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:
- Single environment trial with individual observations
- Single environment trial with trait means
- Multi-environment trials with individual observations
- Multi-environment trials with trait means
Menu Items
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
- AMMI
- 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
- Eigenanalysis
- 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
- QTL data space for using data in QTL menus