About

Collins Bugingo is an Assistant Professor in the Horticulture Section within the School of Integrative Plant Science at Cornell AgriTech, Geneva, N.Y. His role involves advancing seed biology and technology to strengthen agriculture, seed systems, and food security. He is part of the Seed Biology & Technology Program, which focuses on improving seed health science from molecules to cropping systems. His work is aligned with the program's goal of integrating seed health science into digital agriculture and addressing stakeholder needs in seed systems.

Research topics

• Biology
• Horticulture
• Botany
• Agronomy
• Medicine
• Veterinary medicine

Selected publications

• Advances in Seed Health Testing: Integrating Molecular Diagnostics, Imaging, and AI for Enhanced Quality Assurance

  Seeds · 2026-02-23

  articleOpen access1st authorCorresponding

  Seed health testing is a cornerstone of global food security, yet traditional diagnostic workflows often struggle to balance speed, sensitivity, and regulatory confidence under low-prevalence and heterogeneous seed lot conditions. This review synthesizes recent advances in molecular diagnostics (PCR, qPCR, LAMP, and digital PCR), non-destructive imaging technologies (hyperspectral, X-ray, and thermal imaging), and data-driven analytical approaches for pathogen detection in seeds. Emphasis is placed on the practical integration of these tools within high-throughput, ISO/IEC 17025-compliant laboratory workflows, highlighting their respective strengths, limitations, and roles in risk-based decision-making. Comparative discussions address cost, sensitivity, turnaround time, and field deployability across diagnostic platforms, supported by crop- and pathogen-specific examples. Emerging approaches such as CRISPR-based biosensing, advanced sequencing, and imaging-assisted analytics are discussed in the context of validation, regulatory acceptance, and operational feasibility. By focusing on implementation rather than conceptual frameworks, this review provides a pragmatic reference for laboratories, regulators, and seed companies seeking to modernize seed health testing while safeguarding trade integrity and biosecurity.

  PublisherOA PDFDOI

• Optimizing Fungicide Seed Treatments for Early Foliar Disease Management in Wheat Under Northern Great Plains Conditions

  Agronomy · 2025-01-24 · 4 citations

  articleOpen access1st authorCorresponding

  Tan spot (Pyrenophora tritici-repentis) and stripe rust (Puccinia striiformis f. sp. tritici) are major foliar diseases of wheat, causing significant yield losses globally. This study evaluated the efficacy of fungicide seed treatments in managing these diseases during early growth stages under greenhouse, growth chamber, and field conditions in the Northern Great Plains. Winter and spring wheat cultivars were treated with pyraclostrobin or combinations of thiamethoxam, difenoconazole, mefenoxam, fludioxonil, and sedaxane, among others. Greenhouse and growth chamber plants were inoculated with the respective pathogens, while field trials relied on natural inoculum. Fungicide treatments significantly reduced stripe rust severity (up to 36%) (p ≤ 0.05) and moderately reduced tan spot severity during early growth stages (15–20%). Treated plants demonstrated a 30–40% improvement in plant vigor, and a 25–50% increase in winter survival. Additionally, grain yield in treated plots increased by 25–50% (p ≤ 0.05), with test weight and protein content improving by 10% and 15%, respectively. These findings demonstrate the potential of fungicide seed treatments as an integrated pest (or pathogen) management (IPM) strategy to enhance early foliar disease control and wheat productivity.

  PublisherOA PDFDOI

• Bittersweet Challenges: Postharvest Disease Management in Sugarbeet and Sweetpotato

  Plant Disease · 2025-03-26 · 2 citations

  article

  Root crops like sugarbeet and sweetpotato possess an aggregated value that sets them apart from other crops. This aggregated value includes not only their economic importance but also their high nutritional content, which can enhance global food security. However, the economic and nutritional value of these crops is significantly compromised by postharvest diseases, presenting major socioeconomic challenges. Postharvest diseases, caused by various fungal and bacterial pathogens, affect crops during field growth, harvest, handling, and storage. Addressing these challenges requires improving several key aspects of disease management that are often lacking in postharvest pathosystems. These aspects include but are not limited to diagnostic methodologies, cultural practices, chemical control, host resistance, and pathogen monitoring, among others. Emerging technologies and strategies from various fields offer promising solutions to these challenges. In this manuscript, we review new approaches to address common challenges in postharvest diseases of sugarbeet and sweetpotato. This review highlights important considerations for the implementation, modification, and creation of new approaches to maintain or increase the value of these commodities, which are threatened by postharvest diseases.

  PublisherDOI

• From Morphology to Multi-Omics: A New Age of Fusarium Research

  Pathogens · 2025-08-01 · 12 citations

  reviewOpen access1st authorCorresponding

  The Fusarium genus includes some of the most economically and ecologically impactful fungal pathogens affecting global agriculture and human health. Over the past 15 years, rapid advances in molecular biology, genomics, and diagnostic technologies have reshaped our understanding of Fusarium taxonomy, host–pathogen dynamics, mycotoxin biosynthesis, and disease management. This review synthesizes key developments in these areas, focusing on agriculturally important Fusarium species complexes such as the Fusarium oxysporum species complex (FOSC), Fusarium graminearum species complex (FGSC), and a discussion on emerging lineages such as Neocosmospora. We explore recent shifts in species delimitation, functional genomics, and the molecular architecture of pathogenicity. In addition, we examine the global burden of Fusarium-induced mycotoxins by examining their prevalence in three of the world’s most widely consumed staple crops: maize, wheat, and rice. Last, we also evaluate contemporary management strategies, including molecular diagnostics, host resistance, and integrated disease control, positioning this review as a roadmap for future research and practical solutions in Fusarium-related disease and mycotoxin management. By weaving together morphological insights and cutting-edge multi-omics tools, this review captures the transition into a new era of Fusarium research where integrated, high-resolution approaches are transforming diagnosis, classification, and management.

  PublisherDOI

• From Morphology to Multi-Omics: A New Age of Fusarium Research

  Preprints.org · 2025-07-01 · 4 citations

  preprintOpen access1st authorCorresponding

  The Fusarium genus includes some of the most economically and ecologically impactful fungal pathogens affecting global agriculture and human health. Over the past 15 years, rapid advances in molecular biology, genomics, and diagnostic technologies have re-shaped our understanding of Fusarium taxonomy, host-pathogen dynamics, mycotoxin biosynthesis, and disease management. This review synthesizes key developments in these areas, focusing on agriculturally important Fusarium species complexes such as the Fusarium oxysporum species complex (FOSC), Fusarium graminearum species complex (FGSC), and a discussion on emerging lineages such as Neocosmospora. We explore recent shifts in species delimitation, functional genomics, and the molecular architecture of pathogenicity. In addition, we examine the global burden of Fusarium-induced myco-toxins by examining their prevalence in three of the world’s most widely consumed staple crops: maize, wheat, and rice. Last, we also evaluate contemporary management strategies, including molecular diagnostics, host resistance, and integrated disease con-trol, positioning this review as a roadmap for future research and practical solutions in Fusarium-related disease and mycotoxin management.

  PublisherOA PDFDOI

• Rotten to the Core: Challenges With Postharvest Disease Management of Fruit Crops

  Plant Disease · 2025-03-21 · 5 citations

  article

  Postharvest losses are attributed to fungal and bacterial diseases that contribute significantly to food loss and waste. In addition, some of the pathogens produce mycotoxins that contaminate processed food products made from culls and fruit that are not fit for the fresh market. Because consumers expect fresh fruit year-round, coupled with demands for high-quality and low residue levels, new research and tools are needed to combat decay. Hence, this review focuses on the latest advances in detection, control, and cultural practices that can be integrated or stand alone to help thwart rot caused by fungal and bacterial postharvest pathogens of fruit. Although we have chosen a holistic, integrated approach to cover various aspects of postharvest decay control, the manuscript focuses on specific high-value crops such as citrus, apple, avocado, and grapes. In these different crops, we discuss the significant impacts that have been made to understand aspects of pathogen biology, epidemiology, and control. Notwithstanding, postharvest disease management options for both conventional and organic markets are projected to continually increase and will require innovative solutions. We envision the integration of standard, conventional, and novel technologies with the help of artificial intelligence to move the pace of discovery forward that will manifest in paradigm shifting, long-term management solutions.

  PublisherDOI

• Advances in Seed Health Testing: Integrating Molecular, Imaging and AI-Based Diagnostics for Improved Seed Quality Assurance

  Preprints.org · 2025-12-04 · 1 citations

  preprintOpen access1st authorCorresponding

  Seed health testing is undergoing a rapid transformation as emerging technologies supplement and, in some cases, replace conventional diagnostic methods. This review synthesizes recent advances in molecular diagnostics (PCR, qPCR, LAMP, and metabarcoding), non-destructive imaging approaches (hyperspectral, multispectral and X-ray) and AI-assisted pattern recognition for pathogen detection in seeds. Emphasis is placed on integrating these tools into high-throughput seed quality programs, with case studies from vegetable, ornamental and field crop systems. We highlight current limitations in cost, regulatory alignment and global standardization, while identifying future opportunities for rapid, sensitive and field-deployable testing. This review aims to guide researchers, seed technologists and policymakers toward more efficient and reliable seed health assurance strategies.

  PublisherOA PDFDOI

• Microbial Biopesticides’ Efficacy in the Management of Tan Spot in Wheat

  Plant Disease · 2025-05-01

  article1st authorCorresponding

  Tan spot, caused by Pyrenophora tritici-repentis, poses a significant threat to global wheat production, causing yield losses of up to 50% in susceptible cultivars. This study evaluated the efficacy of active ingredients in commercially available microbial biopesticides for managing tan spot under in vitro and greenhouse conditions. In vitro studies demonstrated complete inhibition of mycelial growth by Bacillus subtilis, Bacillus amyloliquefaciens, and Streptomyces lydicus, whereas hydrogen peroxide + peroxyacetic acid exhibited partial inhibition. In greenhouse trials, microbial biopesticides significantly reduced tan spot severity by 10 to 28% compared with untreated controls. Bacillus species showed the highest efficacy, aligning with previous findings on their antagonistic properties and induction of systemic resistance. These results suggest that microbial biopesticides could potentially be used as a tan spot management tool in an integrated pest management program.

  PublisherDOI

• Identification of Fusarium spp. Associated with Chickpea Root Rot in Montana

  Agriculture · 2024 · 7 citations

  • Biology
  • Veterinary medicine
  • Horticulture

  Root rot caused by Fusarium spp. is a significant issue in the chickpea-growing regions of Montana. The specific Fusarium species responsible for the disease and their prevalence remain uncertain. A survey was conducted in 2020 and 2021 to identify Montana’s Fusarium species associated with chickpea. Four hundred and twenty-six Fusarium isolates were recovered from symptomatic chickpea roots across ten counties in the state. Isolates were identified by comparing translation elongation factor 1-α (TEF1-α) sequences in the FUSARIUM-ID database. Among the recovered isolates, Fusarium oxysporum was the most prevalent species (33%), followed by F. acuminatum (21%), F. avenaceum (15%), F. redolens (14%), F. culmorum (6%), F. sporotrichioides (6%), Neocosmospora solani (6%), F. equiseti (2%), F. torulosum (0.9%), F. gamsii (0.8%), F. proliferatum (0.2%), F. pseudograminearum (0.2%), and F. brachygibbosum (0.1%). The aggressiveness of a subset of 51 isolates representing various Fusarium spp. was tested on chickpea cv. ‘CDC Frontier’. A non-parametric variance analysis conducted on disease severity ranks indicated that F. avenaceum isolates were highly aggressive. This study reports for the first time that F. gamsii, F. proliferatum and F. brachygibbosum are causal agents of root rot in chickpea in the United States. This knowledge is invaluable for making informed decisions regarding crop rotation, disease management, and developing resistant chickpea varieties against economically significant Fusarium pathogens.

  PublisherOA PDFDOI

• Optimizing Fungicide Seed Treatments for Early Foliar Disease Management in Wheat under Northern Great Plains Conditions

  Preprints.org · 2024-11-29

  preprintOpen access1st authorCorresponding

  Tan spot (Pyrenophora tritici-repentis) and stripe rust (Puccinia striiformis f. sp. tritici) are major foliar diseases of wheat, causing significant yield losses globally. This study evaluated the efficacy of fungicide seed treatments in managing these diseases during early growth stages under greenhouse, growth chamber, and field conditions in the Northern Great Plains. Winter and spring wheat cultivars were treated with pyraclostrobin or combinations of thiamethoxam, difenoconazole, mefenoxam, fludioxonil, and sedaxane, among others. Greenhouse and growth chamber plants were inoculated with the respective pathogens, while field trials relied on natural inoculum. Fungicide treatments significantly reduced stripe rust severity (up to 36%) and moderately reduced tan spot severity during early growth stages. Treated plants showed improved plant vigor, winter survival, and grain yield, with an increase in test weight and protein content compared to untreated controls. These findings demonstrate the potential of fungicide seed treatments as an integrated pest management strategy to enhance early foliar disease control and wheat productivity.

  PublisherDOI

Frequent coauthors

• Monica Brelsford

  Montana State University

  6 shared

• Mary Burrows

  Montana State University

  6 shared

• Kevin McPhee

  Montana State University

  3 shared

• Swarnalatha Moparthi

  North Carolina State University

  2 shared

• Shaukat Ali

  South Dakota State University

  1 shared

• Oscar Pérez‐Hernández

  Northwest Missouri State University

  1 shared

• Dalitso Yabwalo

  South Dakota State University

  1 shared

• Michael Bradshaw

  North Carolina State University

  1 shared

Labs

• Seed Biology & Technology ProgramPI

Education

• Plant Science Plant Pathology, Plant Science Plant Pathology

  Montana State University

  2022