solGS:  A  Web-­based  Solution  for  Genomic  Selection

Isaak  Y  Tecle,  Naama  Menda,  Guillaume  Bauchet,  Lukas  Mueller

Tecle  et  al.  Bioinformatics  2014,  15:398

Phenotyped  &  

genotyped  individuals

Genomic  selection…

Prediction  model

Predicted  breeding

Values  (GEBVs)

Genotyped  selection  candidates

Training  population

Challenges…

n Data  volume,  storagen Data  structuring,  cleaning,  imputationn Statistical  analysis  complexityn visualization  and  sharing

solGS  webtoolhttp://cassavabase.org/solgs

What  you  can  do  with  solGS…

n Store  datan Chado  Natural  Diversity  schema

n Compose  training  populationsn Build  models  and  predict  breeding  values  of  selection  candidates

n Test  model  accuracy  

What  you  can  do  with  solGS…

n Explore  phenotype  data,  population  structure

n Check  on  relationship  between  GEBVs  vs  observed  phenotypes

n Calculate  selection  indices,  correlation  n Visualize  data  on  interactive  plots

What  is  the  statistical  approach  behind  solGS?

…preparing  data

n Omits  individuals  completely  missing  phenotype  values

n Adjusts  phenotype  values  for  block  effects

n Averages  across  multiple  trials  after  adjusting  for  block  effects

n Imputes  missing  marker  datan Median  substitution

…statistical  modelingn Univariaten RR-­BLUP

n Endelman,  Plant  Genome  (2010)

n GBLUP  n Marker-­based  realized  relationship  matrix

n Prediction  accuracyn Based  on  10-­fold  cross-­validation

How  does  solGS  work?

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…n Store  datan Build  prediction  modelsn Estimate  breeding  valuesn Additional  analyses:  

n Correlation  analysisn Population  structuren Selection  indices

n http://cassavabase.org/solgsn Open  source  code

Thanks  to…

Many  thanks!!

Background  image:  nextgencassava.org