Proof-of-Concept Publicly Accessible Data Dashboards from the US-EPA.pptx
Cassavabase general presentation PAG 2016
1. 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
6. ● 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
7. 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 Diversity
module as database architecture
● Retrieve genomic information
● Sequence visualization ● Open source
https://github.com/solgenomics/
15. CASSAVABASE, a field perspective: Manage Phenotypes
Define phenotypic traits via Cassava
trait dictionaryin CASSAVABASE
Data
collection
via FieldBook
app*
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
-GS
In CASSAVABASE
16. Design genotyping
Trial in CASSAVABASE
TASSEL
pipeline
Data filtering
&
imputation
GBS data uploading
In CASSAVABASE
GS Analysis
& Visualization
in
CASSAVABASE
GBS facility @ Cornell
CASSAVABASE, a lab perspective: Manage Genotypes
18. 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
27. 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:
28. CASSAVABASE Upcoming developments
Search: Integrate trait & values in the wizard search
Manage: extract data subset according to their phenotypic
values, conditionnal choices
Analyze: -Phenotypic analysis developments (ANOVA, GxE)
-Pedigree analysis
-Jbrowse: Mutation prediction of genetic variants
-SolGS: Jobs queuing, trial selection improvement