From Genome to Wheat:From Genome to Wheat:

Emerging opportunities Emerging opportunities for modelling wheat for modelling wheat growth and developmentgrowth and development

Jeff WhiteJeff WhiteUSDA ARS, Phoenix, AZUSDA ARS, Phoenix, AZjwhite@uswcl.ars.ag.govjwhite@uswcl.ars.ag.gov

Current status of crop models:Current status of crop models:Tremendous interest but frustrating level Tremendous interest but frustrating level of scientific output and applicationof scientific output and application

Still too much “snake oil”Still too much “snake oil”–– Prediction vs. understanding Prediction vs. understanding –– Salesmen prosperSalesmen prosper

Model development is often Model development is often independent ofindependent of–– Structured testing Structured testing –– Application for understandingApplication for understanding

Software lacksSoftware lacks–– Version controlVersion control–– DocumentationDocumentation–– True modularityTrue modularity–– MaintenanceMaintenance

OpportunitiesOpportunities–– Improved instrumentationImproved instrumentation–– Functional genomicsFunctional genomics–– Spatial analysis tools

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– Data management tools – Programming strategy– Software management toolsSpatial analysis tools

Model calibration for cultivars...Model calibration for cultivars...

Progress in sequencing the Progress in sequencing the Arabidopsis Arabidopsis genomegenome

Source:

The Arabidopsis Information Resource (TAIR)

Six levels of genetic detail in Six levels of genetic detail in crop simulations modelscrop simulations models1. Generic 1. Generic -- no speciesno species2. Species2. Species--specific specific -- no cultivarsno cultivars3. Cultivar specific parameters3. Cultivar specific parameters4. Cultivar differences represented by 4. Cultivar differences represented by

genotypes with linear effects on model genotypes with linear effects on model parametersparameters

5. Cultivar differences expressed through 5. Cultivar differences expressed through processes described using knowledge of processes described using knowledge of gene expression and gene productsgene expression and gene products

6. Full model of regulators, gene6. Full model of regulators, gene--products, products, etc. etc. –– Systems BiologySystems Biology

Recent landmarks in wheat Recent landmarks in wheat genomicsgenomics

RhtRht : sequenced (Peng et al, 1999): sequenced (Peng et al, 1999)–– Homologous to Homologous to GAIGAI in arabidopsisin arabidopsis

VrnVrn--A1A1 : sequenced (Yan et al., 2003): sequenced (Yan et al., 2003)–– Similar to Similar to APETALA1APETALA1 in arabidopsisin arabidopsis

TaHd1TaHd1 : sequenced (Nemoto et al., 2003) : sequenced (Nemoto et al., 2003) –– Homologous to Homologous to HdHd in rice and in rice and COCO in arabidopsis in arabidopsis

VrnVrn--A2A2 : sequenced (Yan et al., 2004): sequenced (Yan et al., 2004)PpdPpd : [coming soon]: [coming soon]

Are we ready for geneAre we ready for gene--based based wheat modeling?wheat modeling?

Is wheat a suitable target species?Is wheat a suitable target species?–– Genetically “well characterized”Genetically “well characterized”–– Physiologically well studiedPhysiologically well studied–– Abundance of modelsAbundance of models

What are likely benefits?What are likely benefits?–– Dissect error related to calibration of cultivarsDissect error related to calibration of cultivars–– Improve underlying physiologyImprove underlying physiology–– Improve representation of G x EImprove representation of G x E

How to start?How to start?

Wheat Genes: PhenologyWheat Genes: Phenology

Required for vernalization Required for vernalization VrnVrn--A2A2

Earliness Earliness per seper seEpsEps--A1aA1aLong day requirementLong day requirementPpdPpd--D1D1Long day requirementLong day requirementPpdPpd--B1B1Long day requirementLong day requirementPpdPpd--A1A1??VrnVrn--B4B4

Reduces vernalization (spring habit)Reduces vernalization (spring habit)VrnVrn--D1D1Reduces vernalization (spring habit)Reduces vernalization (spring habit)VrnVrn--B1B1Reduces vernalization (spring habit)Reduces vernalization (spring habit)VrnVrn--A1A1DescriptionDescriptionGeneGene

Wheat Genes: Plant height, etc.Wheat Genes: Plant height, etc.

Reduced height (dwarfing)Reduced height (dwarfing)RhtRht--D1cD1c

Tiller inhibitionTiller inhibitionTinTinHairy leafHairy leafHl1, Hl2Hl1, Hl2Awns (and grain size, drought …)Awns (and grain size, drought …)B1, B2B1, B2Awns (and grain size, drought …)Awns (and grain size, drought …)HdHdmore of the samemore of the same……Rht20Rht20

Reduced height (dwarfing)Reduced height (dwarfing)RhtRht--B1cB1cReduced height (dwarfing)Reduced height (dwarfing)RhtRht--D1bD1bReduced height (dwarfing)Reduced height (dwarfing)RhtRht--B1bB1bDescriptionDescriptionGeneGene

Wheat Genes: Other traitsWheat Genes: Other traits

PrePre--harvest sprouting, seed harvest sprouting, seed dormancydormancy

PhsPhs

Frost toleranceFrost toleranceFr1, Fr2Fr1, Fr2AlAl--activated malate transporteractivated malate transporterALMT1ALMT1Copper efficiencyCopper efficiencyCeCeLow cadmium uptakeLow cadmium uptakeCdu1Cdu1Tolerant to high levels of boronTolerant to high levels of boronBo1, Bo2, Bo3Bo1, Bo2, Bo3

Osmotic regulationOsmotic regulationOrOrGrassGrass--DwarfingDwarfingD1D1……D4D4Seed protein contentSeed protein contentPro1, Pro2Pro1, Pro2DescriptionDescriptionGeneGene

Genome size and chromosome Genome size and chromosome numbersnumbers

Genome size(pg DNA)

ChromosomenumberCrop

Arabidopsis 0.4 10

Rice 1.0 24

Corn 5.4 20

Barley 11.1 14

Bread wheat 34.7 42

Common bean 1.2 22Cotton 6.4 52

12.5 14Triticum monococcumTriticum monococcum

Cumulative phenotypic variance in time to Cumulative phenotypic variance in time to silking that is explained by QTLs in the maize silking that is explained by QTLs in the maize cross Ki3 x CML139cross Ki3 x CML139

Data source: Khairallah et al., 1998Data source: Khairallah et al., 1998

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QTLs on Wheat Chromosome 3AQTLs on Wheat Chromosome 3ASource: Shah et al., 1999Source: Shah et al., 1999

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Many genes vs. Many genes vs. thousands of genesthousands of genes

QTL analysis supports many genes, but ...QTL analysis supports many genes, but ...–– Clusters of genesClusters of genes–– Artifact of wide crossesArtifact of wide crosses–– Artifact of statistical analysesArtifact of statistical analyses

Many genes “irrelevant” at the crop levelMany genes “irrelevant” at the crop level–– Basic processesBasic processes–– Disease and pest resistance/responseDisease and pest resistance/response–– Reproductive processReproductive process–– Endosperm proteins and carbohydratesEndosperm proteins and carbohydrates

Wheat:Wheat:Important Important cropcropPublic sectorPublic sectorPure linesPure linesKnown genesKnown genesDeletion linesDeletion linesIsogenic linesIsogenic linesDihaploidsDihaploidsWide crossesWide crossesField dataField dataModelsModelsHomologies Homologies with ricewith rice

THETHEGOODGOOD

Huge genomeHuge genomeTransformation Transformation (but rice works)(but rice works)Limited diversityLimited diversity……

THETHEBADBAD

DiseasesDiseasesUntidy growthUntidy growth……

AND THEAND THEUGLYUGLY

How to Implement GeneHow to Implement Gene--Based Based Modeling in WheatModeling in Wheat

What scale to focus on?What scale to focus on?–– Molecular Molecular –– level 6level 6–– “Macro” “Macro” –– level 4 & 5level 4 & 5Which traits to focus on? Which traits to focus on? How to access genetic and molecular How to access genetic and molecular data?data?ImplementionImplemention per seper se

DNAExon1 Intron1 Exon2

Pre-mRNA

mRNA

Ribosome

Nucleus

Cytoplasm

Transcription

Splicing

Transport

TranslationmRNA

Polypeptide

Conceptual model for control Conceptual model for control of flowering in of flowering in ArabidopsisArabidopsis

Source: John Source: John Innes Centre for Innes Centre for Molecular GeneticsMolecular GeneticsFour pathwaysFour pathways–– PhotoperiodPhotoperiod–– VernalizationVernalization–– AutonomousAutonomous–– GibberellinGibberellin

EE--CELL CELL -- A whole cell simulatorA whole cell simulatorM. Tomita et al., 1999M. Tomita et al., 1999

““Systems Biology”Systems Biology”

Builds on bioinformaticsBuilds on bioinformaticsEmphasizes networksEmphasizes networksSystems Biology Markup Systems Biology Markup LanguageLanguageSeeks a “Theory of Everything”?Seeks a “Theory of Everything”?

Six levels of genetic detail in Six levels of genetic detail in crop simulations modelscrop simulations models1. Generic 1. Generic -- no speciesno species2. Species2. Species--specific specific -- no cultivarsno cultivars3. Cultivar specific parameters3. Cultivar specific parameters4. Cultivar differences represented by 4. Cultivar differences represented by

genotypes with linear effects on model genotypes with linear effects on model parametersparameters

5. Cultivar differences expressed through 5. Cultivar differences expressed through processes described using knowledge of processes described using knowledge of gene expression and gene productsgene expression and gene products

6. Full model of regulators, gene6. Full model of regulators, gene--products, products, etc. etc. –– Systems BiologySystems Biology

GeneGro V1GeneGro V1Based on BEANGROBased on BEANGRO–– Predecessor of CROPGROPredecessor of CROPGRO–– 30 cultivar30 cultivar--specific coefficientsspecific coefficientsLinear effects of seven genesLinear effects of seven genes–– Ppd, Hr, Fin, Fd, SszPpd, Hr, Fin, Fd, Ssz--1, Ssz1, Ssz--2, Ssz2, Ssz--33–– P = a + b G + c H …P = a + b G + c H …Performed very similar to BEANGROPerformed very similar to BEANGRO–– Calibration set: 30 cvs., 14 trialsCalibration set: 30 cvs., 14 trials–– Validation set: 39 cvs., 14 trialsValidation set: 39 cvs., 14 trials

Examples of genotypes specified Examples of genotypes specified for cultivars in GeneGrofor cultivars in GeneGro

00000000000000SeafarerSeafarer00000000000011FleetwoodFleetwood

11000000110000JamapaJamapa

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001111

Ssz2Ssz2

110000110011Porrillo S.Porrillo S.

111111111111Pinto UI114Pinto UI114111100000011CalimaCalima111100000000RedkloudRedkloud

Ssz3Ssz3Ssz1Ssz1FdFdFinFinHrHrPpdPpdCultivarCultivar

Field plot for screening bean cultivars Field plot for screening bean cultivars for photoperiod sensitivityfor photoperiod sensitivity

Photoperiod response of diverse bean Photoperiod response of diverse bean germplasm at germplasm at Palmira (25Palmira (25ooC) and Popayan (19C) and Popayan (19ooC)C)

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Implementing linear effects of Implementing linear effects of genotypegenotype

Genotype cultivars for relevant genes:Genotype cultivars for relevant genes:Photoperiod, phenology Photoperiod, phenology per seper se, growth habit …, growth habit …

Characterize same cultivars for cultivar Characterize same cultivars for cultivar specific model parametersspecific model parametersEstimate effects of genes for each parameter Estimate effects of genes for each parameter using linear regression:using linear regression:–– Genotypes coded as Genotypes coded as 1 = dominant or 1 = dominant or

0 = recessive0 = recessive

–– Equations of form Equations of form P = a + bG + cH ...P = a + bG + cH ...

Examples of genotypes specified Examples of genotypes specified for cultivars in GeneGrofor cultivars in GeneGro

00000000000000SeafarerSeafarer00000000000011FleetwoodFleetwood

11000000110000JamapaJamapa

00

001111

Ssz2Ssz2

110000110011Porrillo S.Porrillo S.

111111111111Pinto UI114Pinto UI114111100000011CalimaCalima111100000000RedkloudRedkloud

Ssz3Ssz3Ssz1Ssz1FdFdFinFinHrHrPpdPpdCultivarCultivar

Examples of gene effects Examples of gene effects assumed in GeneGro V1assumed in GeneGro V1

Single gene, with two allelesSingle gene, with two allelesLFMAX = 1.080 LFMAX = 1.080 -- 0.095 0.095 FinFin RR22 = 0.35**= 0.35**

Two genes, no interactionTwo genes, no interactionPHTHRS[5] = PHTHRS[5] =

21.80 21.80 -- 7.02 7.02 FdFd + 4.56 + 4.56 FinFin RR22 = 0.79**= 0.79**Two genes that interact (epistasis)Two genes that interact (epistasis)CLDVAR = CLDVAR =

16.80 16.80 -- 0.08 0.08 Ppd + Ppd + 0.08 0.08 HrHr + 0.80 + 0.80 Ppd HrPpd HrRR22 = 0.45**= 0.45**

GeneGro V1GeneGro V1Performed as well as Performed as well as original original BEANGROBEANGRO–– Validation data set: Validation data set:

39 cvs.39 cvs.14 trials14 trials4 countries4 countries

How to Implement GeneHow to Implement Gene--Based Based Modeling in WheatModeling in Wheat

What scale to focus on?What scale to focus on?–– Molecular Molecular –– level 6 and systems biology level 6 and systems biology –– “Macro” “Macro” –– level 4 & 5level 4 & 5Which traits to focus on? Which traits to focus on? How to access genetic and molecular How to access genetic and molecular data?data?ImplementionImplemention per seper se

Grain yield vs. days to maturity Grain yield vs. days to maturity PBW 34, 8 dates, 7 years, Ludhiana, Punjab, IndiaPBW 34, 8 dates, 7 years, Ludhiana, Punjab, IndiaSource: S.S. Dhillon Source: S.S. Dhillon

y = 34.305x - 1839

R2= 0.67**

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Observed response of anthesis date to time of Observed response of anthesis date to time of sowing for two wheat cvs. sowing for two wheat cvs. at Ludhiana, Punjabat Ludhiana, PunjabSource: S.S. DhillonSource: S.S. Dhillon

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Conceptual model for transition from Conceptual model for transition from vegetative to reproductive growth in vegetative to reproductive growth in wheat. wheat. Source: Murai et al., 2003Source: Murai et al., 2003

VegetativeVegetative ReproductiveReproductive

VrnVrn

Photoperiod Photoperiod pathwaypathway

PpdPpd

Vernalization Vernalization pathwaypathway

Short daysShort days Long daysLong daysLow Low temperaturestemperatures

Major wheat genes affecting Major wheat genes affecting phenologyphenology

Awns may accelerate heading and Awns may accelerate heading and maturitymaturity

Hd, B1Hd, B1

Reduced height can affect phenologyReduced height can affect phenologyRhtRht

Photoperiod response (effect unclear)Photoperiod response (effect unclear)TaHd1TaHd1Earliness Earliness per seper seEpsEps

Reduces vernalization requirementReduces vernalization requirementVrnVrn

Long day responseLong day responsePpdPpd

DescriptionDescriptionGene Gene familyfamily

Reported effects of Reported effects of Rht Rht genegeneInternode lengths (Internode lengths (--))Leaf blade and sheath length (Leaf blade and sheath length (--))Assimilate partitioning, HI (+)Assimilate partitioning, HI (+)Development (+/Development (+/--))Kernel weight (Kernel weight (--) ) Cell length (not width)Cell length (not width)WUE (+/WUE (+/--))RUE (+)RUE (+)Roots: Length (0), RLD (+)Roots: Length (0), RLD (+)Coleoptile length (Coleoptile length (--), seedling vigor (), seedling vigor (--))

Implementing linear effects of Implementing linear effects of genotypegenotype

Characterize cultivars for relevant genes:Characterize cultivars for relevant genes:Photoperiod, phenology Photoperiod, phenology per seper se, growth habit …, growth habit …

Characterize same cultivars for cultivar Characterize same cultivars for cultivar specific model parametersspecific model parametersEstimate effects of genes for each parameter Estimate effects of genes for each parameter using linear regression:using linear regression:–– Genotypes coded as Genotypes coded as 1 = dominant or 1 = dominant or

0 = recessive0 = recessive

–– Equations of form Equations of form P = a + bG + cH ...P = a + bG + cH ...

How to access required data?How to access required data?

Genotype listGenotype list–– GCTE databaseGCTE databaseGenesGenes–– DatabasesDatabases–– Expert opinionExpert opinion–– Rapid screeningRapid screeningCrop response/environmentsCrop response/environments–– GCTE databaseGCTE database–– Isogenic linesIsogenic lines

Options for characterizing Options for characterizing wheat genotypeswheat genotypes

****$$$$******Screening toolsScreening tools

******$$$$********Molecular toolsMolecular tools

********$$******DatabaseDatabase

********$$**Pedigree analysisPedigree analysis

**$$$$$$$$********Test crossesTest crosses

SpeedSpeedCostCostReliabilityReliability

Examples of interesting wheat Examples of interesting wheat studies using nearstudies using near--isogenic linesisogenic lines

Phillips (1992): Winter/Spring, 6 Phillips (1992): Winter/Spring, 6 backgrounds, 15 environments (plus Turkey)backgrounds, 15 environments (plus Turkey)GAWYT: CIMMYT trial, various GAWYT: CIMMYT trial, various Vrn & Ppd Vrn & Ppd xx30+ locations (200030+ locations (2000--2001)2001)Borrell et al. (1993): Borrell et al. (1993): Rht Rht in Triple Dirkin Triple DirkWorland & Worland & SayresSayres (1996): (1996): PpdPpd--D1D1FlinthamFlintham et al. (1997):et al. (1997): Rht Rht in winter wheatsin winter wheats……

Conceptual model for transition from Conceptual model for transition from vegetative to reproductive growth in vegetative to reproductive growth in wheat. wheat. Source: Murai et al., 2003Source: Murai et al., 2003

VegetativeVegetative ReproductiveReproductive

VrnVrn

Photoperiod Photoperiod pathwaypathway

PpdPpd

Vernalization Vernalization pathwaypathway

Short daysShort days Long daysLong daysLow Low temperaturestemperatures

Variation in tissueVariation in tissue--level expression of level expression of FLFFLF gene in gene in Arabidopsis. Arabidopsis. Source: Sheldon et al., 1999Source: Sheldon et al., 1999

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For actual image see For actual image see Sheldon, C.C., Sheldon, C.C., J.E. Burn, P.P. Perez, J. Metzger, J.A. J.E. Burn, P.P. Perez, J. Metzger, J.A. Edwards, W.J. Peacock, and E.S. Edwards, W.J. Peacock, and E.S. Dennis. 1999. The FLF MADS box Dennis. 1999. The FLF MADS box gene a repressor of flowering in gene a repressor of flowering in Arabidopsis regulated by vernalization Arabidopsis regulated by vernalization and and methylationmethylation. The Plant Cell 11445. The Plant Cell 11445--458.458.

Effects of vernalization regime on Effects of vernalization regime on expression of VIN3 gene in expression of VIN3 gene in Arabidopsis.Arabidopsis.Source: Sung & Amasino, 2004Source: Sung & Amasino, 2004

No No vernalizationvernalization

40 days 40 days vernalizationvernalization

40 days 40 days vernvern. . + 5 days 22+ 5 days 22°°CC

For actual image see:For actual image see:

Sung, S., and R.M. Sung, S., and R.M. AmasinoAmasino. . 2004. Vernalization in Arabidopsis 2004. Vernalization in Arabidopsis thalinathalina is is mediaedmediaed by the PHD by the PHD finger protein VIN3. Nature finger protein VIN3. Nature 427:159.427:159.

Steps toward geneSteps toward gene--based based wheat modelswheat models

Two pronged approach: Two pronged approach: –– Cultivar variationCultivar variation–– Underlying processesUnderlying processes

Start with:Start with:–– PhenologyPhenology–– Growth habitGrowth habit

Characterize genotypes of cultivars in Characterize genotypes of cultivars in GCTE data setsGCTE data sets“Rescue” field data for near isogenic lines“Rescue” field data for near isogenic linesNew research:New research:–– Gene expression studies: timing & tissues Gene expression studies: timing & tissues –– Gene controversies (e.g., Gene controversies (e.g., Eps, Or, TaHd1)Eps, Or, TaHd1)–– Gene discovery for Gene discovery for traits in modelstraits in models