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SolGS Hyderabad conference 2016

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Presentation of SolGS, a web-based tool for genomic selection in crops.
http://isas70.icrisat.ac.in/prog/

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SolGS Hyderabad conference 2016

  1. 1. solGS: A Web-based Genomic Selection Analysis Tool Isaak Y Tecle, Naama Menda, Guillaume Bauchet, Lukas Mueller
  2. 2. Websites with solGS…
  3. 3. Phenotyped & genotyped individuals Genomic selection… Prediction model Predicted breeding Values (GEBVs) Genotyped selection candidates Training population
  4. 4. Genomic Selection advantages…  Little or no phenotyping  reduced cost  Shorter breeding cycles  Higher selection gain per unit time  Increased prediction accuracy
  5. 5. Genomic Selection challenges…  ‘Big data’  Data organization, cleaning, imputation  Data storage and accessibility  Raw data and results visualization and sharing  Statistical analysis complexity
  6. 6. solGS http://cassavabase.org/solgs
  7. 7. Data storage… Jung et.al., 2011. Database. Chado schema
  8. 8. Data access interfaces Search wizard
  9. 9. pre-modeling data processing
  10. 10. Phenotype data processing…  Missing phenotype data handling  Adjusts phenotype means for environmental effects  lme4  Combines multiple trials
  11. 11. Genotype data processing  Filters out  monomorphic markers  markers with > 60% missing values  markers with MAF < 5%  individuals with > 80% missing values  Imputes missing marker data  Median substitution  Genotype coding  [-1, 0, 1], [0, 1, 2]
  12. 12. Prediction modeling
  13. 13. 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
  14. 14. Use case
  15. 15. Creating a training dataset
  16. 16. Creating a custom training dataset…
  17. 17. Building a prediction model
  18. 18. Exploring model input
  19. 19. Exploring model accuracy
  20. 20. Exploring model output
  21. 21. Estimating breeding values of selection candidates Applying the model…
  22. 22. Selection gain?
  23. 23. Prediction modeling for multiple traits
  24. 24. Estimating breeding values of a selection candidates for multiple traits Applying the models…
  25. 25. Estimating genetic correlations
  26. 26. Calculating selection indices
  27. 27. To sum up…solGS  Stores data  Builds prediction models  Estimates breeding values  Additional analyses:  Correlation analysis  Population structure  Selection indices  Genetic gain  Open source  Organism agnostic
  28. 28. Thanks to…
  29. 29. Many thanks!!

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