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SolGS: A Bioinformatics Solution for Genomic Selection Isaak Y Tecle, Naama Menda, Jeremy Edwards, Lukas Mueller.

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Presentation on theme: "SolGS: A Bioinformatics Solution for Genomic Selection Isaak Y Tecle, Naama Menda, Jeremy Edwards, Lukas Mueller."— Presentation transcript:

1 solGS: A Bioinformatics Solution for Genomic Selection Isaak Y Tecle, Naama Menda, Jeremy Edwards, Lukas Mueller

2 Phenotyped & Genotyped Lines Genomic Selection Prediction Model Predicted Breeding Values Genotyped Lines

3 What solGS does… Builds prediction models Predicts breeding values Calculates selection index Correlation analysis Interactive data visualization

4 Building a prediction model... 3 options

5 http://cassavabase.org/solgs

6 Building a prediction model Option 1: Search using a trait name

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15 Estimating breeding values of a selection population Applying the model

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18 Building a prediction model Option 2: using a trial as a training population

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21 Building a prediction model Option 3: use your own list of clones

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24 Build multiple models simultaneously

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27 Estimating breeding values of a selection population for multiple traits Applying the models

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30 Calculating selection index

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33 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

34 Database Chado ND Schema Co-developed by SGN, GDR, VectorBase and Medicago Jung et al. Database 2011.

35 To sum up… Build models Estimate breeding values Additional tools: correlation analysis selection index http://cassavabase.org/solgs Feedback

36 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

37 Thanks to…

38 Cassavabase team

39 Many thanks!! Background image: nextgencassava.org


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