CABANA Workshop: Genotyping by Sequencing Applied to Plant Breeding

Date:

 Tuesday 6 Friday 9 August 2019

Venue: 

University of Costa Rica (UCR) - Ciudad universitaria Rodrigo Facio Brenes, San Pedro, San Jose, Costa Rica

Application opens: 

Friday 31 May 2019

Application deadline: 

Sunday 30 June 2019

Contact: 

Laura Brenes Guillén

Registration fee: 

18000 CRC

Course Overview

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. 
 

Audience

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.

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 

Learning outcomes

After this workshop 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
  • Practice the different applications of GBS data, mainly focused on plant breeding, conservation and genetics

Programme

This course is currently under development and full details about the course are not yet available.  Once the programme is confirmed we will post it here along with details on how to apply and registration costs.  If you would like to be informed when applications open for this course then please click on the “Register your interest” button above.