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