Integrated Breeding Workflow System Update

GCP General Research Meeting September 27 – 30, 2013

Lisbon, Portugal

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)

Analytical Tools

Breeding View – GenStat Current pipelines Single environment field trial analysis GxE analysis QTL linkage analysis

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

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)

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

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.

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.

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)

What is planned for MBDT

Full integration into IBWS Enhancements to UI display (e.g. similar flapjack

format) Include unmapped markers

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

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

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

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

SNP markers at GCP

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)

Crop #Samples #Data PointsCassava 294 404,100Chickpeas 520 430,730Common bean 189 214,595Cowpea 200 213,249Groundnut 259 18,855Maize 144 166,542Pigeonpea 293 390,288Rice 528 567,150Sorghum 646 320,154Soybean 246 255,254Wheat 200 356,576Total 3,337,493

Includes SNP conversion projects, fingerprinting and mapping pops.

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

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

Finally

Sunday 1-5 PM “Introduction to the IBWS”