Introduction to QTL mapping and association mapping in GenStat

  • Date: 15-16th July 2010 
  • Location: Apsley Paper Trail Project, Apsley, Hertfordshire, UK
  • Time: Start 9am, Finish 5pm
  • Duration: 2 days.
  • Price includes all materials and lunches.
Who Should Attend Individuals interested in a flexible QTL mapping approach, applicable in standard situations (SIM, CIM) as well as more specialized situations (multi-environment QTL mapping, QTLxE, multi-trait QTL mapping, association mapping, in- and outbreeders). QTL mapping is presented as a natural extension of the analysis of (field) trials within a mixed model framework. Although most of the QTL analyses will be presented in Windows dialogue form, it is recommended that attendants have some familiarity with mixed models and quantitative genetics.
Overview Standard QTL mapping is introduced as an extension of mixed model analysis of single traits in single trials. Effectively, on a genomic grid genetic covariates are fitted that represent contrasts in unobserved QTL genotype probabilities given marker information. The calculation of these genetic covariates will be explained for various types of populations: inbreeders, outbreeders and association panels. After mixed model QTL analysis for single traits in single trials, extensions will be described for multiple trials and multiple traits, where the modeling of the variance-covariance structure for trials and traits is crucial.
Learning Objectives By the end of the course you should be able to:

  • Perform a QTL analysis for a wide array of single populations, for single and multiple environments, and single and multiple traits
  • Use various inference procedures for assessing QTL evidence
  • Report QTL locations and effects
Instructors Fred van Eeuwijk, Marcos Malosetti and Martin Boer, WUR-Biometris, P.O. Box 100, 6700 AC Wageningen, The Netherlands.
Training Methods Theory will be presented in the form of lectures. Supervised practicals will allow attendants to become familiar with the details of the actions required to perform a QTL analysis in Genstat using Windows’ dialogues. These practicals will also serve to learn how to interpret QTL mixed model analysis output.

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