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: 

Monday 10 June 2019

Application deadline: 

Monday 01 July 2019

Participation: 

Open application with selection

Contact: 

Laura Brenes Guillén, Andrés Gatica-Arias

Registration fee: 

$30000 CRC

Registration closed

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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.

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.

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

Programme

Day 1 – Tuesday 6 August
08:00-08:30 Welcome and instructions Andrés Gatica
08:30-09:00 Introduction and CABANA presentation Andrés Gatica
09:00-10:00 Methodologies for genotyping and NGS overview TBD
10:00-10:30 Break
10:30-11:30 Trainee flash talks Organizers
11:30-12:30 GBS methods overview Bradley Till
12:30-13:30 Lunch
13:30-15:30 Planning a GBS experiment: the technology and lab Carla Filippi
15:30-16:00 Break and poster session
16:00-17:30 Review of computational skills Bradley Till
17:30 End of day 1  
Day 2 – Wednesday 7th August
08:30-09:00 Q&A of previous day  
09:00-10:30 Working with model organisms Bradley Till
10:30-11:00 Break and poster session
11:00-12:30 Working with non model organisms Bradley Till
12:30-13:30 Lunch
13:30-14:30 Stacks (Catchen et al 2013) - SNP calling for species with reference genome Carla Filippi
14:30-15:30 Stacks (Catchen et al 2013) - SNP calling for species with no reference genome Carla Filippi
15:30-16:00 Break and poster session
16:00-17:30 Imputation strategies 1 Gabriela Merino
17:30 End of day 2  
Day 3 – Thursday 8th August
08:30-09:00 Q&A of previous day  
09:00-10:30 Imputation strategies 2 Gabriela Merino
10:30-11:00 Break
11:00-12:30 EBI resources for accessing Plant data Rebeca Campos
12:30-13:30 Lunch
13:30-15:00 Applications: Population genomics analysis, Genomic Selection accuracy (comparing GBS data vs SNP-chip panels)  Carla Filippi
15:00-15:30 Break and poster session
15:30-16:30 Applications: GWAS, Genetic Map construction, GWAS and QTL mapping Carla Filippi
16:30-17:30 PCR amplicon sequencing Bradley Till
17:30 End of day 3  
Day 4 – Friday 9th August
08:30-09:00 Q&A of previous day  
09:00-10:30 Practical application: tGBS and mapping of QTLs in papaya  Luis Barboza
10:30-11:00 Break
11:00-12:30 Self-paced practical All trainers
12:30-12:45 Course Wrap-up and feedback Rebeca Campos, Andrés Gatica
12:45 Lunch