solgs hyderabad conference 2016
TRANSCRIPT
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solGS: A Web-based Genomic Selection Analysis
Tool Isaak Y Tecle, Naama Menda,
Guillaume Bauchet, Lukas Mueller
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Websites with solGS…
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Phenotyped &
genotyped individuals
Genomic selection…
Prediction model
Predicted breeding
Values (GEBVs)
Genotyped selection candidates
Training population
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Genomic Selection advantages… Little or no phenotyping
reduced cost Shorter breeding cycles Higher selection gain per unit time
Increased prediction accuracy
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Genomic Selection challenges…
‘Big data’ Data organization, cleaning, imputation
Data storage and accessibility Raw data and results visualization and sharing
Statistical analysis complexity
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solGShttp://cassavabase.org/solgs
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Data storage…
Jung et.al., 2011. Database.
Chado schema
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Data access interfaces
Search wizard
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pre-modeling data processing
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Phenotype data processing…
Missing phenotype data handling
Adjusts phenotype means for environmental effects lme4
Combines multiple trials
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Genotype data processing Filters out
monomorphic markers markers with > 60% missing values markers with MAF < 5% individuals with > 80% missing values
Imputes missing marker data Median substitution
Genotype coding [-1, 0, 1], [0, 1, 2]
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Prediction modeling
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statistical modeling
Univariate Two-stage analysis RR-BLUP
Endelman, Plant Genome (2010) GBLUP
Marker-based realized relationship matrix
Prediction accuracy Based on 10-fold cross-validation
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Use case
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Creating a training dataset
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Creating a custom training dataset…
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Building a prediction model
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Exploring model input
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Exploring model accuracy
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Exploring model output
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Estimating breeding values of selection
candidates
Applying the model…
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Selection gain?
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Prediction modeling for multiple traits
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Estimating breeding values of a selection candidates for multiple traits
Applying the models…
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Estimating genetic correlations
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Calculating selection indices
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To sum up…solGS Stores data Builds prediction models Estimates breeding values Additional analyses:
Correlation analysis Population structure Selection indices Genetic gain
Open source Organism agnostic
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Thanks to…
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Many thanks!!