CAGE Project meetingAdelaide March 2006

• Generation Challenge Program projects– QTLxE (Wageningen University Research)– Simulating MAS (CSIRO PI)– Whole-plant modelling (CIRAD)

• DArT results for IAT• Some ideas for future of IAT research

Eco-physiological models for QTLxEIntegrating statistical and physiological approaches

Ky Mathews, Scott Chapman (CSIRO, Australia)Fred van Eeuwijk, Marcos Malosetti, Martin Boer, Marco Bink (WUR) Matthew Reynolds, Jose Crossa, Jean-Marcel Ribaut (CIMMYT)Mateo Vargas (Univ. Chapingo, MX)

Aims

Develop a statistical methodology for modelling QTL effects in mult-environment, multi-trait datasets. Subsequently incorporate environment covariates to explain QTL by environment interaction

Approach• built on factorial regression• flexible for incorporation of multi-QTLs, and multi-

environment• implemented in standard statistical packages• being applied in maize and wheat

Results for wheat population SeriBabax, yield

BABAX

SERI

yield (t/ha)4.703.502.446.412.204.183.22

Further work & other approaches

Further work• Incorporate environmental covariates• Extend to multi-traitMalosetti M et al (2004) Euphytica 137:139-145Other approaches

Verybla, Cullis and Thompson (2007) accepted by TAG (under revision)The full linkage map is included in a working model and outlier techniques are used to select putative QTL

Optimizing marker-assisted breeding systems for drought tolerance in cereals through linkage of physiological and genetic models

Scott Chapman, David Bonnett, Greg Rebetzke (CSIRO Plant Industry)Jiankang Wang, Jonathan Crouch (CIMMYT)Graeme Hammer, Mark Dieters (University of Queensland)Francois Tardieu, Claude Welcker (INRA)CGIAR plant breeders

ENGINE

QUG

GESG-E System

POPGermplasm

POPGermplasm

QMPParameters

QU-LINE

QU-MASS

QU-PEDRRS

G-P Plugin

Output1

Output2

Output...

Outputn

QU-RRS

QU-MAS

QU-LINEQU-LINE

QU-RRS

QU-MAS

• Models populations of genotypes undergoing recombination, crossing and selection

• Project Aims– develop software tools

to capture and use molecular map data in simulation

• ‘map’ editor• phenotype ‘plug-ins’

• Example simulations– parent building– MAS to increase

coleoptile length without affecting height

• Contact for licence:mark.dieters@uq.edu.au

Exploring Landscapes with QU-Gene

New interface to capture and select gene and marker information

• Create an XLS file with Info on genes, markers, effects, populations

• Read into gene editor

• Sets of QTL and markers can be selected for MAS simulations

Interface with Triticarte 4A chromosome for Cranbrook/Halberd

• complete chromosome with 1 ‘real’ QTL and 2 ‘noisy’ QTL

Interface with Triticarte 4A chromosome for Cranbrook/Halberd

• Same chromosome after selecting QTL and only flanking markers

‘Physiological’ model plug-ins

• Allows testing of module with inputs of weather and QTL coefficients

• Currently testing various selection and QTL scenarios for drought related traits

MAS for long coleoptilesResults of 1000 simulations

• Coleoptile length – 2 major (height) QTL + 5 minor QTL• Aim to retain large number of lines at end of selection• Compared MAS, PS and combinations of MAS and PS at different

stages of selection (F2, DH etc)• Found best strategies to maximise number of desired DH lines

Wang et al. (2007) Application of Population Genetic Theory and Simulation Models to Efficiently Pyramid Multiple Genes via Marker-assisted Selection. Crop Science (in press)

B. Selection conducted with 400 DH lines derived from F2 individuals fixed at Rht8

0

10

20

30

10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250

Number of DH lines with coleoptile length > 120 mm

Fre

quen

cy (

%) No selection

MASPSMAS+PSPS+MAS

Qu-Gene extensions

• QUG file editor– allows separate incorporation of genes (QTL); markers; and ‘noise’– could be connected to databases of molecular marker locations,

and QTL locations and effect sizes– allows simulation of value of markers in terms of potential genetic

gain rather than % variance explained– (Cooper et al 2005, AJAR)

• Phenotype plug-ins– allows phenotype to be provided by external module for infinite

expansion– e.g. can have genes that control coleoptile length or leaf growth

directly, or control these processes via a combination of genes with environment…

1A 1A z 4B 4B 7A 3B z z 3A 4A 4A 3B 7B 7B 7B 7B z z 2B_ 3A 5A 1A 1B 7B_ 3A 2A 3A 6A 6A 5A 6A z 1D 6A 6Az 1B z 5B 7A 7A 6A 6A z 1B 6A z z z 1B 1B z z z 1B z z z 3B 3BL 1B 5B 3A 4A 4A 4B 2Dz

6D 4A 2D 7B 2D 2D 1Bz 7B 7B_ 1B z z 2B 2B 2B z 2A 3Dz 2B 4B 3B 3B 3B 7B z 4A 6B 6B 6B 6B 6B 1A

3.0/

23 1D 1D 1A1A

/7A 7A z 1A 1A 5B z z 3B z 4A

7D/L

G2

7D 6Bz z z z z z z z z z z z z z 1A 4A 7D 7D 5D 5A 1A 7B 5D 4A 4A 4A 4A 4Az z 2B 2B 1D 6Dz

1D 3A 7A 7A 7B 6B 3DL

1D 2B 2B 6B 6B 3A 7B 7B 5B 3Az 6B 7B 3A 4A 4A 7A z 2A 7B 1A 2B 2B 2B 5B 6B z z z 5B z 5Dz 3B 3BL 6B z z 4B 5A 3B 3B 3B 3B 3B 5B 4A 6B z z 4B 1B 2A 2A 7B 3A z z z 7B z 5A 7B 2B 2B 1B 2B 2B 2B 2B 6A 1A 1D 1D 3Az z 5A 1D 1Az 3B 6B 5B z 7A 4A z 4A 4A 4A 4A z 4A z 3B 4A z 6A 2B 2B 5B 3B 7B z 2A 4A 3B 3B 3B 3A 6B z z z 1B 6B z 6B 2B 2B

2B_2 z 7B 6D 2A 5B 5B 2Bz z z 1B 1B 1B 6B z z 5A z 1D 3Dz z 1B z 2B z z z z z 2B

2.0/

62.

0/6 5B z z z z z

KAUZTALL - CIMMYTKAUZDWARF - CIMMYTPROINTAFEDERAL - CIMMYTSITTA - CIMMYTKennedy - LRCDOLLARBIRD - WWATTILA - CIMMYTINQALAB91 - CIMMYTSERI-M82 - CIMMYTSERITALL - CIMMYTSERI-cross - CIMMYTSERIDWARF - CIMMYTSCHOMBURGK - WARIKrichauff - WARIBT-SCHOMBURGK - WARIYR10-WARIGAL - WARIWW425 - CIMMYTFrame - WARIExcalibur - RACSunlin - SUNCADOUX - WAGoroke - VIC-HCROC_1/AE.SQUARROSA(205)//KAUZ - CIMMYTJanz - LRCSunvale - SUNPelsart - LRCSunco - SUNSAAR - CIMMYTBATAVIA - LRCGATCHER - SUGATCHERGS50A - SUWARIGAL - WARIKATUNGA - VICPRL/SARA//TSI/VEE&5 - CIMMYTBarunga - WARICHIL/PRL - CIMMYTTUI - CIMMYTBaxter - LRCTrident - RACCETTIA - CIMMYTTAM200/TUI - CIMMYTSILVERSTAR - WWVULCAN - SPSBabax - CIMMYTBabax-cross - CIMMYTNESSERTALL - CIMMYTNESSERDWARF - CIMMYTWestonia - WWGALVEZDWARF - CIMMYTGALVEZTALL - CIMMYTJUN/BOMB - CIMMYTPAVONTALL - CIMMYTPAVONDWARF - CIMMYTDiamondbird - WWHartog - LRCSONALIKA - CIMMYTDHARWARDRY - CIMMYTHXL7573/2*BAU - CIMMYTPastor - CIMMYTIATline44 - CIMMYTURES/JUN//KAUZ - CIMMYTPASTOR*2/OPATA - CIMMYTSUPERSERI-1 - CIMMYT

2005 resultsJaccard dist

clustered and coloured by

chromosome and breeding program

1618

216

158

1641

016

415

1544

620

461

1695

516

645

2064

415

693

2113

516

631

2006

316

651

1643

166

594

6661

966

463

1638

916

841

2156

516

497

1637

715

403

1546

963

453

7371

866

475

1951

477

884

7264

415

211

6352

577

752

7797

573

887

1658

619

506

2004

263

386

7805

920

066

2147

920

763

2153

566

665

1657

666

518

1945

966

713

1668

116

910

2043

420

067

1609

916

501

1963

116

338

1693

716

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1611

016

554

1521

220

152

1544

217

439

1667

417

079

1550

263

501

1561

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722

7795

916

437

7804

716

056

1703

016

375

7802

716

626

1653

019

886

1547

715

547

1950

721

714

2030

416

154

6678

215

252

2021

416

369

2011

220

136

2087

416

436

1676

416

207

1639

619

937

1630

163

403

6366

416

357

1951

966

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2108

319

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1527

815

475

1556

816

608

1662

216

553

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277

2061

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716

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215

289

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661

2144

519

688

1653

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512

1586

321

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116

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1640

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1561

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151

1570

520

770

1649

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145

1678

919

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6677

615

526

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416

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1952

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291

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489

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276

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766

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244

2039

666

541

1660

716

523

2094

772

373

7247

916

367

2057

516

934

1550

421

315

1971

166

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1555

315

576

1555

277

823

1638

416

445

1532

466

714

1681

319

876

6368

219

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2050

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280

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543

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237

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2167

415

734

6664

216

662

1624

616

009

1651

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313

1633

716

652

6667

815

833

1959

315

617

1624

415

860

1540

516

833

7792

516

614

1602

821

254

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619

551

1628

516

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377

889

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363

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567

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7802

216

930

1708

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539

1552

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096

1607

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977

1638

515

345

1697

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1952

416

268

1526

616

408

7389

215

263

1700

316

697

1672

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301

1613

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543

1525

915

503

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916

912

1530

319

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2081

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819

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752

1673

316

465

1644

216

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1527

715

307

1535

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838

7795

216

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1594

115

658

1662

116

840

1976

666

759

7789

516

732

1644

115

494

1657

516

596

1685

916

932

1659

816

692

2014

720

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171

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1631

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644

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242

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629

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1951

616

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300

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708

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616

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232

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721

617

6364

616

391

6362

116

472

1634

215

827

1521

815

746

1567

216

881

1522

766

610

1970

115

387

1624

515

234

1639

416

101

1645

621

256

2138

815

228

1646

719

770

6358

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479

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116

722

1632

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116

505

7271

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840

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1990

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314

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1949

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1697

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1955

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484

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516

232

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815

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2141

521

212

1540

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734

1532

115

546

1957

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565

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295

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286

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2100

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1963

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2059

116

038

1710

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599

1710

315

819

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983

1700

721

406

2115

678

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1982

317

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2024

216

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7381

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471

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1659

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600

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1600

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098

1527

566

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6669

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511

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1968

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1988

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488

2080

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1948

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1656

7

CNDO/R143//ENTE/MEXI_2/3/AEGILOPSVEE/MJI//2*TUI/3/PASTORKAUZ TALLTOB/ERA//TOB/CNO67/3/PLO/4/VEE#5/5URES/JUN//KAUZSITTASERI DWARFSERI TALLSUNLINKAUZ DWARFTRIDENTHALBERDFRAMEPUGSLEYBARUNGASCHOMBURGKPROINTA FEDERALKRICHAUFFYR10-WARIGALWARIGALBT-SCHOMBURGKBAXTERBJY/COC//PRL/BOW/3/ATTILACADOUXGATCHERGATCHER GS50AKATUNGACARNAMAHWYALKATCHEMTUIYITPIANNUELLOWYLAHJANZSUNCOPELSARTSUNVALESUNBRINESSER TALLNESSER DWARFEGA HUMEBATAVIAVULCANCHARAROSELLAGOROKEGBA COMBATBABBLERCROC_1/AE.SQUARROSA (205)//KAUZURES/PRL//BAV92MILAN/KAUZ//BABAX/3/BABAXWEEBILL1CHEN/AE.SQ//WEAVERPASTOR/3/ALTAR 84/AEGILOPS SQUARCROC_1/AE.SQUARROSA (224)//OPATA/PRL/2*PASTORSAARIRENA/BABAX//PASTORPASTOR/BAV92BABAXPASTOR/3/VEE#5//DOVE/BUCGEN*2//BUC/FLK/3/2*PASTORFILIN/2*PASTORPASTORSONALIKADHARWAR DRYEGA BONNIE ROCKWW425HXL7573/2*BAUATTILA*2/PBW65ATTILASILVERSTARKENNEDYSUPER SERI #1INQALAB 91TAM200/TUICETTIACHIL/PRLWESTONIAPRL/SARA//TSI/VEE#5JUN/BOMBGALVEZ TALLGALVEZ DWARFDRYSDALEVENTURASUNSTATEHARTOGDOLLARBIRDPASTOR*2/OPATADIAMONDBIRDEXCALIBURREESPAVON TALLPAVON DWARF

02/2007 results

PCA of DArT data (NAs set to 0.5)

-15 -10 -5 0 5 10

-10

-50

510

PC1

PC

2

SCHOMBURGKBT-SCHOMBURGK

TRIDENT

FRAME

WARIGALYR10-WARIGAL

EXCALIBUR

KATUNGA

BARUNGA

GOROKE

CADOUX

KRICHAUFF

DOLLARBIRD

WESTONIAJANZPELSART

HARTOG

GATCHER GS50AGATCHER

SUNCOSUNVALE

BATAVIA

KENNEDY

DIAMONDBIRD

WW425 SILVERSTAR

VULCANSUNLIN

ATTILA

SITTA

CETTIACHIL/PRL

TUI

JUN/BOMB

PASTOR*2/OPATA

TAM200/TUI

SUPER SERI #1INQALAB 91

PRL/SARA//TSI/VEE#5

CROC_1/AE.SQUARROSA (205)//KAUZ PASTOR

URES/JUN//KAUZ

CNDO/R143//ENTE/MEXI_2/3/AEGILOPS SQUARROSA (TAUS)/4/W

HXL7573/2*BAUPROINTA FEDERAL

DHARWAR DRY

SAAR

BABAX

SONALIKA

PAVON DWARFPAVON TALL

SERI DWARFSERI TALL

KAUZ DWARF

KAUZ TALL

NESSER DWARFNESSER TALL

GALVEZ DWARFGALVEZ TALL

BABBLER

CHARA

VENTURA

WYLAHSUNBRIBAXTEREGA HUME

REES

HALBERDPUGSLEY

DRYSDALE

GBA COMBAT

SUNSTATE

ANNUELLO

ROSELLA

YITPICARNAMAH

EGA BONNIE ROCKWYALKATCHEMWEEBILL1PASTOR/BAV92

FILIN/2*PASTORPRL/2*PASTORPASTOR/3/VEE#5//DOVE/B

URES/PRL//BAV92

CHEN/AE.SQ//WEAVERATTILA*2/PBW65

VEE/MJI//2*TUI/3/PASTO

IRENA/BABAX//PASTOR

CROC_1/AE.SQUARROSA (224)//OPATA/3/PASTOR

BJY/COC//PRL/BOW/3/ATTILA

GEN*2//BUC/FLK/3/2*PASTO

MILAN/KAUZ//BABAX/3/BABAX

TOB/ERA//TOB/CNO67/3/PLO/4/VEE#5/5/KAUZ/6/URES/JUN

PASTOR/3/ALTAR 84/AEGILOPS SQUARROSA (TAUS)//OPATA

Pavon

Cook

1BS/1RS?

??

BJY/COC//PRL/BOW/3/ATTILCADOUXGATCHERGATCHER GS50AKATUNGACARNAMAHWYALKATCHEMTUIYITPIANNUELLOWYLAHJANZSUNCOPELSARTSUNVALESUNBRINESSER TALLNESSER DWARFEGA HUMEBATAVIAVULCANCHARAROSELLAGOROKEGBA COMBATBABBLERCROC_1/AE.SQUARROSA (2URES/PRL//BAV92MILAN/KAUZ//BABAX/3/BABWEEBILL1

Australianadaptation?

Northern?

IAT – what next?

• have established strong relationships between Australian locations and CIMMYT testing locations

• Window-on-Wheat can help identify potentially useful germplasm from relevant nurseries (ESWYT, HRWYT, SAWYT) and relevant locations

• Can we identify potentially useful genomic regionsin a similar manner?

• Analysis of CIMMYT nurseries using a ‘filter’ of genetic correlations between Oz and world

LD mapping needs- historical phenotype data; many markers; lots? of lines