Introduction to BIGapp for Plant Breeding
Workshop Materials
Welcome! This hands-on workshop introduces BIGapp — a free, web-based tool for analyzing genomic data in plant breeding programs. No coding required.
Who Is This For?
This workshop is designed for:
- Undergraduate and graduate students in plant sciences
- Researchers working with genomic data in breeding programs
- Anyone interested in applying genomics to crop improvement
No prior experience with R or bioinformatics is required. BIGapp provides a point-and-click interface for analyses that traditionally require programming skills.
What You’ll Learn
By the end of this workshop, you’ll understand:
- Why genomic data matters for breeding decisions
- How to filter and quality-check your genotyping data
- What population structure is and how to visualize it with PCA
- How GWAS works to find markers associated with traits
More importantly, you’ll be able to do all of this yourself using BIGapp.
Workshop Overview
Duration: 2 hours
Format: Live demonstration + hands-on practice
Schedule
| Time | Topic |
|---|---|
| 0:00 - 0:10 | Welcome & Setup Check |
| 0:10 - 0:25 | Why Genomics in Breeding? — The big picture |
| 0:25 - 0:50 | Module 1: Data Import & Quality Control |
| 0:50 - 1:00 | Short Break |
| 1:00 - 1:25 | Module 2: Population Structure & PCA |
| 1:25 - 1:55 | Module 3: GWAS — Finding marker-trait associations |
| 1:55 - 2:00 | Wrap-up & Questions |
If you finish early or want to continue learning after the workshop, check out Module 4: Genomic Selection — predicting breeding values from markers.
Before the Workshop
We’ll use the online version of BIGapp, so you just need a web browser and internet connection.
Bookmark this link: big-demo.shinyapps.io/bigapp-main
If you’d like to install BIGapp locally for use after the workshop, see the Setup Instructions.
Materials
| Resource | Description |
|---|---|
| Setup Instructions | Optional local installation guide |
| Module 1: Data & QC | Import data, filter SNPs and samples |
| Module 2: Population Structure | Understand and run PCA |
| Module 3: GWAS | Find marker-trait associations |
| Module 4: Genomic Selection | (Optional) Predict breeding values |
Workshop Data
We’ll use a simulated Atlantic Giant Pumpkin diversity panel — 200 samples from breeding programs across the US, with 1,200 SNPs.
Download these files before the workshop:
| File | Description |
|---|---|
| Genotype VCF | Genotype data (3 MB) |
| Phenotypes CSV | Sample info + fruit weight trait |
| Dataset README | Full dataset documentation |
This dataset simulates realistic GWAS scenarios: population structure from geographic regions (Eastern, Midwest, Western US) and a QTL for fruit weight on Chromosome 4.
Questions?
- During the workshop: Raise your hand or type in the chat
- After the workshop: Open an issue on GitHub or email me
Additional Resources
New to genomics in plant breeding? These resources provide more background:
- BIGapp Tutorials on Scribehow — Step-by-step guides with screenshots