About

Marcio Resende is an Associate Professor and the Principal Investigator at the Sweet Corn and Potato Lab. He holds a Ph.D. and leads research efforts focused on sweet corn and potato breeding and genetics. As the principal investigator, he oversees projects aimed at improving these crops through genetic and breeding approaches, contributing to advancements in agricultural science and crop development.

Research topics

• Biology
• Botany
• Food science
• Biochemistry
• Chemistry
• Genetics
• Machine Learning
• Computer Science
• Biotechnology
• Cell biology

Selected publications

• Integrating image‐based phenotyping and marker‐assisted selection to optimize the selection of potato clones for chipping and resistance to viruses X and Y

  Crop Science · 2026-04-27

  articleOpen access

  Abstract Potato ( Solanum tuberosum L.) is the most important non‐cereal crop for global food security. To meet the demands of the processing, potato clones with good frying quality and industrial yield and resistance to major viral diseases are required. This study aimed to integrate image‐based phenotyping and marker‐assisted selection to optimize the selection of potato clones for potato chip processing and virus resistance. A total of 39 clones were evaluated in comparison with the cultivar Atlantic at two locations in Minas Gerais, Brazil. The trials were conducted during the 2022 and 2023 winter seasons. Agronomic traits included total tuber yield and dry matter content, while image‐based phenotyping quantified chips color through the L * axis of the CIELAB color system. The data were subjected to individual and multi‐environment analyses of variance. All clones were compared with the cultivar Atlantic using Dunnett's test, based on the means of the multi‐environment analysis. Clones were also tested for molecular markers linked to the Ry adg and Rx 1 alleles, which provide resistance to potato virus Y and potato virus X, respectively. The clone CCF25‐08 exhibited high tuber yield and dry matter content with simultaneous resistance to both viral diseases, suggesting it is a promising candidate as a parental line or for release as a new cultivar. The integration of image‐based phenotyping and marker‐assisted selection proved effective for the colorimetric differentiation of chips and the identification of virus‐resistant clones. This approach can improve experimental accuracy in potato breeding programs by reducing subjectivity in evaluations and accelerating the development of potato clones suitable for the processing.

  PublisherDOI

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

  PLoS ONE · 2025-09-10 · 2 citations

  articleOpen access

  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

• Convergent evolution of <i>NFP</i> -facilitated root nodule symbiosis

  Proceedings of the National Academy of Sciences · 2025-09-09 · 2 citations

  articleOpen access

  The origin and phylogenetic distribution of symbiotic associations between nodulating angiosperms and nitrogen-fixing bacteria have long intrigued biologists. Recent comparative evolutionary analyses have yielded alternative hypotheses: a multistep pathway of independent gains and losses of root nodule symbiosis vs. a single gain followed by numerous losses. A detailed reconstruction of the history of genes involved in signaling between nitrogen-fixing bacteria and potential hosts, particularly lipo-chitooligosaccharide (LCO) signaling, is needed to distinguish between these hypotheses. LCO recognition by plants involves the Nod Factor Perception ( NFP ) gene family; in the legume model Medicago truncatula (Fabales), MtNFP is essential for establishing rhizobial symbiosis. Here, we document convergent evolution of NFP , indicating multiple origins of LCO-driven symbiosis. In contrast to previous models that explain the recruitment of NFP via a single duplication in the ancestor of the nitrogen-fixing clade, our phylogenomic and synteny results suggest this duplication does not span the entire clade. Tandem duplication in a common ancestor of Cucurbitales and Rosales resulted in the NFP1 and NFP2 groups. In contrast, the phylogenetically closest paralog of MtNFP is MtLYR1 , located on a different chromosome within a large syntenic block. All available data indicate that a large-scale duplication resulted in MtNFP and MtLYR1 , likely corresponding to a whole-genome duplication in an ancestor of subfamily Papilionoideae of Fabaceae. We show that MtNFP and the NFP2 -like group are not orthologous, indicating multiple independent gains of NFP -based LCO signaling. This molecular convergence provides a possible mechanism for multiple gains of root nodule symbiosis across the nitrogen-fixing clade.

  PublisherOA PDFDOI

• InteracTor: Feature engineering and explainable AI for profiling protein structure-interaction-function relationships

  PLoS Computational Biology · 2025-10-13 · 3 citations

  articleOpen accessCorresponding

  Characterizing protein families' structural and functional diversity is essential for understanding their biological roles. Traditional analyses often focus on primary and secondary structures, which may not fully capture complex protein interactions. Here we introduce InteracTor, a novel toolkit that extracts multimodal features from protein three-dimensional (3D) structures, including interatomic interactions like hydrogen bonds, van der Waals forces, and hydrophobic contacts. By integrating eXplainable Artificial Intelligence (XAI) techniques, we quantified the importance of the extracted features in the classification of protein structural and functional families. InteracTor's interpref features enable mechanistic insights into the determinants of protein structure, function, and dynamics, offering a transparent means to assess their predictive power within machine learning models. Interatomic interaction features extracted by InteracTor demonstrated superior predictive power for protein family classification compared to features based solely on primary or secondary structure, revealing the importance of considering specific tertiary contacts in computational protein analysis. This work provides a robust framework for future studies aiming to enhance the capabilities of models for protein function prediction and drug discovery.

  PublisherDOI

• Tar Spot on Maize: Impact of Soil Types and Environmental Conditions on the Survival of Phyllachora maydis in the Subtropical Climate of Florida

  Journal of Fungi · 2025-06-11

  articleOpen access

  Tar spot, caused by Phyllachora maydis, is an established maize disease in the Midwest of the United States but remains an emerging concern in Florida. While this pathogen can overwinter on plant residue, its survival in Florida’s subtropical environment is not well understood. This study evaluated how environmental factors affect the germination of P. maydis ascospores and stroma integrity. Symptomatic maize leaves were incubated under four conditions: Histosol soil (muck), Krome soil (rocky), 4 °C, and 23 °C. Extensive leaf decomposition occurred in both soil types, with most plant material degraded after eight weeks, while the stroma maintained its structure. Despite this, ascospore germination declined across all conditions. After eight weeks, ascospores incubated at 4 °C retained 25% viability, while those at 23 °C had the lowest germination (0.7%). Ascospores from leaves buried in soil exhibited low viability (1–6%), with no significant differences between soil types (p=0.9944). Weather analysis revealed that increased temperature reduced germination rates, while higher humidity enhanced them. These findings suggest that P. maydis displays limited survivability under Florida-like conditions, with germination rates declining over time. Therefore, cultural practices such as tillage, already employed by corn producers in Florida, may be effective in reducing sources of P. maydis inoculum.

  PublisherOA PDFDOI

• 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

• Tropical potato breeding: population structure, genetic diversity and putative regions under selection in a Brazilian tetraploid potato germplasm

  Research Square · 2025-06-17

  preprintOpen access
  PublisherOA PDFDOI

• Pathobiome Analyses Reveal Structural Changes in Maize Microbiomes Associated with <i>Phyllachora maydis</i> and Tar Spot Disease

  Phytobiomes Journal · 2025-06-13 · 2 citations

  articleOpen access

  Pathobiomes, the complex microbial communities associated with plant diseases, play a crucial role in shaping host–pathogen interactions. In crops such as maize, understanding these microbial dynamics is essential for managing diseases such as tar spot, caused by the fungus Phyllachora maydis. Thus, the objectives of this study were to investigate the mycobiome composition associated with tar spot disease in corn and to evaluate the genetic diversity of P. maydis in Florida. Amplicon sequencing of the internal transcribed spacer (ITS) region revealed 1,267 unique amplicon sequence variants (ASVs) across asymptomatic and symptomatic (tar spot stroma) maize tissues, with Ascomycota dominating both tissue types. Although the overall fungal diversity was similar between symptomatic and asymptomatic tissues, P. maydis was significantly more abundant in symptomatic samples. Key taxa, such as Fusarium and Epicoccum, were enriched in tar spot lesions, contributing to a distinct fungal community structure. Co-occurrence network analysis further demonstrated a more complex fungal interaction network in tar spot-affected tissues, suggesting the importance of Fusarium, Curvularia, and Phaeosphaeria, among others, in shaping these interactions. Low genetic diversity within the P. maydis population in Florida was confirmed based on nucleotide diversity and phylogenetic analysis of 16 ASVs and 88 individual isolates collected from single tar spots across different fields during 2022 and 2023, showing minimal nucleotide variations across the ITS, large subunit, and small subunit regions. These findings enhance our understanding of the fungal community dynamics and P. maydis population structure in tar spot disease. By framing these dynamics within a pathobiome perspective, this study offers insights that could inform future microbiome-based management strategies. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

  PublisherOA PDFDOI

• Genetic insights into non-additive effects in tetraploid potato breeding

  Euphytica · 2025-05-21

  article
  PublisherDOI

• Association mapping of haploid male fertility in sweet corn

  Theoretical and Applied Genetics · 2025-04-16 · 1 citations

  article
  PublisherDOI

Frequent coauthors

• Matias Kirst

  University of Florida

  37 shared

• Patricio R. Muñoz

  University of Florida

  35 shared

• Luís Felipe V. Ferrão

  University of Florida

  15 shared

• Leandro G. Neves

  15 shared

• Marcos Deon Vilela de Resende

  Universidade Federal de Viçosa

  15 shared

• Marco Antônio Peixoto

  University of Florida

  11 shared

• Leonardo Lopes Bhering

  Universidade Federal de Viçosa

  10 shared

• M. D. V. de Resende

  Brazilian Agricultural Research Corporation

  10 shared

Labs

• Marcio Resende LabPI