Flapjack takes global spotlight at Wheat Initiative online training sessions

“These workshops were a fantastic opportunity to showcase not only Flapjack, but the wide variety of free and open-source visualization, database, and decision support tools that we produce at the Hutton in support of breeders all around the globe”

The advantages of Flapjack, the James Hutton Institute’s multi-platform application providing interactive visualizations of high-throughput genotype data, were demonstrated at a recent workshop organised with the purpose of helping wheat breeders across the globe to modernise their molecular breeding skills.

The online event, sponsored by the Wheat Initiative with the CGIAR Excellence in Breeding Platform (EiB), and the International Maize and Wheat Improvement Center (CIMMYT), focused on training in three open-source tools used in molecular breeding: GOBii-GDM for genomic data management, Flapjack for data visualization and breeding analysis, and Galaxy for Genomic Selection. These tools help breeders make selections more quickly and precisely, and ultimately lead to more cost effective and efficient improvement of varieties.

The workshop series, “Transforming Wheat Breeding Through Integrated Data Management with GOBii and Analysis in Flapjack,” aims to benefit breeders from wheat-producing countries all over the world, with sessions over two different time zones – for US/Europe, and Australasia – spread out over 3 days to reduce “zoom fatigue.” Participants joined the first session from Australia, Canada, Ethiopia, France, India, Ireland, Italy, Morocco, Pakistan, Switzerland, Tunisia, the UK, and the United States.

The training team included: 

• Iain Milne from the James Hutton Institute, developer of the Flapjack genotyping visualization tool that includes analysis for pedigree verification, marker-assisted backcrossing and forward breeding
• Elizabeth Jones, EiB Adoption Lead and former GOBii project director
• Clay Sneller, wheat breeder at Ohio State University and major contributor towards training materials for important molecular breeding tools
• Carlos Ignacio, previously based at IRRI as a GOBii team member and a major contributor towards the design of Flapjack tools, and who is now working on a PhD in Genomic Selection at Ohio State University
• Star Gao, application specialist with GOBii and now a requirements analyst for the Enterprise Breeding System, and Andrew Kowalczyk, developer of the genotyping data QC tool DArTView at Diversity Arrays Technology, Australia.

Iain Milne, from the James Hutton Institute’s Information and Computational Sciences, said: “These workshops were a fantastic opportunity to showcase not only Flapjack, but the wide variety of free and open-source visualization, database, and decision support tools that we produce at the Hutton in support of breeders all around the globe.”

Many of the tools will be incorporated into Excellence in Breeding’s Enterprise Breeding System (EBS), a new integrated data management system being developed for CGIAR breeders. Elizabeth Jones also plans to design training modules for these molecular breeding tools that will be accessible to anyone through the EiB Toolbox.

In the meantime, the tools used in the workshop are all freely available, or logins are available upon request:

• DArtView
• Flapjack and training videos
• GOBii-GDM. Visit this site to request access or email ej245@cornell.edu
• Galaxy Genomic Selection.