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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, [email protected]@uswcl.ars.ag.gov
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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
0
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5 10 15 20 25 30 35
Temperature (oC)G
rain
yie
ld (k
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CERES IWIS
– Data management tools – Programming strategy– Software management toolsSpatial analysis tools
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Model calibration for cultivars...Model calibration for cultivars...
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Progress in sequencing the Progress in sequencing the Arabidopsis Arabidopsis genomegenome
Source:
The Arabidopsis Information Resource (TAIR)
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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
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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]
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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?
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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
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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
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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
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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
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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
0
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QTL
Phen
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ic v
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nce
(%)
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QTLs on Wheat Chromosome 3AQTLs on Wheat Chromosome 3ASource: Shah et al., 1999Source: Shah et al., 1999
0
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Plant height Kernels/spike Kernel weight Spikes/m2
Phen
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expl
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d (%
)Eps Xbcd1555 Xtam61 Xcdo638 Xbcd141Locus:Locus:
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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
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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
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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
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DNAExon1 Intron1 Exon2
Pre-mRNA
mRNA
Ribosome
Nucleus
Cytoplasm
Transcription
Splicing
Transport
TranslationmRNA
Polypeptide
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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
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EE--CELL CELL -- A whole cell simulatorA whole cell simulatorM. Tomita et al., 1999M. Tomita et al., 1999
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““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”?
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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
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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
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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
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Field plot for screening bean cultivars Field plot for screening bean cultivars for photoperiod sensitivityfor photoperiod sensitivity
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Photoperiod response of diverse bean Photoperiod response of diverse bean germplasm at germplasm at Palmira (25Palmira (25ooC) and Popayan (19C) and Popayan (19ooC)C)
-0.2
0.0
0.2
0.4
0.6
0.8
1.0
-0.2 0.0 0.2 0.4 0.6 0.8 1.0
Palmira
Popa
yan
1:1
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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 ...
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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
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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**
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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
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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
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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**
1000
2000
3000
4000
5000
100 110 120 130 140 150 160 170 180
Days to maturity
Gra
in y
ield
(kg
ha-1)
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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
60
70
80
90
100
110
120
15-Oct 25-Oct 4-Nov 14-Nov 24-Nov 4-Dic 14-Dic 24-Dic
Sowing date
Day
s to
ant
hesi
s
PBW 34
HD 2329
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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
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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
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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 (--))
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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 ...
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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
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Options for characterizing Options for characterizing wheat genotypeswheat genotypes
****$$$$******Screening toolsScreening tools
******$$$$********Molecular toolsMolecular tools
********$$******DatabaseDatabase
********$$**Pedigree analysisPedigree analysis
**$$$$$$$$********Test crossesTest crosses
SpeedSpeedCostCostReliabilityReliability
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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……
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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
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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
Root
sRo
ots
Rose
ttRo
sett
leav
esle
aves
Caul
inCa
ulin
leav
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aves
Bolt
Bolt
stem
sst
ems
uds
Buds
Flow
ers
Flow
erSi
lique
sSi
lique
ee ee s s
B
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.
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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.
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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
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