About

Dr. Kelly Balmant is an Assistant Professor in the Department of Horticultural Sciences at the University of Florida, where she specializes in designing biological systems for breeding horticultural crops. Her research focuses on consumer-oriented traits of horticultural crops, integrating multi-omics strategies such as transcriptomics, single-cell RNA-seq, metabolomics, and genomics to dissect the genetic and molecular basis of complex quality traits, including flavor, nutritional content, and post-harvest shelf-life. Her goal is to translate these discoveries into molecular markers for breeding and to engineer or select for varieties with improved quality and shelf stability, benefiting both producers and consumers. Dr. Balmant also serves as the Trait Biology Lead of the Crop Transformation Center at the University of Florida. She holds a PhD in Plant Molecular and Cellular Biology from the University of Florida, a MSc in Genetics and Plant Breeding from the Federal University of Viçosa in Brazil, and a BSc in Biology with a minor in Genetics and Molecular Biology from the same university. Her teaching responsibilities include courses in Plant Molecular Biology and Genomics, Genomics and Bioinformatics, and Laboratory Methods in Plant Molecular Biology. She has been recognized with the IFAS CALS Innovation Teaching Award for 2023-2024.

Research topics

• Biology
• Genetics
• Botany
• Cell biology
• Evolutionary biology
• Computational biology

Selected publications

• Food Rx: Integrating horticulture research to improve nutrition and health

  Proceedings of the National Academy of Sciences · 2025-05-19

  articleOpen access

  It is clear that the escalating epidemic of insulin resistance and type 2 diabetes has reached a crisis level in the United States, that overweight and obesity are drivers, and that diets and the food system have major roles. It is also clear that nutrition and medical research point to increased healthful fruit and vegetable intake as a key part of any strategy to manage the crisis. But although increasing healthful intake entails both expanding production of fruits and vegetables and improving their healthful characteristics, horticulture has generally been sidelined or taken for granted when strategies are envisioned. This article makes the case that horticulture research and practice can and should be equal partners with nutrition and medicine in the pressing search for effective crisis-management strategies. To do so, it first "runs the numbers" for the scale of the crisis, for trends in fruit and vegetable intake and production, for the scant federal support for horticultural crop production and research, and for horticulture research's high return on investment. The article then sketches a roadmap to integrate horticulture research and community outreach with nutrition and healthcare, stressing new opportunities. The goal is a US food system that i) makes healthful fruits and vegetables accessible, affordable, and appealing for all and ii) complements a healthcare system spanning patient-based to population-based nutrition.

  PublisherOA PDFDOI

• Beyond the Wood Log: Relationships Among Bark Anatomy, Stem Diameter, and Tolerance to Eucalypt Physiological Disorder (EPD) in Cultivated Clones of Eucalyptus grandis Hill Ex Maiden and E. urophylla T. Blake

  International Journal of Plant Biology · 2025-10-31

  articleOpen access

  Eucalyptus plantation forests play an important role in the global trade balance, and have been challenged with the Eucalypt Physiological Disorder (EPD) exhibiting symptoms on barks. Despite of that, there is little information on the anatomical features of phloem and periderm associated with this disorder. Although tolerant and susceptible commercial clones exhibited similar anatomical structures, they differed in the proportions of conducting and total phloem tissue and the amount of phloem containing Calcium oxalate (CaOx) crystals. The frequency and diameter of sieve tube elements (STEs) also varied among the tested clones. The increased area of phloem with non-collapsed STE and CaOx crystals were linked to the EPD tolerant phenotype. Bark, secondary phloem, and periderm thickness were correlated with EPD scores. Structural characteristics of phloem cells is correlated with increasing stem diameter. Bark and phloem thickness exhibited significant and positive associations with EPD-tolerant clones and stem diameter, while negative correlations with EPD scores. These connections corroborate the positive impact of increasing the proportion of total phloem thickness on stem diameter growth and EPD tolerance. The present results were based on restricted, yet commercially important, Eucalyptus species (E. grandis, E. urophylla and E. grandis × E. urophylla hybrids) highlighting bark and phloem traits linked to plant growth and EPD tolerance.

  PublisherOA PDFDOI

• Artificial intelligence‐powered plant phenomics: Progress, challenges, and opportunities

  The Plant Phenome Journal · 2025-12-29 · 1 citations

  articleOpen access

  Abstract Artificial intelligence (AI), a key driver of the Fourth Industrial Revolution, is being rapidly integrated into plant phenomics to automate sensing, accelerate data analysis, and support decision‐making in phenomic prediction and genomic selection. This perspective paper synthesizes current advances, identifies major barriers, and proposes future directions to realize the transformative potential of AI‐enabled plant phenomics. We first provide an overview of AI technologies with the potential to address key challenges in phenomics, from data collection to phenotypic trait extraction and environmental sensing. We then present three case studies focusing on specialty crops (blueberry [ Vaccinium corymbosum L.] mechanical harvestability traits, strawberry [ Fragaria × ananassa (Duchesne ex Weston)] production, and citrus [ Citrus L.] disease) to illustrate practical applications of AI‐driven phenomics. Moreover, we highlight future perspectives and opportunities for further research and innovation. These include large foundation models, real‐time inference on edge devices, explainable AI, generative AI and digital twins, AI‐enhanced multi‐omics, agentic AI, and knowledge‐guided and data‐driven hybrid approaches. Finally, we discuss key challenges and limitations of applying AI to plant phenomics, including data curation, model generalization and bias, and ethical considerations related to equitable access to AI tools.

  PublisherOA PDFDOI

• An improved nuclei isolation protocol from leaf tissue for single-cell transcriptomics

  PLoS ONE · 2025-09-10 · 2 citations

  articleOpen accessSenior author

  The study of plant biology has traditionally focused on investigations conducted at the tissue, organ, or whole plant level. However, single-cell transcriptomics has recently emerged as an important tool for plant biology, enabling researchers to uncover the expression profiles of individual cell types within a tissue. The application of this tool has revealed new insights into cell-to-cell gene expression heterogeneity and has opened new avenues for research in plant biology. A critical step in the successful application of single-cell and single-nuclei RNA-seq (scRNA-seq and snRNA-seq) is the isolation of individual cells or nuclei, respectively, from tissue to recover their transcriptional profile. A critical step during nuclei isolation for snRNA-seq studies is Fluorescent-Activated Cell Sorting (FACS). During this step, nuclei stained with DAPI (4',6-diamidino-2-phenylindole) can be sorted and separated from cell debris and organelles. Leaf tissue presents a unique challenge due to its high content of chloroplasts, which can interfere with obtaining high-quality results. Because DAPI can also bind to the plastid genome, these organelles will be sorted as nuclei. Thus, in tissues with a high content of chloroplasts, we have a high contamination of these organelles and an overestimation of the number of nuclei. In this study, we introduce a straightforward alternative method for isolating nuclei from Zea mays leaves with reduced chloroplast contamination. By effectively removing chloroplasts during the FACS step of our protocol, using the autofluorescence from the chloroplasts, we achieved improved alignment of reads to the genome and transcriptome. Our enhanced protocol offers a valuable solution for applying snRNA-seq in tissues with a high content of chloroplasts.

  PublisherDOI

• Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks

  Genome biology · 2025-08-28 · 4 citations

  articleOpen access

  BACKGROUND: Single-cell genomics is revolutionizing plant developmental biology, enabling the transcriptome profiling of individual cells and their lineage relationships. However, plant cell walls polymers hamper the dissociation and analysis of intact cells. This rigid structure can conceal cell types embedded in complex, lignified, multi-cell layered tissues such as those undergoing secondary growth. Their absence leads to incomplete single-cell genomic atlases and lineage inferences. RESULTS: We isolate nuclei to capture transcripts representing the diversity of cells throughout the stem of the woody perennial Populus trichocarpa generating a high-resolution transcriptome atlas of cell types and lineage trajectories. RNA sequencing of 11,673 nuclei identifies 26 clusters representing cell types in the cambium, xylem, phloem, and periderm. Comparative analysis with protoplast-derived transcriptome data reveals significant biases, with nuclei-based sequencing providing a higher representation of cells in lignified inner xylem tissues. Among previously underrepresented types, we uncover vessel-associated cells (VAC), a largely uncharacterized parenchyma subtype and the terminus of a xylem cell lineage. Gene regulatory analysis identifies a VAC-specific network and the Populus MYB48 as its primary regulator. Functional validation of MYB48 knockout mutants show an increase in vessel number and size, pointing to a role of VACs in vessel development. CONCLUSIONS: Our study demonstrates the capture and transcriptome characterization of cell types embedded in plant secondary growth, identifying novel regulators of xylem development and stress adaptation. The discovery of MYB48 as a key regulator of VAC function highlights a previously uncharacterized mechanism influencing vessel development, with applications to improving wood formation and stress resilience.

  PublisherOA PDFDOI

• Linking bark anatomy to Eucalyptus Physiological Disorder (EPD) in commercial clones

  International Journal of Horticultural Science · 2025-07-08

  articleOpen access

  Abiotic stresses trigger the Eucalyptus Physiological Disorder (EPD) which poses a threat to planted and native stands. This research seeks links between eucalyptus bark histological features and EPD, in which the descriptive bark anatomy and histochemistry are approached. Barks from 5-year eucalyptus trees, from commercial clones of E. grandis, E. urophylla and its hybrids, were collected at breast height (DBH), and 50% and 75% of the commercial height, and evaluated. The eucalyptus bark consisted of a periderm (or rhytidome) and a secondary phloem with conspicuous solitary sieve tube elements (STE). The outer bark revealed a secondary phloem with collapsed STE, whereas its inner counterpart displayed non-collapsed STEs. A region crowded with calcium oxalate (CaOx) crystals in axial parenchyma, covering the non-collapsed and partially overlapped collapsed secondary phloem, was observed. Eucalyptus barks exhibited similar anatomical organization at DBH, 50% and 75% of the commercial height, irrespective of expected EPD phenotype or scores. Notwithstanding, there are qualitative differences that are associated with the proportion of non-collapsed phloem and phloem with crystals, which were higher in the tolerant clones and in trees with score 0. The more resistant clones or samples with lower EPD scores exhibited a higher proportion of the regions of living phloem, phloem with CaOx crystals, and non-collapsed phloem. These results support the hypothesis that an increased proportion of STE collapse will occur concurrently with elevated EPD scores and are the basis for an ongoing histometric approach.

  PublisherDOI

• Complementary files - The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in <i>Medicago truncatula</i>

  Figshare · 2024-01-01

  datasetOpen access

  RDS files containing the clustered datasets from "The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in <i>Medicago truncatula</i>"

  PublisherDOI

• Rapid detection of bromatological and chemical biomarkers of clones tolerant to eucalyptus physiological disorder

  South African Journal of Botany · 2024-11-09 · 1 citations

  article
  PublisherDOI

• The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

  Cell Reports · 2024-02-01 · 37 citations

  articleOpen access

  Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

  PublisherOA PDFDOI

• SnRK1a1, a new player in the sucrose–Opaque2 network during endosperm filling

  Molecular Plant · 2024-07-06 · 2 citations

  letter1st authorCorresponding
  PublisherDOI

Frequent coauthors

• Daniel Conde

  Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

  31 shared

• Paolo M. Triozzi

  Scuola Superiore Sant'Anna

  24 shared

• Matias Kirst

  University of Florida

  21 shared

• Sara Knaack

  Wisconsin Institutes for Discovery

  20 shared

• Christopher Dervinis

  University of Florida

  20 shared

• Sushmita Roy

  University of Wisconsin–Madison

  19 shared

• Henry W. Schmidt

  University of Florida

  19 shared

• Wendell Pereira

  University of Florida

  17 shared

Awards & honors

• IFAS CALS Innovation Teaching Award (2023-2024)