solGS: Web-based Genomic Selection Analysis Tool

Purposes

Gain understanding of genomic selection, GS model building, breeding values prediction, assessing model data input and output quality.

Brainstorm for ideas to make the tool suit better your research purposes.

Outline

Overview GS and solGS

Demo Exercise, bug watching, feedback

Brainstorming

Phenotyped &

genotyped individuals

Genomic selection…

Prediction model

Predicted breeding

Values (GEBVs)

Genotyped selection candidates

Training population

GS advantages

Little or no phenotyping reduced cost

Shorter breeding cycles Higher selection gain per unit time

Increased prediction accuracy

Phenotyped &

genotyped individuals

Genomic selection…

Prediction model

Predicted breeding

Values (GEBVs)

Genotyped selection candidates

Training population

Challenges…

Data volume, storage Data structuring, cleaning, imputation

Statistical analysis complexity

visualization and sharing

solGShttp://cassavabase.org/solgs

What you can do with solGS…

Store data Chado Natural Diversity schema

Create training dataset Build models and predict breeding values of selection candidates

Test model accuracy

What you can do with solGS…

Explore phenotype data Evaluate population structure Check on relationship between GEBVs vs observed phenotypes

Calculate selection indices, correlation

Visualize data on interactive plots

Calculate selection response

What is the statistical approach behind solGS?

…preparing phenotype data

Omits individuals completely missing phenotype values

Adjusts phenotype values for block effects

Averages across multiple trials after adjusting for block effects

…preparing genotype data

Removes out monomorphic markers Removes markers with > 60% missing values

Removes markers with MAF < 5% Removes individuals with > 80% missing values

Imputes missing marker data Median substitution

…statistical modeling Univariate Two-stage analysis RR-BLUP

Endelman, Plant Genome (2010) GBLUP

Marker-based realized relationship matrix

Prediction accuracy Based on 10-fold cross-validation

How does solGS work?

Websites for exercise

Cassava-devel.sgn.cornell.edu Cassava-test.sgn.cornell.edu Review.cassavabase.org Cassavabase.org https://iita-mirror.cassavabase.org

https://172.30.2.199 Username: sgn Password: eggplant

Phenotyped &

genotyped individuals

Genomic selection steps…

Prediction model

Predicted breeding

Values (GEBVs)

Selection candidates

Training dataset

Demo: Part I

Create training data set & build modelExplore model input and outputPhenotype and genetic correlationPopulation structureSelection index

Things to consider when creating a training data set & building a model

Things to consider…Phenotype data

Number of phenotyped individuals Minimum 20 clones

Relevant to target environment Data quality

Experimental design Measurement accuracy Missing values outliers

Things to consider…genotype data Marker number, genome distribution, polymorphism,

Data quality Allele calling accuracy Missing values (Per marker, individual)

Minor alleles Heterozygosity, LD

Population structure

Let’s do stuff!

single trial – single trait Create training data set and build model Trial method

Search for trial ‘Cassava Ibadan 2002/03’

Create a training dataset with that trial

Description, correlation Build a model for FRW

Explore model input and output, model accuracy Download GEBVs

Exercise: single trial – single trait Create training data set and build model

Search for your trial Create a training dataset with that trial

Check description, correlation Build a model for your trait

Explore model input and output, Population structure model accuracy Download GEBVs

single trial – multiple traits Create training data set and build models

Search for trial ‘Cassava Ibadan 2002/03’

Create a training dataset with that trial

Description, correlation Build models for FRW and CMDS

Explore model input and output for each model,

Genetic correlation Selection index

Exercise: single trial – multiple traits Create training data set and build models

Search for your trial Create a training dataset with that trial

Check description, correlation Build models for two traits at the same time

Explore model input and output for each model,

Genetic correlation Calculate and download selection index

Combined trials – single trait Create training data set and build models using two trials Search for ‘cassava ibadan 02/03 & 01/02’ Create a training dataset with the trials

Check description, correlation Build a model for FRW

Explore model input and output for the model, Population structure Prediction accuracy Download GEBV

Exercise: combined trials – single trait Create training data set and build models using two trials

Search for your trials Create a training dataset with the trials

Check description, correlation Build a model for your trait

Explore model input and output for the model,

Population structure Prediction accuracy Download GEBV

Using list – single trait Create training data set and build a model using plots list

Using the search wizard create a plots list from trial ‘cassava ibadan 2002/03 plots’

Create a training dataset with the list Check description, correlation

Build a model for your FRW Explore model input and output for the model, Population structure Prediction accuracy Download GEBV

Exercise: Using list – single trait Create training data set and build a model using plots list

Using the search wizard create a plots list from a trial… select all plots..

Create a training dataset with the list Check description, correlation

Build a model for your trait Explore model input and output for the model, Population structure Prediction accuracy Download GEBV

Demo: Part II

Predict breeding values of selection populationsGenetic correlationSelection indexSelection gain

Things to consider when applying a model to predict breeding values of selection populations

Things to consider…applying the model Training population vs selection population genetic relationship

Target environment Marker types used Population structure

Predict GEBVs of a Selection population Create training data set & build model Cassava Ibadan 2002/03 FRW

Search for a selection population Cassava Ibadan 2003/04

Predict GEBVs for the selection population Check selection response Download GEBVs

Exercise: Selection Population Prediction Create training data set & build model use one of the models you already built

Search for a selection population Related to the training population

Predict GEBVs for the selection population Check selection response Download GEBVs

Multiple Traits: Predict GEBVs of a Selection population

Create training data set & build model Cassava Ibadan 2002/03 FRW, CMDS

Search for a selection population Cassava Ibadan 2003/04

Predict GEBVs for both traits for the selection population Check selection response Download GEBVs

Exercise: Multiple Traits selection population prediction

Create training data set & build model Use previous two models from your training populations

Search for a selection population

Predict GEBVs for both traits for the selection population Check genetic correlation Calculate selection index

List: Predict GEBVs of a Selection population Create training data set & build model Cassava Ibadan 2002/03 FRW

Search for a selection candidates list Cassava Ibadan 213 genotypes

Predict GEBVs for the selection population Check selection response Download GEBVs

Exercise: selection candidates list Create training data set & build model Go to a previous model page

Create a selection candidates list Use search wizard to create accessions list

Using the model predict GEBVs of the list Check selection response Download GEBVs

Demo: Part III

Trait search Search for ‘fresh root weight’ Select trial ‘cassava ibadan 2002/03’

Check model output

Demo: Part III

PCA using accessions list

Brainstorm for new featuresMake priority list

What features do you like in BMS?What features do you like in to be added in cassavabase?

Thanks to…

Composing a training population: Fitting a

prediction model...3 options

Fitting a prediction model…

Option 1: Search using a trait name

Estimating breeding values of selection

candidates

Applying the model…

Fitting a prediction model…

Option 2: Search for trials

Estimating breeding values of a selection candidates for multiple traits

Applying the models…

Estimating genetic correlations

Calculating selection indices

Fitting a prediction model…

Option 3: use your own list of

individuals

To sum up… Store data Build prediction models Estimate breeding values Additional analyses:

Correlation analysis Population structure Selection indices

http://cassavabase.org/solgs Open source code

Thanks to…

Many thanks!!

Background image: nextgencassava.org