CABANA Workshop: Analysis of Crop Genomics Data

Date:

 Monday 2 Friday 6 December 2019

Venue: 

Universidad de los Andes - UniAndes - Cra 1 Nº 18A - 12, 111711,  Bogota,  CUN, Colombia

Application opens: 

Thursday 25 July 2019

Application deadline: 

Sunday 29 September 2019

Participation: 

Open application with selection

Contact: 

Marco Cristancho, Derrin Crawte

Registration fee: 

$112000 COP

Course Overview

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.

 

Syllabus, Tools and Resources

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)

Audience

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, 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.
 

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

Programme

Day 1: Overview of genotyping, NGS, variant calling
Day 2: Ensembl Plants, Variant Effect Predictor, Expression Atlas, Pan-genome analysis
Day 3: R-gene identification and crop diversity analysis
Day 4: Crop diversity analysis (continued)
Day 5: GWAS

 

Day 1 – Monday 2 December 2019
08:30-09:00 Arrival, registration  
09:00-09:30 Welcome and introduction Marco Cristancho / Diana López
09:30-10:30 Methodologies for genotyping and NGS overview Diana López
10:30-11:00 Break
11:00-11:45 Methodologies for genotyping and NGS overview Diana López
11:45-12:30 Planning a genotyping experiment Diana López
12:30-14:00 Lunch
14:00-15:00 Whole genome variant calling: Strategies for SNP, small indels and SSR whole genome calling Carla Filippi
15:00-16:00 Structural Variant calling: Large insertions, deletions, translocations Carla Filippi
16:00-16:30 Break  
16:30-17:45 Introduction to the Ensembl Plants browser Bruno Contreras
17:45 End of day 1  
19:30 Dinner  
Day 2 – Tuesday 3 December 2019
08:30-10:00 VEP and Expression Atlas Bruno Contreras
10:00-10:30 Break
10:30-12:00 Retrieving data from Ensembl Compara Bruno Contreras
12:00-12:30 Interacting with Ensembl: requesting new genomes, annotations or variants Bruno Contreras
12:30-14:00 Lunch
14:00-16:00 Pan-genome Analysis Bruno Contreras
16:00-16:30 Break  
16:30-17:45 Pan-genome Analysis Bruno Contreras
17:45 End of day 2  
Day 3 – Wednesday 4 December 2019
08:30-10:00 R-genes identification and characterisation Carla Filippi
10:00-10:30 Break
10:30-12:00 Overview of R Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
12:00-13:30 Lunch
13:30-15:00 Genomic Molecular Markers Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
15:00-16:15 Measuring diversity Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
16:15-16:45 Break
16:45-17:15 Wheat data from CIMMYT Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
17:15-18:15 Assessing and summarizing diversity in wheat data Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
18:15 End of day 3  
Day 4 – Thursday 5 December 2019
09:00-09:30 Maize microsatellites Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
09:30-10:30 Assessing diversity in maize microsatellites  Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
10:30-11:00 Break
11:00-11:30 Summarizing diversity in maize microsatellites Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
11:30-12:30 Testing diversity in maize microsatellites Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
12:30-14:00 Lunch
14:00-15:30 Core Subset selection: concepts Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
15:30-16:00 Break
16:00-17:30 Core Subset selection in maize and wheat Octavio Martinez de la Vega/Manuel Humberto Reyes-Valdés
18:00 Course dinner  
Day 5 – Friday 6 December 2019
09:00-10:00 Introduction to genome wide association studies (GWAS) Hannele Lindqvist-Kreuze
10:00-10:15 Break
10:15-11:45 Practical: GWAS in polyploid potato using RStudio and GWASPoly Hannele Lindqvist-Kreuze
11:45-12:15 Q&A on Molecular markers Hannele Lindqvist-Kreuze
12:15-12:30 Wrap-up and feedback Marco Cristancho
12:30 End of course