This workshop will provide training around the experimental design and multiple applications of Genotyping by Sequencing (GBS) in plants. In addition, detailed computational analysis of GBS data and resources will be explored. Genomic analysis tools for GBS, such as Tassel, iPyrad, STACKS, as well as publicly available resources for plant data process and application will we implemented during the workshop.

The analysis of genomic variation is an essential part of plant genetics and crop improvement programs. DNA polymorphisms can be directly related to phenotype differences, be genetically linked to its causative factor, or indicate relationships between individuals in populations. Over the last years, the use of genotyping has enabled the characterization and mapping of genes and metabolic pathways in plants as well as the study of species diversity and evolution, marker-assisted selection (MAS), germplasm characterization and seed purity. Genotyping by sequencing (GBS) is a high throughput method to identify and genotype, at the same time, molecular markers as part of breeding activities, genetic mapping, and population genomics. Another advantage is that this method can be applied to organisms without reference genome and imputation of SNPs can be done as part of haplotype blocks. It was first published in 2011 and since then multiple crops have been improved including maize, potato, and rice. 

Who is this course for?

This course is aimed at wet-lab researchers at within Latin America undertaking plant breeding and population genetics interested in applying next-generation sequencing to screen individuals.

Please note this course will be taught in English, however the trainers are fluent in either Spanish or Portuguese, and can offer language support where feasible.

A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form.

Knowledge in UNIX and NGS technologies is required. Therefore, these free resources should be studied beforehand: 

Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix

Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training 

Basic R concept tutorials: www.r-tutor.com/r-introduction 

You may also find this video overview of GBS useful.

What will I learn?

Learning outcomes

After this course you should be able to:

• Plan and design your own GBS experiment for plant material
• Assess NGS data for GBS applications 
• Implement pipelines for analyzing GBS data with and without reference genomes
• Describe the differences in data analysis when working with polyploids
• Use public EMBL databases for plant genomics

Trainers

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.

The registration fee includes:

• Use of a computer in the Training Room at Educación Continua throughout the course
• Tea/coffee,lunch and dinner for the duration of the course
• Course dinner on August 8th
• Course materials provided
• Course certificate

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