Please note this course was postponed in 2020 due to the COVID-19 pandemic and will take place virtually in 2021.

This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping. During the course participants will learn about genotyping experimental design, variant calling, comparative genomics using Ensembl, analyse variation data with Ensembl Variant Effect Predictor and the European Variation Archive and explore concepts of genome wide association studies (GWAS).  The content will explain how to make use of existing public data, retrieve, submit and share your data with the community.

It will also provide training on using R in genomics applications for crop genotyping. Trainers will cover the basics of diversity analysis using R, before analyzing various genomes to assess diversity. This will include hierarchical clustering, correlating genomic data with geographic and phenotypic information and investigating gene-phenotype relationships and microsatellites. This course will use genomic data of wheat, maize and potato as training datasets throughout the week. The course will be delivered through a combination of hands-on training sessions and lectures.

Please note: The course will use genomic data from crop plant species throughout the week. It will not explore in detail methods for assembling genomes.

Who is this course for?

This course is aimed at researchers at graduate level upwards within Latin America who are working with and/or generating their own crop genomic data or who are working on genotyping technologies, including data analysis software development. 

Prerequisites: Basic computational or previous bioinformatics experience is required for this workshop, such as basic commands in R. Undergraduate-level knowledge of plant biology would be an advantage. 

Please note this course will be taught in English. There will be assistants fluent in Spanish who can offer language support where feasible.

What will I learn?

Learning outcomes

By the end of this course, participants should be able to:

• Describe how to design a crop genotyping experiment
• Conduct variant calling and search for a variety of crop genomic motifs such as SSRs and indels 
• Use Ensembl for comparative analysis to explore plant genomes
• Access plant variation data from public resources and use appropriate tools to analyse variation
• Input and study genomics data using R to evaluate genomic diversity
• Select the best method to investigate genomic diversity

Course content

During this course you will learn about: 

• How to design sequence-based genotyping experiments and conduct variant calling
• Ensembl tools for browsing plant genomes and variant data
• Using R to assess crop diversity
• Genome wide association studies (GWAS)

Trainers

Please note this course was postponed in 2020 due to the COVID-19 pandemic and will take place virtually in 2021.

In order to be considered for a place on this course applicants must complete the online application form.

Incomplete applications will NOT be considered. 

If you have any queries about the registration process please email Guilherme Oliveira and Piv Gopalasingam.

There will be a maximum of 30 participants on this course and registration is dependent on selection after successful completion of the application process

Applications will close on 9th February 2020 at 23:30 (GMT)