SolGS Hyderabad conference 2016
53
solGS: A Web-based Genomic Selection Analysis Tool Isaak Y Tecle, Naama Menda, Guillaume Bauchet, Lukas Mueller
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Transcript of SolGS Hyderabad conference 2016
solGS: A Web-based Genomic Selection Analysis
Tool Isaak Y Tecle, Naama Menda,
Guillaume Bauchet, Lukas Mueller
Websites with solGS…
Phenotyped &
genotyped individuals
Genomic selection…
Prediction model
Predicted breeding
Values (GEBVs)
Genotyped selection candidates
Training population
Genomic Selection advantages… Little or no phenotyping
reduced cost Shorter breeding cycles Higher selection gain per unit time
Increased prediction accuracy
Genomic Selection challenges…
‘Big data’ Data organization, cleaning, imputation
Data storage and accessibility Raw data and results visualization and sharing
Statistical analysis complexity
solGShttp://cassavabase.org/solgs
Data storage…
Jung et.al., 2011. Database.
Chado schema
Data access interfaces
Search wizard
pre-modeling data processing
Phenotype data processing…
Missing phenotype data handling
Adjusts phenotype means for environmental effects lme4
Combines multiple trials
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]
Isaak Tecle
Prediction modeling
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
Isaak Tecle
Use case
Creating a training dataset
Creating a custom training dataset…
Building a prediction model
Exploring model input
Exploring model accuracy
Exploring model output
Estimating breeding values of selection
candidates
Applying the model…
Selection gain?
Prediction modeling for multiple traits
Estimating breeding values of a selection candidates for multiple traits
Applying the models…
Estimating genetic correlations
Calculating selection indices
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
Thanks to…
Many thanks!!
