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Published byFrank Brett Ray Modified over 9 years ago
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solGS: A Bioinformatics Solution for Genomic Selection Isaak Y Tecle, Naama Menda, Jeremy Edwards, Lukas Mueller
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Phenotyped & Genotyped Lines Genomic Selection Prediction Model Predicted Breeding Values Genotyped Lines
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What solGS does… Builds prediction models Predicts breeding values Calculates selection index Correlation analysis Interactive data visualization
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Building a prediction model... 3 options
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http://cassavabase.org/solgs
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Building a prediction model Option 1: Search using a trait name
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Estimating breeding values of a selection population Applying the model
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Building a prediction model Option 2: using a trial as a training population
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Building a prediction model Option 3: use your own list of clones
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Build multiple models simultaneously
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Estimating breeding values of a selection population for multiple traits Applying the models
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Calculating selection index
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Statistical method Ridge regression, mixed-model rrBLUP (Endelman, Plant Genome (2010)) Kinship-BLUP Marker-based realized relationship matrix Model accuracy Based on 10-fold cross-validation
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Database Chado ND Schema Co-developed by SGN, GDR, VectorBase and Medicago Jung et al. Database 2011.
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To sum up… Build models Estimate breeding values Additional tools: correlation analysis selection index http://cassavabase.org/solgs Feedback
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Next... Incorporate G x E effects Correlation analyses: phenotype values vs. breeding values, selection indices vs breeding values. PCA and clustering Add more prediction methods Computational speed improvement
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Thanks to…
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Cassavabase team
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Many thanks!! Background image: nextgencassava.org
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