizania palustris</i>) in Minnesota

  Plant Disease · 2025-02-21

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Referee report. For: The genome sequence of Inga laurina (Sw.) Willd. [version 1; peer review: 2 approved]

  Faculty of 1000 Research Ltd · 2024-01-01

  articleOpen access1st authorCorresponding
  PublisherDOI

• Interactive transcriptome analyses of Northern Wild Rice (Zizania palustris L.) and Bipolaris oryzae show convoluted communications during the early stages of fungal brown spot development

  Frontiers in Plant Science · 2024-04-26

  articleOpen accessSenior authorCorresponding

  Fungal diseases, caused mainly by Bipolaris spp., are past and current threats to Northern Wild Rice (NWR) grain production and germplasm preservation in both natural and cultivated settings. Genetic resistance against the pathogen is scarce. Toward expanding our understanding of the global gene communications of NWR and Bipolaris oryzae interaction, we designed an RNA sequencing study encompassing the first 12 h and 48 h of their encounter. NWR activated numerous plant recognition receptors after pathogen infection, followed by active transcriptional reprogramming of signaling mechanisms driven by Ca 2+ and its sensors, mitogen-activated protein kinase cascades, activation of an oxidative burst, and phytohormone signaling-bound mechanisms. Several transcription factors associated with plant defense were found to be expressed. Importantly, evidence of diterpenoid phytoalexins, especially phytocassane biosynthesis, among expression of other defense genes was found. In B. oryzae , predicted genes associated with pathogenicity including secreted effectors that could target plant defense mechanisms were expressed. This study uncovered the early molecular communication between the NWR– B. oryzae pathosystem, which could guide selection for allele-specific genes to boost NWR defenses, and overall aid in the development of more efficient selection methods in NWR breeding through the use of the most virulent fungal isolates.

  PublisherOA PDFDOI

• Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustris L.)

  2024-08-30 · 1 citations

  preprintSenior author

  Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping-by-sequencing (GBS) and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and a Zizania aquatica outgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. The first genome-wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

  PublisherDOI

• Impact of polyphenol oxidase on the bioavailability of flavan-3-ols in fruit smoothies: a controlled, single blinded, cross-over study

  Food & Function · 2023-01-01 · 17 citations

  articleOpen access

  = 11), flavan-3-ols were co-ingested with a high-PPO banana drink but contact prior to intake was prevented. In this context, plasma flavan-3-ol levels were still reduced, suggesting an effect possibly related to post-ingestion PPO activity degrading flavan-3-ols in the stomach. There was a substantial range in the PPO activity detected in 18 different fruits, vegetables and plant-derived dietary products. In conclusion, bioavailability of flavan-3-ols, and most likely other dietary polyphenol bioactives, can be reduced substantially by the co-ingestion of high PPO-containing products, the implications of which are of importance for dietary advice and food preparation both at home and in industrial settings.

  PublisherOA PDFDOI

• Flavan-3-ol-methylxanthine interactions: Modulation of flavan-3-ol bioavailability in volunteers with a functional colon and an ileostomy

  Free Radical Biology and Medicine · 2023-01-05 · 13 citations

  articleOpen access
  PublisherOA PDFDOI

Frequent coauthors

• Ralph A. Reisfeld

  25 shared

• Jens C. Eickhoff

  University of Wisconsin–Madison

  25 shared

• Stephan D. Voss

  Dana-Farber/Harvard Cancer Center

  25 shared

• Barrett Wagner

  Hennepin Healthcare Research Institute

  25 shared

• Paul M. Sondel

  University of Wisconsin–Madison

  25 shared

• Robert C. Seeger

  25 shared

• Wendy B. London

  25 shared

• Mark R. Albertini

  University of Wisconsin Carbone Cancer Center

  25 shared

Labs

• Kimball LabPI