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Plant Breeding Consortium

Computing Skills in Plant Breeding Workshop

Organized by the NC State University Plant Breeding Consortium and Tree Improvement Program.

Registration and Deadline

The registration cost includes two coffee breaks, five lunches (Monday through Friday), one dinner (Wednesday), and electronic copies of handouts of lectures. The registration is limited to 80 people. A maximum of 30 students are accepted to the workshop.

Prerequisites: You will need to bring your laptop each day and have familiarity with linear mixed models and R programming.

Save money when you register by Friday, Jan. 30, 2026. Early registration for graduate students is $500 and for others $1250. The cancellation deadline is Friday, Feb. 20, 2026, and includes a $40 fee.

The regular registration deadline is Friday, Feb. 27, 2026. For graduate students, it is $600 and for others, $1500. The cancellation deadline is Friday, Feb. 20, 2026, and includes a $40 fee.

Professionals Registration

Early registration for plant breeding professionals is $1250 and regular registration is $1500. The cancellation deadline is Friday, Feb. 20, 2026, and includes a $40 fee.

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Student, Postdoc, and Visiting Scholar Registration

Early registration for students, postdocs, and visiting scholars is $500. Regular registration is $600. The cancellation deadline is Friday, Feb. 20, 2026, and includes a $40 fee.

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Locations

Overnight Lodging

Ramada Raleigh
(approximately 4 miles or 15 minutes drive from campus)
1520 Blue Ridge Rd, Raleigh, NC 27607
Phone: (919) 832-4100
ramadaraleigh.com
$89 per night plus taxes

Be sure to mention that you are participating in an NC State workshop in order to get the discounted rate.

Aloft Raleigh
(approximately 1.7 miles or 10 minutes drive)
2100 Hillsborough Street, Raleigh, North Carolina, USA, 27607
Phone: (919) 828-9900
Book your room

Parking on Campus

All individuals parking on campus must acquire a parking permit, which is linked to the vehicle’s license plate. If you are renting a car, please wait to purchase a parking permit until you have the license plate information. Permits can be purchased online or in person at the Transportation Office. Please note that everything is electronic; there is no physical permit required for display.

Why should you attend the workshop?

Computing skills are essential for plant breeders in various aspects of your work, enabling you to manage large genetic, phenotypic, and environmental datasets and conduct complex statistical analyses for decision-making. During this five-day, hands-on workshop, you will master computing skills that enhance efficiency, accuracy, and innovation in plant breeding, ultimately leading to the development of improved crop varieties.

  • Gain an understanding of theoretical concepts.
  • Develop practical skills through hands-on experience.
  • Enhanced collaboration and teamwork with your fellow participants.

Teaching Format:

Introduction and Theory (1 hour):

  • Research teams present the foundational concepts.
  • Cover key theories, principles, and methodologies.
  • Provide context and session objectives.

Demos (1 hour):

  • Present demonstrations to illustrate theoretical concepts.
  • Use practical examples and applications to enhance understanding.
  • Encourage interactive engagement and ask participants questions.

Practice Session (2 hours):

  • Participants work in small teams to apply the concepts they have learned.
  • Provide sample data sets and practical exercises.
  • Encourage collaboration, problem-solving, and critical thinking.
  • Faculty, post-docs, and students provide guidance and support as needed.

Software:

A free ASReml-R license will be available to all participants. Any additional software and computing requirements will be communicated two weeks before the workshop.

Workshop Modules:

Module 1: Experimental Designs in Plant Breeding

Instructor: Jonathan Stallrich
Monday, Mar 16, 2026, 13:00-17:00

This module provides an overview of proper randomization and analysis of classical experimental designs used in plant breeding. It covers experiments with one or multiple treatment factors, including both fixed and random effects. Blocking factors are introduced, with a discussion of how blocking influences randomization and statistical efficiency. The module concludes with an introduction to split-plot designs. The R package agricolae will be used throughout to demonstrate practical approaches to experimental layout and randomization. 

Module 2: Exploring Linear Mixed Models

Instructor: Christian Maltecca
Tuesday, Mar 17, 2026, 8:30-12:00

This module introduces linear mixed models as a cornerstone of data analysis in plant and animal breeding. Participants will learn both the theoretical foundations and practical applications of mixed models using ASReml. The focus is on plant breeding datasets, with skills that provide a foundation for advanced topics such as multi-environment and multi-year trials and genomic selection models.

Module 3: Analysis of Multi-Environment Trials (MET)

Instructor: James Holland
Tuesday, Mar 17, 2026, 13:00-17:00

This module provides comprehensive coverage of analyzing multi-environment and multi-year trial data to predict the genetic merit of individuals for selection. It will describe fitting a range of variance-covariance structures to capture complex patterns in GxE interactions and within-environment residual effects. Participants will learn how to estimate heritability and obtain predictions from complex genotype-by-environment (G×E) covariance structures using ASReml.

Modules 4 & 5: Image Analysis for High-Throughput Phenotyping and AI

Instructors: Jing Zhang, Nick Garrity, Alexis Suero Mirabal, Caiwang Zheng
Wednesday, Mar 18, 2026, 8:30 – 17:00

High-throughput phenotyping generates large and complex datasets, including images collected from field and controlled environments. These modules introduce software tools and workflows for efficient image processing and trait extraction in plant breeding. Participants will gain practical skills to streamline phenotypic data collection and integrate image-based traits into breeding and selection pipelines, including applications of machine learning and AI.

Module 6: Marker-Assisted Selection

Instructors: Jeffrey Dunne, Ryan Andres
Thursday, Mar 19, 2026, 8:30-12:00

This module covers the principles and applications of marker-assisted selection, with emphasis on traits controlled by major genes, such as disease resistance. Participants will learn how to integrate validated major-effect markers identified through linkage mapping or GWAS into routine breeding and selection decisions. This module will introduce Python protocol development for the Opentrons OT-2 robot and developing custom web-based breeding applications using R Shiny and Plotly Dash.

Modules 7 & 8: Genomic Selection-Theory and Practice

Instructors: Fikret Isik, Roberto Fritsche Neto, Nasir Shalizi
Thursday, Mar 19, 2026, 13:00-17:00
Friday,  Mar 20, 2026, 8:30-12:00

These modules provide an in-depth treatment of the theory and practical implementation of genomic selection, highlighting how it differs from conventional mixed-model prediction based on pedigree alone. Topics include the construction and scaling of pedigree- and marker-based relationship matrices, the integration of genomic and pedigree information in single-step and two-step GBLUP models, and the evaluation of prediction accuracy and bias. Real-world examples from both crop and forest tree breeding programs will be used to illustrate best practices and common challenges.

Sponsored by

BASF logo

BASF

Company Website

Sponsorship Opportunities

Platinum – $10,000

Recognition as an elite sponsor with the organization’s logo on the workshop registration page, event signage and program, and looping slideshow thanking sponsors; recognized at the evening reception and during welcoming remarks on Day 2; includes a sponsor table and four (3) workshop registrations.

Gold – $7,500

signage and program, and looping slideshow thanking sponsors; recognized at the evening reception on Day 1 and during welcoming remarks on Day 2; includes a sponsor table and three (2) conference registrations.

Silver – $5,000

Recognition with the organization’s logo on the conference registration page, event signage and program, and looping slideshow thanking sponsors; includes a sponsor table and two (1) conference registrations.

Bronze – $2,500

Recognition with the organization’s logo on the conference registration page, event signage and program, and looping slideshow thanking sponsors.

Friend/Student – $1,000

Recognition as a sponsor on the conference registration page and in the event program.

Important Information for ALL Sponsorship Levels

  • All logos must be high resolution for website and print (EPS) and provided within two weeks of any signed sponsorship agreement.  Logos will be sized and placed accordingly based on sponsorship level, depending on use.
  • It may take up to five business days to upload material onto the workshop website.
  • Recognition in any promotional material, per sponsorship package, is subject to pre-determined deadlines.
  • Sponsorship registration and payment must be completed before recognition is received.
  • Sponsors should upload their logo at https://forms.gle/7rDiC75sh9cUkwD8A or email the file to jdsitzes@ncsu.edu

Questions

For questions regarding registration and logistics, contact Janice Sitzes (jdsitzes@ncsu.edu). For all other questions, contact Dr. Fikret Isik (fisik@ncsu.edu).

Organizing Committee

  • Fikret Isik, Chair, Co-Director NCSU Tree Improvement Program, College of Natural Resources
  • Carlos Iglesias, Director of the Plant Breeding Consortium, College of Agriculture & Life Sciences
  • Kathleen Denya, Director of Innovation Partnerships, Plant Sciences Initiative
  • Gina Brown-Guedira, USDA Professor, Department of Crop and Soil Sciences
  • Jeffrey Dunne, Associate Professor, Department of Crop and Soil Sciences
  • Grant Billings, Bioinformatics doctoral student; Genomic Sciences Program