Download - Cassavabase SolGS presentation PAG 2016
![Page 1: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/1.jpg)
solGS: A Web-based Solution for Genomic Selection
Isaak Y Tecle, Naama Menda, Guillaume Bauchet, Lukas Mueller
Tecle et al. Bioinformatics 2014, 15:398
![Page 2: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/2.jpg)
Phenotyped &
genotyped individuals
Genomic selection…
Prediction model
Predicted breeding
Values (GEBVs)
Genotyped selection candidates
Training population
![Page 3: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/3.jpg)
Challenges…
n Data volume, storagen Data structuring, cleaning, imputationn Statistical analysis complexityn visualization and sharing
![Page 4: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/4.jpg)
solGS webtoolhttp://cassavabase.org/solgs
![Page 5: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/5.jpg)
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
![Page 6: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/6.jpg)
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
![Page 7: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/7.jpg)
What is the statistical approach behind solGS?
![Page 8: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/8.jpg)
…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
![Page 9: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/9.jpg)
…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
![Page 10: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/10.jpg)
How does solGS work?
![Page 11: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/11.jpg)
![Page 12: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/12.jpg)
Composing a training population: Fitting a prediction model...
3 options
![Page 13: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/13.jpg)
![Page 14: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/14.jpg)
Fitting a prediction model…
Option 1: Search using a trait name
![Page 15: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/15.jpg)
![Page 16: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/16.jpg)
![Page 17: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/17.jpg)
![Page 18: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/18.jpg)
![Page 19: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/19.jpg)
![Page 20: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/20.jpg)
![Page 21: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/21.jpg)
![Page 22: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/22.jpg)
![Page 23: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/23.jpg)
![Page 24: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/24.jpg)
![Page 25: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/25.jpg)
![Page 26: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/26.jpg)
Estimating breeding values of selection candidates
Applying the model…
![Page 27: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/27.jpg)
![Page 28: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/28.jpg)
![Page 29: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/29.jpg)
Fitting a prediction model…
Option 2: Search for trials
![Page 30: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/30.jpg)
![Page 31: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/31.jpg)
![Page 32: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/32.jpg)
![Page 33: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/33.jpg)
![Page 34: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/34.jpg)
![Page 35: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/35.jpg)
![Page 36: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/36.jpg)
Estimating breeding values of a selection candidates for multiple traits
Applying the models…
![Page 37: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/37.jpg)
![Page 38: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/38.jpg)
![Page 39: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/39.jpg)
Estimating genetic correlations
![Page 40: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/40.jpg)
![Page 41: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/41.jpg)
Calculating selection indices
![Page 42: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/42.jpg)
![Page 43: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/43.jpg)
Fitting a prediction model…
Option 3: use your own list of individuals
![Page 44: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/44.jpg)
![Page 45: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/45.jpg)
![Page 46: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/46.jpg)
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
![Page 47: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/47.jpg)
Thanks to…
![Page 48: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/48.jpg)
![Page 49: Cassavabase SolGS presentation PAG 2016](https://reader033.vdocuments.net/reader033/viewer/2022042604/587fd0161a28ab58248b48e3/html5/thumbnails/49.jpg)
Many thanks!!
Background image: nextgencassava.org