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Workshops

The workshops will  take place in person on Monday June 15th, 2026.

 

Workshops are free for NAFGS members. Additional US $75 fees apply to non-members.​

TreeSnap

Instructors and organizers

Fiorence Caldwell

University of Tennessee Knoxville

Meg Staton

University of Tennessee Knoxville

Time: 9:00 AM - 10:00 AM

Location: La Laurentienne Building

Description

Community science engagement can strengthen forest research by expanding geographic coverage, increasing the frequency of observations, and enabling early detection of forest health threats. Successfully integrating non-professional scientists requires intuitive, accessible platforms that lower barriers to participation while maintaining data quality. We have developed TreeSnap, a mobile application that encourages the public to locate and document trees affected by pests and diseases, including ash, chestnut, beech, hemlock, and elm. Using the free app, volunteers submit GPS locations, photographs, and trait information relevant to ongoing tree research. Species-specific, customizable questions guide data collection, while the companion TreeSnap website allows researchers to sort and filter submissions and access user observations efficiently. With more than 3,400 active users and over 26,000 tagged trees, TreeSnap has become a valuable tool for identifying candidate trees with potential genetic resistance. In parallel, we are developing TreeSnap Plots, a new software system for long-term plot monitoring that enables participants to report tree survival and health over multiple years, with an initial focus on hemlock species threatened by hemlock woolly adelgid. This workshop will focus on how to use these digital tools in forest research projects to generate high-value datasets while sustaining strong participant engagement.

* Language of Instruction: English

CartograPlant

CartograPlant: A Web Tool for the Storage, Integration, and Analysis of Global Georeferenced Plant Genotypes, Phenotypes, and Environmental Data

Instructors and organizers

Meghan Myles

University of Connecticut

Brandon Lind

University of Connecticut

Gabriel Barrett

University of Connecticut

Time: 10:00 AM - 12:00 PM

Location: La Laurentienne Building

Description

Talk 1 - Welcoming Remarks This session will demonstrate the use of CartograPlant (https://cartograplant.org/), a web application which facilitates access to genotypic, phenotypic, and environmental data about globally georeferenced plants. It contains three talks: the first introduces CartograPlant as a whole; the second describes the process of data ingestion, ontology mapping, and integration; and the third describes its analytical and data retrieval capabilities. CartograPlant supports the community need for FAIR (Findable, Accessible, Interoperable, and Reusable) plant data storage and access. Currently, CartograPlant enables access to genetic and phenotypic data for 1,160 unique plant species across 635 genera in addition to 964 global, North American, and regional environmental layers. Together, TPPS and CartograPlant work to increase data reuse. This framework itself is continually updated, ensuring that its database structure and tools consistently meet the evolving storage and analysis needs of researchers, conservationists, land managers, and plant breeders as they assess global change, support resilient breeding, and guide informed agricultural and ecosystem management decisions. Talk 2 - FAIR Data Submission and Integration for Plant Population Studies This session will describe the process of data submission to CartograPlant and post-submission automated processes. Data ingestion is completed with the Tripal Plant Population Submit (TPPS) pipeline, a dynamic set of questions which aim to collect data consistent with the Minimum Information About Plant Phenotyping Experiments (MIAPPE) guidelines. Upon data submission, vocabulary terms are mapped to common ontology frameworks including the Sequence Ontology (SO) and the Phenotype And Trait Ontology (PATO). Such ontology mapping permits the multidimensional integration of datasets generated across time and heterogeneous methodologies, enabling meta- and mega-analysis. Long-term data storage and Digital Object Identifier (DOI) generation are offered for eligible datasets. Talk 3 - Analytics for Plant Population Studies This session will include a demonstration of the analytical capabilities of CartograPlant. Following ingestion, data is made available for visualization, retrieval, and analysis through CartograPlant. Users can filter data by taxon, measured traits, marker type, region, and publication, enabling precise selection of genotypic, phenotypic, and environmental datasets. These modular filters facilitate downstream analyses such as population structure inference, genotype-environment associations, and genotype-trait associations. CartograPlant offers registered users free access to pre-built analytic pipelines and High-Performance Computing (HPC) resources, accessed through an intuitive Graphical User Interface (GUI). We will provide a demonstration of these capabilities and walk through this process with attendees. We will also prepare datasets to enable hands-on training, and will guide attendees through analyses in real time.

* Language of Instruction: English

An Introduction to Genomic Selection and GWAS in Forest Tree Breeding

Quantitative Genetics

Instructors and organizers

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Ogut_Funda_Quantitative_Genetics.jpg
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Patrick Lenz

Natural Resources Canada

Funda Ogut

Natural Resources Canada

Fikret Isik

North Carolina State University

With support from Simon Nadeau (NRCan) and Jean-Philippe Laverdière (NRCan)

Time:

Part 1: 9:00 AM - 12:00 PM 

Part 2: 1:30 PM - 4:30 PM 

Location: La Laurentienne Building

Description

Advances in genomics have transformed quantitative genetics by bridging classical theory with molecular biology and expanding its application in plant and animal breeding. Genome-wide DNA markers are now routinely combined with field data to predict genetic merit, improve selection efficiency, and better understand the genetic basis of complex traits in forest trees. Using examples from forest breeding programs in eastern Canada and the Southern USA, this workshop will focus on genomic selection and an overview of genome-wide association studies. Emphasis will be placed on building intuition around how these methods work, when they are most useful, and their key assumptions and limitations in long-lived, outcrossing species. The workshop is designed for students and early-career researchers. It combines short lectures with demonstrations of data analysis. Participants will gain practical experience with modern tools in forest genetics and tree breeding.

* Language of Instruction: English

Support offered in French

Demographic Modelling

Demographic Modelling of Forest Tree Species

Instructors and organizers

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Eduardo Mendoza-Maya

Universidad Nacional Autónoma de México

Juan Pablo Jaramillo-Correa

Universidad Nacional Autónoma de México

Time: 9:00 AM - 12:00 PM

Location: La Laurentienne Building

Description

Understanding how population expansions, collapses, or secondary contacts modify genetic diversity provides critical insights for the management, breeding and conservation of forest trees. In this workshop, we will explore basic concepts in population genetics/genomics, we will learn what is and how to estimate a site frequency spectrum (SFS), and we will discover how an SFS changes when a population grows, declines, or is submitted to strong selective forces. We will also examine examples from endangered Mexican conifers with demographic modelling tools and will exchange ideas regarding the use of these tools in forest management, conservation and breeding. This workshop is intended for students, technicians, postdocs, or early career scientists with limited knowledge of evolutionary/population genetics, but who have a broad interest in the use and preservation of genetic diversity. Although the main topics will be discussed in English, specific questions in French or Spanish will also be welcomed and addressed during the final discussion of the workshop.

* Language of Instruction: English

Support offered in Spanish and French

AI in Genomics

Instructors and organizers

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Jérôme Laroche

Université Laval

Julien Prunier

Université Laval

Time: 2:00 PM - 4:00 PM

Location: La Laurentienne Building

Description

Artificial Intelligence (AI) holds the promise of major societal advancements. Although AI has existed since the early days of computing, recent improvements in computer hardware have enabled the emergence of highly powerful modern AI systems. This evolution is happening so rapidly that many of us in genomics have not yet explored the potential of earlier AI tools that preceded Large Language Models (LLMs; e.g., ChatGPT), particularly machine learning (ML) methods. ML represents a paradigm shift in data analysis compared with traditional statistics and remains underused, partly due to challenges related to model interpretability. However, ML algorithms can solve complex problems and are highly transferable to decision-support tools. In addition, new approaches now enable the interpretation of complex models, which represents a turning point for AI trustworthiness and for advancing scientific knowledge. Genovalia is a Université Laval platform providing services in data storage, advanced genomic data analysis, and web application development for agriculture/forestry and environmental sciences. In this workshop, we will present the foundations of AI with a particular focus on ML concepts and methods. We will then use a demonstration dataset to illustrate the complete workflow, from genomic and phenotypic data to ML models integrated into a web application.

* Language of Instruction: English

Support offered in French

Metabarcoding

 Introduction to DNA Metabarcoding in Ecological Research

Instructors and organizers

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Escolástico-Ortiz_Dennis_Metabarcoding.jpg
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Najoua Mghazli

Natural Resources Canada and Université du Québec en Abitibi-Témiscamingue

Dennis A. Escolástico-Ortiz

Natural Resources Canada

Christine Martineau

Natural Resources Canada

Time: 1:30 PM - 4:30 PM

Location: La Laurentienne Building

Description

Understanding microbial communities in the environment is essential for advancing research in ecology, particularly regarding plant–microbe interactions. DNA metabarcoding has become a powerful tool for characterizing microbial communities, but its effective application relies on experimental design, appropriate laboratory methods, and rigorous data analysis. This lecture-based workshop introduces DNA metabarcoding for studying microbial communities found in environmental (e.g., soil) and biological samples (e.g., roots). This session will outline the fundamental steps to conduct a metabarcoding study, guiding participants through initial sampling strategies and sample preservation, essential molecular techniques, bioinformatics and subsequent data analysis. Illustrated by examples of microbial analyses drawn from ecological projects, the session will emphasize best practices, common pitfalls and methodological decisions that would help participants to design reproducible research. This session aims to provide a comprehensive overview of a complete metabarcoding workflow and its potential applications in plant ecology.

* Language of Instruction: English

Support offered in French

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