New Plant Breeding Strategies - University of Pittsburghsuper7/30011-31001/30921.pdf · New Plant...
Transcript of New Plant Breeding Strategies - University of Pittsburghsuper7/30011-31001/30921.pdf · New Plant...
Diversity Arrays Technology
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New Plant Breeding Strategies Using an Affordable and Effective Whole-Genome
Profiling MethodEric Huttner
Diversity Arrays Technology, Canberra, Australia
Diversity Arrays Technology
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Molecular technologies for crop improvementMolecular technologies for crop improvement
Transgenic (GM) plantsTransgenic (GM) plantsSuccessful deployment for simple traitsSmall number of widely used useful genes
Molecular genetic markersMolecular genetic markersIdentification of polymorphism associated with specific traitsSmall number of markers used in routine breeding (substitute to phenotyping)
Mostly used in “first world” cropsMostly used in “first world” crops
Can we do better ?Can we do better ?For complex traitsFor orphan crops
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Multigenic: many genes involvedMultigenic: many genes involved
Genes are interactingGenes are interacting
Many possible combinations of alleles for the Many possible combinations of alleles for the genes involvedgenes involved
Allele-specific quantitative contribution, Allele-specific quantitative contribution, modulated by the other genesmodulated by the other genes
Epigenetic variation (e.g. methylation)Epigenetic variation (e.g. methylation)plays a role not fully establishedplays a role not fully established
Whole-genome molecular marker profiles: a Whole-genome molecular marker profiles: a useful tool to deal with this complexityuseful tool to deal with this complexity
Complex traitsComplex traits
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The need for whole-genome analysisThe need for whole-genome analysis
Complex traitsComplex traitsNeed to recombine several regions simultaneously
New sources of genesNew sources of genesUsing more exotic germplasmAccelerate the transfer of small genomic regions
Speed to marketSpeed to market
Capture the results of genomics programsCapture the results of genomics programs
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Molecular markers and their limitationsMolecular markers and their limitations
HistoricHistoricBiochemical, morphologicalGenetic (DNA based): RFLP, RAPD
CurrentCurrentSSR, AFLP®, coming … soon ? SNPAnd DArT !
LimitationsLimitationsDiscovery: cost, choice of genetic diversityAssay: cost, throughput, data integrityFreedom To Operate
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Diversity Arrays TechnologyDiversity Arrays Technology
Andrzej Kilian, the inventor of Diversity Arrays Technology, with Norman Borlaug
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Diversity Arrays Technology (DArT)Diversity Arrays Technology (DArT)DArT genome scansDArT genome scans
Parallel analysis of several hundred markers on microarrays Sequence independent, affordable for orphan cropsDiscovery and Typing on the same platform: no assay development requiredAmenable to full automation → data integrityApproximately 10-fold cost reduction
Technology described at the last BioVision conferenceTechnology described at the last BioVision conference
Description and references: www.DiversityArrays.comDescription and references: www.DiversityArrays.com
Demonstrated on 18 cropsDemonstrated on 18 crops
This talk: Applying the technology to wheat and bananaThis talk: Applying the technology to wheat and banana
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DArTFWCentromer
1H 2H 3H 4H 5H 6H 7H
Workflowlibrary and target preparation
slide spotting
hybridization with targets
slide scanning
DArTsoft:dataanalysis
results
DArTdb: LIMS
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Current statusCurrent statusSpecies Marker collections Note
Rice 14 Service available Barley (H. vulgare and H. spontaneum) 10 Triticarte service available
Wheat (T. aestivum) 5 Triticarte service available Triticum durum and other Triticum sp 4 Triticarte service available
Sorghum 3 Service available. Lupin 1 Service available
Chickpea 1 POC done. Routine typing under development Sugarcane 10 POC done. Routine typing under development Cassava 4 Generation Challenge Program Coconut 1 Generation Challenge Program
Musa sp (Banana) 2 Generation Challenge Program Pigeon pea (Cajanus cajan) 4 POC done.
Apple 3 Used for varietal ID service Tomato* 2 POC done One breeding application.
Arabidopsis*** 2 Wittenberg et al, Mol. Genet. Genom. 274, 30-39 Perennial rye grass 5 POC done. Routine typing under development
Quinoa** 2 Asplenium sp (fern) and Garovaglia sp (moss) 2 Biodiversity.
Fungal wheat*** and barley pathogen**** various Map built for wheat pathogen
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WheatWheatAustralian company Triticarte delivering the service Australian company Triticarte delivering the service since Dec 2004 (since Dec 2004 (www.triticarte.com.auwww.triticarte.com.au))
DNA-to-data serviceDNA-to-data service
6545 samples analysed over past 12 months6545 samples analysed over past 12 months
About 2.7 millions data pointAbout 2.7 millions data point
Average cost to customers: 8 US c. / data pointAverage cost to customers: 8 US c. / data point
35 customers, 9 countries35 customers, 9 countries
32 mapping populations, 2000 markers located to 21 32 mapping populations, 2000 markers located to 21 chromosomeschromosomes
Initial marker-trait associations reportedInitial marker-trait associations reported
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F1E1D1C1B1A1Call RateQualityChromosomeMarker
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Banana and plantainsBanana and plantains4th most important crop in the world4th most important crop in the world
food for millions of people
a herb not a tree a herb not a tree belong to the Musaceae (monocot)Musa acuminata (A) – dessert bananaMusa balbisiana (B) – cooking banana
Genome size 540-600 MbGenome size 540-600 Mb(1.5 x rice genome size)(1.5 x rice genome size)
Complex genomeComplex genomestructure and evolutionstructure and evolution
Image © INIBAP
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Establishing DArT for BananaEstablishing DArT for BananaA project of Generation Challenge ProgramA project of Generation Challenge Program
One visitor from CIRAD (France), 3 monthsOne visitor from CIRAD (France), 3 monthsIdentified about 1000 polymorphic markersIdentified about 1000 polymorphic markersTyped 187 samples of diverse banana clonesTyped 187 samples of diverse banana clones
Triploid AAA (dessert), AAB (plantain) and ABB (cooking) genomeDiploid AA and BB genomes and others
Markers now availableMarkers now available
Management of collectionsManagement of collections
Understand the phenotypic variation in the plantain Understand the phenotypic variation in the plantain groupgroup
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Diversity analysis of 187 cultivars based on 373 markersDiversity analysis of 187 cultivars based on 373 markers
BBBB ABB AAB AA AAAASOthers
Predominance of the A vs B differentiationWide diversity within A: two domestication routes ?
NB Possible bias due to excessive weight of triploid clones
Axis 1 42.1 %
Axis 2 9.5 %
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A close up on the plantain groupA close up on the plantain groupA clone
Several origins
• Fragment of Neighbor Joining dendrogram based on Dice Index• Source of variation among the clonal material: epigenetics and/or genome rearrangements
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ApplicationsApplications of DArT of DArT““Whole-genome profile” applicationsWhole-genome profile” applications
Comprehensive single-step characterisation of germplasmGenetic background screening in Back CrossesAccelerated introgression from exotic germplasmIdentification of multiple regions responsible for complex traits (QTL and association mapping)Mapping of genome rearrangementsBulk segregant analysis in a single stepMarker-assisted selection for many traits simultaneously
Will this enable new breeding methodologies ?Will this enable new breeding methodologies ?“Bolder” use of genetic diversity, increased use of exotic germplasmData mining approaches to marker-trait association
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AcknowledgementsAcknowledgements
The Grains R&D Corporation of AustraliaThe Grains R&D Corporation of Australia
Dr Neil Howes, Plant Breeding Institute of the Dr Neil Howes, Plant Breeding Institute of the University of SydneyUniversity of Sydney
The Generation Challenge Program of the CGIARThe Generation Challenge Program of the CGIAR
Dr Ange-Marie Risterucci and colleagues, CIRAD Dr Ange-Marie Risterucci and colleagues, CIRAD (Montpellier, France)(Montpellier, France)
BioVision AlexandriaBioVision Alexandria