1. Home
  2. QTL analysis using menus in Genstat

QTL analysis using menus in Genstat

The QTL menus provide easy access to QTL analysis within Genstat. Two sources of data are required: phenotypic data (measurements of trait values) and genotypic/map data (evaluation of genotyping at markers and positions of markers on a genetic map). The phenotypic data can arise from either a single trial (single environment analysis) or multiple trials (multi-environment analysis). In the latter case, the QTL analysis can detect both QTL and QTLxE (QTL by environment) interactions. The phenotypic data can be loaded into Genstat either as individual observations (ie. plot data in the case of field trials) or genotype means. A QTL data space is available to manage the data structures required for QTL analysis.

The links below give a step-by-step description of the suggested analysis path for four cases:

  1. Single environment trial with individual observations
  2. Single environment trial with trait means
  3. Multi-environment trials with individual observations
  4. Multi-environment trials with trait means

The QTL menu bar has been designed to help you progress easily through each step of an analysis. It includes facilities for loading the two sources of data and QTL analysis of single or multi-environment trials.

Data Import/Export
Load Phenotypic data
Load Genotypic (Marker and Map) data
Load Genetic Relationship data
Load QTL Data space
Save Genotypic (Marker and Map) data
Save Flapjack Project file
Save QTL Data space
Data Manipulation
Compatibility Check
Subset Phenotypic and Genotypic Data by Genotypes
Subset Genotypic Data by Markers
Remove Subsetting
Replace Missing Values in Marker Scores
Data Exploration
Summary Statistics for Environments
Summary Statistics Between Environments
Summary Statistics Between Traits
GGE Biplot
Display Genetic Map
Genotype Data Plots
Summary Statistics for Markers
Map Construction
Calculate Number of Recombinations
Form Linkage Groups
Construct a Linkage Map
Phenotypic Analysis
Preliminary single environment analysis
Select Best Variance-covariance model for Multiple Environments
Genotypic Analysis
Calculate Genetic Predictors
Form Kinship Matrix
Linkage Disequilibrium (LD) Decay
QTL Analysis
Single Trait Linkage Analysis (Single Environment)
Multi-trait Linkage Analysis (Single Environment)
Single Trait Association Analysis (Single Environment)
Single Trait Linkage Analysis (Multiple Environments)
Single Trait Association Analysis (Multiple Environments)
View QTL data space

See also

Updated on June 13, 2019

Was this article helpful?