MBP Davenport

8/9/2019 MBP Davenport

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Present at ion T i t le Goes Here

…presentation subtitle.

“Next” generation of decision supporttools

Guy Davenport

CIMMYT Leader

IRRI-CIMMYT Crop Research Informatics LaboratoryJayashree B.

Bioinformatics

ICRISAT





:: color, composition, and layout

What is decision support in breeding?

• Decide breeding strategy

o Decisions on mating designs, population sizes,phenotyping and genotyping strategies, selectionmethods and intensities

• Choice of parental lineso Integration, analysis and presentation of all

available information on potential parents withrespect to the target traits and environments.

• Recurrent selection

o Selection and advancement decisions based

relevant genotypic and phenotypic information




ParentalLines

Phenotype/Genotype

Cross/Self/Inter-mate

Selection

Make a selectionbased on phenotype

or genotype

NewLines

Parental line

selection

Where do we need it?

Devise breeding

Strategy

Simulation / Prediction




Why do we need decision support inbreeding?

• Increased speed in making decisions

o Quick turnover essential especially in multi-seasonbreed programs

• More/better information for making decisionso More markers means better decisions, but

increases complexity

• Better analysiso New analyses need to be made user friendly and

integrated with existing tools and data






Methodology and tools are available toassist breeders

• Analysis of the data such as marker effects orselection indices

• Visualization tools relying on combination of sortingand filtering.

• These tools range from

o standalone tools for visualization that oftencarryout a limited range of tasks

o to command-line statistical applications that havea great deal of flexibly but require seriousprogramming knowledge.




Problems with current support• Phenotypic, genotypic and genetic data required for

these tools are usually available from disparatesources and formats

• Are not integrated with databases

• Labour intensiveo Requires a lot of reformatting of data from one

format to another

o Not user friendlyo Requires statistics / programming knowledge

• Does not support large numbers of markers

• Software not fully open/free!




MB Support Tool - Development plans

• A single desktop application that will consist of

o Molecular Breeding Design (MBD) Module toprovide support for design of initial crosses andstrategy

o Molecular Selection (MoSel) Module to providesupport for subsequent selections

• Will use the extended GCP informatics platform toretrieve both breeding and public data from local andweb resources and create new germplasm lists

• Integrate with simulation tools




Molecular Breeding Design (MBD) Module

• Select parental germplasm based on

o presence or absence of traits in potential parents

o compatibility between donors and recipients

o genetic distance matrices based on pedigree(COP) and where available molecular data

o analysis of background similarity via geneticdistance matrices

• Design target genotype and create crossinglists/input files for Molecular Breeding Platform

• In development at ICRISAT




MBD Module – Current functionality (1)• Read germplasm lists,

genotype data, trait data, map

data• Display graphical genotypesof potential donors &recipients

• Display linkage maps andQTL

• Check availability ofgenotyping data for selectedmarkers

• Generate list of unscreenedmarkers, file to be passed tomolecular LIMS

Graphical

genotypes

Linkagemap

QTLs

Unscreened

markers list

Export files

to LIMS






MBD – User feedback

Demonstrated tobreeders atICRISAT. Furtherdevelopment willfollow closely twoMAB projectsDonor

Recurrent

Target

Distance

matrix

Allele drag and

drop from donor to

target




MBD Module – Future functionality• Overlaying of QTL data: multiple populations, multiple

environments, multiple traits.

• Provide for integration and display of additional trait metadata

• Input file formats for QTL data – currently PlabQTL (iMAS), toadd QTL cartographer besides a generic QTL data template.

• Allow flanking markers to multiple QTLs to be selected and sortfor multiple markers before a choice of suitable recurrent ismade.

• Allow display of consensus linkage maps and positioning ofQTLs by marker name rather than map position.

• Expanded tool tip to include color coded information on additiveeffects and LOD scores of individual QTLs.




Molecular Selection (MoSel) Module

• Facilitate the selection of the most promising lines in terms of

closeness to the target genotype and likelihood of reaching thetarget according to a proposed development strategy.

o Integrate and display genotype and phenotype information

o Order, group and filter lines• Based on selection indices, marker associations

o Send data to simulation tool to predict how the program maycontinue

o Choose lines and crossing schemes for further development

• Send to MB informatics platform (MB)

• In development at CIMMYT




MoSel – Current functionality

Query integrate anddisplay genotypeand phenotype

information

Filter and sort




MoSel Module – Future functionality (1)

• Partitioned display of foreground and background

markers• Integration with R statistical software to assign and

useo

marker effects for different loci.o Selection Indices• Extendable so that newly developed analytical

measures can quickly integrated and tested

• Filter, sort and scroll genotype displays for test linesby proximity to target and recurrent lines based ongenetic and phenotypic values




MoSel Module – Future functionality (2)

• Aid selection of lines and send back to the MB

platform as crossing lists for the next cycle• Markers fixed in recipient populations should also be

identified so that they do not need to be processedfor subsequent generations.

• Highlight suitable polymorphic markers for use in thedefinition of marker-trait associationso For example identification of x number of evenly

distributed polymorphic markers for mapping






GIDs must bepresent in ICIS forall parental lines

Record Phenotype

and Genotype data

in ICIS

Generate phenotypeor genotypeworkbooks

Generate derivativeGIDs in ICIS / MFB

Initial genotypingpolymorphisms

detected

Parental

Lines

Phenotype

/GenotypeSelf/Cross

Selection

Molecular Selection(MoSel)

New

Lines

Molecular BreedingDesign (MBD)

Simulation ToolsQuLine / QuMARS

etc















Latest version on DTMA wiki http://wiki.cimmyt.org/confluence/display/DTMAunder Molecular Breeding




AcknowledgmentsDevelopment Team

• Luis Avila, Martin Senger, Richard Bruskiewich, Jose Crossa(IRRI-CIMMYT)

• Jayashree B, Prathyusha C, Reetu T (ICRISAT)

• Graham McLaren (GCP)

Proposed User Teams

• Gary Atlin, Yunbi Xu (CIMMYT) and Sarah Hearne (IITA) -

Maize• Yann Mannes and Susanne Dreisigacker (CIMMYT) - Wheat

• Tom Hash, Nepolean T (ICRISAT) – Pearl millet

• Pooran Gaur (ICRISAT) - Chickpea

Documents

MBP Davenport