solgs: a bioinformatics solution for genomic selection isaak y tecle, naama menda, jeremy edwards,...
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solGS: A Bioinformatics Solution for Genomic Selection
Isaak Y Tecle, Naama Menda, Jeremy Edwards, Lukas Mueller
Phenotyped &
Genotyped Lines
Genomic Selection
Prediction Model
Predicted BreedingValues
GenotypedLines
What solGS does…
Builds prediction models Predicts breeding values Calculates selection index Correlation analysis Interactive data visualization
Building a prediction model...3 options
http://cassavabase.org/solgs
Building a prediction model
Option 1: Search using a trait name
Estimating breeding values of a selection population
Applying the model
Building a prediction model
Option 2: using a trial as a training population
Building a prediction model
Option 3: use your own list of clones
Build multiple models simultaneously
Estimating breeding values of a selection population for multiple traits
Applying the models
Calculating selection index
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
Database Chado ND Schema Co-developed by SGN, GDR,
VectorBase and Medicago Jung et al. Database 2011.
To sum up… Build models Estimate breeding values Additional tools:
correlation analysis selection index
http://cassavabase.org/solgs Feedback
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
Thanks to…
Cassavabase team
Many thanks!!
Background image: nextgencassava.org