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Unlocking breeding potential of African crops through data management an
example with CASSAVABASE
Guillaume Bauchet
Plant and Animal Genome Conference San Diego January 2016
gjb99@cornell.edu
OUTLINE
http://nextgencassava.org/
CASSAVABASE , What for?
CASSAVABASE , a user perspective
CASSAVABASE , search, manage, analyze
CASSAVABASE , a view
The Central data store for NEXTGEN CASSAVA :Genomic selection in African cassava breeding programs
http://nextgencassava.org/
NEXTGEN CASSAVA
What are the major challenges?
● Multi trait and Multi breeding environments for cassava phenotypic data collection
● Large scale production of genomic data using GBS
● Integrate Genomic Selection tool via web interface
What are the major challenges?
● Make the most of this resource for cassava breeders: speed up the analysis and decision making
What are the needs?● Search various data types (phenotypes and germplasm) in a large datastore
●Manage data and daily breeding activity through comprehensive interface
●Analyse and retrieve data for genomic assisted breeding
What are our solutions?● Integrate phenomic & genomic data with breeding tools
●Use Perl with the Bio::Chado::Schema and Natural Diversitymodule as database architecture
●Retrieve genomic information
●Sequence visualization ●Open source
https://github.com/solgenomics/
http://cassavabase.org/
New search bar
Navigation bar always visible on top Expandable search box
Caroussel
New responsive design
CASSAVABASEby numbers
2016: + 80,000 accessions, 2,5 billion genetic observations
2014:
+360 registered users
From Phenotype to Genotype to Breeding: Harvesting the fruits of CASSAVABASE
CASSAVABASE, an Office perspective: Search
Search breeding program, location, trial, trait, year, accession
CASSAVABASE, a field perspective: Manage Phenotypes
Define phenotypic traits via Cassava trait dictionaryin CASSAVABASE
Data collection
via FieldBookapp*
Design trials, barcodes & field maps
in CASSAVABASE*
Data uploading in CASSAVABASE
via .xls and .txt file **See Alex Ogbonna PAG presentation
“Managing Phenotypic Data through Cassavabase with Fieldbook App”“
Data analysis in CASSAVABASE
-Sum. stat-ANOVA-BLUP-GSIn CASSAVABASE
Design genotyping Trial in CASSAVABASE
TASSEL pipeline
Data filtering &
imputationGBS data uploading
In CASSAVABASE
GS Analysis & Visualization
in CASSAVABASE
GBS facility @ Cornell
CASSAVABASE, a lab perspective: Manage Genotypes
CASSAVABASE an office perspective: ManageBreeding programs, trial, accession
CASSAVABASE : Analyze with SolGS
Phenotypic values Population Structure GEBV vs phenotypes
See Isaak Tecle PAG presentation & poster 342“solGS: A Web-based Solution for Genomic Selection”
GEBV
CASSAVABASE : Analyze with SolGS
CASSAVABASE from the Office: Analyze phenotypesQC to phenotypes
Single trial
CASSAVABASE from the Office: Analyze phenotypesQC to phenotypes
Single trial
CASSAVABASE tools: Analyze pedigree
CASSAVABASE from the Office: Analyze phenotypes
data_2011_B1
4 6 8 10
r= 0.68
p<0.001
r= 0.66
p<0.001
4 6 8 10 14
r= 0.70
p<0.001
46
810
12
r= 0.63
p<0.001
46
810
data_2011_B2
r= 0.76
p<0.001
r= 0.79
p<0.001
r= 0.73
p<0.001
data_2011_B3
r= 0.76
p<0.001
46
810
r= 0.68
p<0.001
46
810
14 data_2012_B1
r= 0.75
p<0.001
4 6 8 10 12 4 6 8 10 4 6 8 12
46
812
data_2012_B2
30 31 32 33 34 35 36 37
-1.5
-0.5
0.5
1.5
Fitted values
Residuals
Residuals vs Fitted
26
9
15
-2 -1 0 1 2
-10
12
Theoretical Quantiles
Sta
ndar
dize
d re
sidu
als
Normal Q-Q
26
9
15
30 31 32 33 34 35 36 37
0.0
0.4
0.8
1.2
Fitted values
Standardized residuals
Scale-Location269
15
0.0 0.1 0.2 0.3 0.4 0.5
-2-1
01
2
Leverage
Sta
ndar
dize
d re
sidu
als
Cook's distance
Residuals vs Leverage
9
2615
ANOVA, h2,
BLUP, GxE
QC phenotypesMultiple trials
JBrowse
CASSAVABASE tools: Analyze sequence
Variant effects
prediction
VIGS tool
CASSAVABASE tools: Analyze sequence
BLAST
CASSAVABASE, a User perspective: support & interaction
CASSAVABASE, a User perspective: support & interaction
-> Provide support on technical issues ( data management)-> Gather user request for tool improvement and new developments (pedigree queries, VIGS)-> 2016: Install Mirror site @ IITA Ibadan, Nigeria
Weekly meetings with users in Africa: Wiki, FB pages & mailing list:
CASSAVABASE Upcoming developments
Search: Integrate trait & values in the wizard search
Manage: extract data subset according to their phenotypicvalues, conditionnal choices
Analyze: -Phenotypic analysis developments (ANOVA, GxE)-Pedigree analysis-Jbrowse: Mutation prediction of genetic variants-SolGS: Jobs queuing, trial selection improvement
LukasMueller
AlexOgbonna
BryanEllerbrock
NaamaMenda
IsaakTecle
NickMorales
AKNOWLEDGEMENTS
Jeremy Edwards
BMGF
ChiedozieEgesi
PeterKulakow
Robert Kawuki
IsmailRabbi
Questions?
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