solGS: A Web-based Solution for Genomic Selection
Isaak Y Tecle, Naama Menda, Guillaume Bauchet, Lukas Mueller
Tecle et al. Bioinformatics 2014, 15:398
Phenotyped &
genotyped individuals
Genomic selection…
Prediction model
Predicted breeding
Values (GEBVs)
Genotyped selection candidates
Training population
Challenges…
n Data volume, storagen Data structuring, cleaning, imputationn Statistical analysis complexityn visualization and sharing
solGS webtoolhttp://cassavabase.org/solgs
What you can do with solGS…
n Store datan Chado Natural Diversity schema
n Compose training populationsn Build models and predict breeding values of selection candidates
n Test model accuracy
What you can do with solGS…
n Explore phenotype data, population structure
n Check on relationship between GEBVs vs observed phenotypes
n Calculate selection indices, correlation n Visualize data on interactive plots
What is the statistical approach behind solGS?
…preparing data
n Omits individuals completely missing phenotype values
n Adjusts phenotype values for block effects
n Averages across multiple trials after adjusting for block effects
n Imputes missing marker datan Median substitution
…statistical modelingn Univariaten RR-BLUP
n Endelman, Plant Genome (2010)
n GBLUP n Marker-based realized relationship matrix
n Prediction accuracyn Based on 10-fold cross-validation
How does solGS work?
Composing a training population: Fitting a prediction model...
3 options
Fitting a prediction model…
Option 1: Search using a trait name
Estimating breeding values of selection candidates
Applying the model…
Fitting a prediction model…
Option 2: Search for trials
Estimating breeding values of a selection candidates for multiple traits
Applying the models…
Estimating genetic correlations
Calculating selection indices
Fitting a prediction model…
Option 3: use your own list of individuals
To sum up…n Store datan Build prediction modelsn Estimate breeding valuesn Additional analyses:
n Correlation analysisn Population structuren Selection indices
n http://cassavabase.org/solgsn Open source code
Thanks to…
Many thanks!!
Background image: nextgencassava.org
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