SNP Data Analysis

Course Description

New sequencing and marker genotyping technologies promise to accelerate the pace of genetic diversity research and gains in selection through molecular breeding. At the same time, these technologies can often overwhelm researchers because of the large amounts of new data being produced. Recently, single nucleotide polymorphism (SNP) markers have become popular because of several key advantages: SNP markers are more abundant in the genome and multiplexed SNP genotyping is more efficient and cost-effective than SSR genotyping. SNP chips can enable rapid scans of the rice genome at different levels of resolution for applications such as diversity analysis, fingerprinting, QTL and association mapping, and marker-assisted selection. At the same time, a wealth of genetic information can enable candidate gene discovery for important traits at fine-mapped gene and QTL regions. These new methods require a deep understanding of advanced bioinformatics and data analysis techniques to extract useful information from large sets of data for rice diversity and breeding applications.

The SNP Analysis and Candidate Gene Discovery Training Course will provide IRRI researchers and scholars with the essential knowledge required to navigate the new DNA sequence and SNP data sets. The goal is to introduce participants to the available tools to handle these types of data and to apply them in their own research projects. The course will include hands-on sessions to allow participants to become familiar with the different software programs and online tools for SNP analysis and candidate gene discovery.


To develop skills for SNP analysis and bioinformatics for candidate gene discovery for rice researchers.

  • To present an overview of methodologies for rice SNP analysis;
  • To train participants in the use of stand-alone and online tools for SNP analysis and candidate gene discovery;
  • To demonstrate SNP analysis and gene discovery workflows for rice research.

The course includes hands-on computer training, where the participants work on exercises individually with assistance from resource persons, to raise the participant’s level of skill in:
  • Searching and retrieving SNP data from online SNP databases;
  • Allele calling using the Alchemy software;
  • Navigating and using the tools for graphical genotyping using Flapjack;
  • Conduct diversity analysis using PowerMarker/Structure;
  • Perform QTL analysis using QGene;
  • Make association studies using Tassel
  • Using bioinformatics tools to support SNP analysis and Candidate Gene Discovery.

The course is offered to IRRI researchers and scholars who conduct SNP analysis with bioinformatics support in their project. Maximum of 20 participants will be accepted.  Each participant must bring a laptop for use in the training.

To apply for a slot in the course, download application and screening form. Priority of selecting participants is based on screening criteria.

Course Content
  • Introduction to SNP Discovery
  • Navigating Online SNP Databases
  • Using SNPs for Graphical Genotyping
  • Diversity and Population Structure Analysis
  • Linkage Disequilibrium Analysis
  • Association Studies
  • Bioinformatics for Gene Discovery
  • Candidate Gene Discovery for SNP regions
Date & Venue

May 11-15, 2015
International Rice Research Institute (IRRI)
Los Baños, Laguna, Philippines

Course Coordinator/Organizer

Dr. Michael R. Thomson
Scientist, Molecular Genetics
Plant Breeding, Genetics and Biotechnology Division

International Rice Research Institute
DAPO Box 7777, Metro Manila, Philippines
Fax: (63- 2) 891-1292; 580 5699
Phone: (63- 2) 845-0563; 580-5600 ext 2538