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

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

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

Building a prediction model... 3 options

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 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