2. IBWS Update
What has happened since the last meeting?
Analytical Pipeline
Breeding View (GenStat and R versions)
Decision support tools
OptiMAS
Molecular Breeding Decision Tool (backcrossing)
GDMS – genotyping data management system
Genotyping support services (GSS)
3. Analytical Tools
Breeding View – GenStat
Current pipelines
Single environment field trial analysis
GxE analysis
QTL linkage analysis
4. Breeding View
GenStat Pipelines
Breeding View - GenStat Pipelines
Single environment field trial
analysis
Analysis for row-column designs
including spatial analysis
Run multiple traits simultaneously
Automatic generation of
diagnostic plots
Options added to control layout
of report
Integration in IBWS
5. Breeding View
GenStat Pipelines
Single trait linkage analysis
(QTL)
Run multiple traits simultaneously
Improved output, including
graphics (e.g., profile plots)
Additional output file containing
QTL results
GxE/multi-site analysis
Includes FW regression, AMMI,
GGE biplots and stability
coefficients
Run multiple traits simultaneously
Select environments
IBWS integration (input only)
6. What is planned for
Breeding View
Enhancement of existing pipelines
Sequential analysis of a series of environments in SSA pipeline
Implementation of additional pipelines
Field design generation pipeline
Genomic selection pipeline
QTLxE
Update installation program to include Breeding View – R
Same interface, same output files
SSA pipeline already implemented
Initial implementation of GxE pipeline
Enhanced integration in IBWS
Improvements/changes in the reporting of results
7. OptiMAS
Improvements to OptiMAS algorithms to reduce calculation time and
memory consumption
Previous analyses can be reloaded with chosen with previous
configuration/preferences
Marker QC step to check for inconsistencies in genotyping
Improvements to the website including online and offline (within
software) documentation and tutorial.
8. What is planned for OptiMAS
Full integration into IBWS
Development of a wizard for automated decision making
(selection of crosses).
Computation of diversity score based on the pedigree or
markers.
Inclusion of QTL position uncertainty in score computation
Use of allele effects at QTL in order to compute expected
gain for different traits and possibility to weight different
traits to compute indexes.
9. Molecular Breeding
Decision Tool (MBDT)
Selection of polymorphic markers including those linked
to chosen trait and export of list to a text file between
parental lines.
Improvements to calculation of % recovery recurrent
parent. Export function added to export the list of
genotypes.
Be able to view individual chromosomes.
Option added to prioritize recombination (heterozygotes)
at a flanking marker over percentage of recovery
Partial integration into the IBWS
Be able to use different marker types (i.e. combination of
SSR and SNP markers)
10. What is planned for MBDT
Full integration into IBWS
Enhancements to UI display (e.g. similar flapjack
format)
Include unmapped markers
11. Genotyping data management
system (GDMS)
Select polymorphic markers between two lines
(including trait specific markers) and export as
genotyping order form
Improvements made in importing genotyping
data direct into GDMS
Tools to help in the selection of parental lines
Select set of lines and send to flapjack for
visualization, including unmapped markers
Investigate relationships among selected germplasm
by calculating similarity matrix direct from GDMS
12. What is planned for GDMS
Implement the new interface for GDMS
Enhance functionality to help in parental selection
Relatedness; Trait specific markers; visual selection of
polymorphic markers
Further integration in the IBWS to improve the uploading
of genotyping datasets
Enhance the selection of diagnostic markers and display
of results for progeny selection in a MAS experiment
Implement additional QC steps
Ability to edit part of a dataset
13.
14. Conclusion
Following the first release of the IBWS
Enhancements in functionality of tools have
continued and will continue
Better integration (retrieval and saving of data)
Series of user feedback sessions being
conducted with breeders
Identify any gaps in current functionality or
changes in existing functionality
Refactor the entire IBWS interface to improve
the user experience
15. IBP marker services
The new marker services concept based on
high-throughput SNP genotyping was operational
in 2011
Decision to focus on a single SNP genotyping
provider (KBioscience, UK)
SNP conversion to KBioscience platform with
1,000-2,000 SNPs for each crop of interest
SSR genotyping support still being provided by
current labs as needed
BecA
ICRISAT
17. GSS Projects at GCP
See poster 8.3
2007 2008 2009 2010 2011 2012 2013 2014
GSS-II (35)
GSS-III (16)
GSS-Commissioned B (WACCI) (14)
SNP Conversion (18)
Multi-year course-I (MYC1) (30)
Multi-year course-II (MYC2) (36)
Forensic (QA/QC) (180)**
GSS (open call)
*This is an estimated number
GSS-I (19)
GSS-Commissioned A (NARS&ACCI) (25)
Fingerprinting-A (non-TL crops) (8)
Fingerprinting-B (TL crops) (11)
18. Crop #Samples #Data Points
Cassava 294 404,100
Chickpeas 520 430,730
Common bean 189 214,595
Cowpea 200 213,249
Groundnut 259 18,855
Maize 144 166,542
Pigeonpea 293 390,288
Rice 528 567,150
Sorghum 646 320,154
Soybean 246 255,254
Wheat 200 356,576
Total 3,337,493
Includes SNP conversion projects, fingerprinting
and mapping pops.
19. Diagnostic markers from within
and outside the GCP
Construction of consensus genetic maps for all
crops
For use in SNP selection tool
To identify KASPar markers as replacements for
existing diagnostic markers
Populating GDMS with marker information
Populating GDMS with fingerprint information
Populating GDMS with QTL/MTA information
20. Predictive markers outside of
GCP
Triticeae-CAP project
One activity to transform existing wheat and barley
diagnostic markers to SNP markers (KASPar)
Discussion with Cristobal Uauy (JIC), Susanne
Dreisigacker (CIMMYT) and Gina Brown-Guerida
(USDA)
Sent the list of predictive markers for wheat
Notified LGCGenomics that GCP should have access
to them
Information to be incorporated as part of the IBWS
Barley markers are also available