CABANA Workshop: Genomic Analysis of Crop Biodiversity using R

Date:

 Tuesday 25 Friday 28 June 2019

Venue: 

LANGEBIO, Cinvestav - LANGEBIO, Cinvestav, Libramiento Norte Carretera Leon Km 9.6, Irapuato,  GUA,  36821, Mexico

Application opens: 

Monday 29 April 2019

Application deadline: 

Tuesday 28 May 2019

Participation: 

Open application with selection

Contact: 

Derrin Crawte

Registration fee: 

$700 MXN

Dates additional information: 

This course runs over 4 days and includes lunch and refreshments breaks.

Course Overview

This course will provide training on using R in genomics applications for crop biodiversity. The first day will cover the basics of biodiversity and R, before analyzing various genomes to assess biodiversity. 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 chilli pepper as training datasets throughout the week.

This course will be jointly taught by Octavio Martinez de la Vega (LANGEBIO, Cinvestav) and Manuel Humberto Reyes-Valdes (UAAAN).

Audience

This course is aimed at researchers from postgraduate level upwards interested in using R to analyse genomics data for crop biodiversity studies.


Please note this course will be taught in English, however the trainers are 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.

 

Prerequisites
An undergraduate level degree in plant biology or a related discipline would be an advantage. 


You will need to know basic commands in R in order to get the most from this course, though a review of basic concepts and commands in R will be covered on the first day. You can find a good introduction to R here: http://www.r-tutor.com/r-introduction

You will also need to bring a laptop with R installed and working knowledge of how to navigate your working directory effectively using R commands.

To download R please visit: https://www.r-project.org/

To download RStudio please visit: https://www.rstudio.com/products/rstudio/download/

Learning outcomes

After this course you should be able to:

  • Input and analyze genomic data into R to evaluate genomic diversity
  • Discuss advantages and limitations of different data types
  • Select the best method to analyze genomic diversity
  • Draw and evaluate dendrograms showing genomic relations
  • Plan genomic experiments to optimal evaluation of genomic diversity

Programme

Day 1 – Tuesday 25 June 2019
09:00-10:00 Welcome and Introduction  
10:00-11:00 Genomic Molecular Markers  
11:00-11:30 Coffee Break
11:30-13:00 R packages for biodiversity  
13:00-14:00 Lunch
14:00-15:30 Overview of R  
15:30-16:00 Coffee Break  
16:00-17:00 Guidelines for analysis of biodiversity  
17:00-17:30 Data simulation: Dummy examples   
17:30 End of day 1  
Day 2 – Wednesday 26 June 2019
09:00-10:00 Measuring diversity  
10:00-11:00 Hierarchical clustering and dendrograms  
11:00-11:30 Coffee Break
11:30-13:00 Resampling methods  
13:00-14:00 Lunch
14:00-15:30 Wheat data from CIMMYT  
15:30-16:00 Coffee Break
16:00-17:00 Assessing diversity in wheat data  
17:00-17:30 Summarizing diversity in wheat data  
17:30 End of day 2  
Day 3 – Thursday 27 June 2019
09:00-10:00 Testing diversity in wheat data  
10:00-11:00 Selecting for conservation in wheat data  
11:00-11:30 Coffee Break
11:30-13:00 Maize microsatellites  
13:00-14:00 Lunch
14:00-15:30 Assessing diversity in maize microsatellites  
15:30-16:00 Coffee Break
16:00-17:00 Summarizing diversity in maize microsatellites  
17:00-17:30 Testing diversity in maize microsatellites  
17:30 End of day 3  
Day 4 – Friday 28 June 2019
09:00-10:00 Selecting for conservation in maize microsatellites  
10:00-11:00 Genome-wide Phenotypes  
11:00-11:30 Coffee Break
11:30-13:00 Assessing diversity in Genome-wide Phenotypes  
13:00-14:00 Lunch
14:00-15:30 Summarizing diversity in Genome-wide Phenotypes  
15:30-16:00 Coffee Break
16:00-17:00 Testing diversity in Genome-wide Phenotypes  
17:00-17:30 Design of biodiversity studies  
17:30-17:45 Course close and feedback