How far should the CGIAR genebanks dare to go Ruaraidh Sackville Hamilton 17 June 2021 Background needs and opportunities for genetic resources Conserving and delivering the right resources Conserving and delivering resources the right way ID: 933558
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Slide1
The future of genebanks:
How far should the CGIAR genebanks dare to go?Ruaraidh Sackville Hamilton17 June 2021
Slide2Background: needs and opportunities for genetic resourcesConserving and delivering the right resourcesConserving and delivering resources the right wayWhat will CGIAR genebanks do?
Outline
Slide3Coevolution of technology and policyRoa
et al 2016Plant genetic resources: needs, rights and opportunities
Slide4In some cases,
AlphaFold’s structure predictions were indistinguishable from those determined using ‘gold standard’ experimental methods such as X-ray crystallography and, in recent years, cryo-electron microscopy
Slide5Global Crop Diversity Trust created to reduce conflictBy funding essential genebank operationsNot adequate: need synergies
CGIAR Excellence in Breeding: Optimizing breeding schemes“It is a common practice for breeding programs to make wide crosses based on the belief that genetic diversity needs to be expanded, rather than [build] an understanding of quantitative genetics principles or knowledge of how diversity changes in a breeding program. As a result, the allele frequency of important traits can be negatively impacted”https://excellenceinbreeding.org/sites/default/files/manual/EiB-M2_Germplasm%20%20%20trait%20introgression_01-06-20.pdf Rate of genetic gain:
Immediate impact
vs
long term sustainability
Slide6What are the CGIAR genebanks for?
Conserving and facilitating use of diversity of mandate species:
The diversity that was lost in the green revolution?
Slide7What are the CGIAR genebanks for?
Conserving and facilitating use of diversity of mandate species:
The diversity that was lost in the green revolution?
Heritage varieties?
Slide8What are the CGIAR genebanks for?
Conserving and facilitating use of diversity of mandate species:
The diversity that was lost in the green revolution?
Heritage varieties?
Functional variants of genes not in breeders’ working collections?
Slide9What are the CGIAR genebanks for?
Conserving and facilitating use of diversity of mandate species:
The diversity that was lost in the green revolution?
Heritage varieties?
Functional variants of genes not in breeders’ working collections?
Genomes of immediate interest to breeders?
Slide10In rice:~ 50,000 gene modelsOn average, ~ 10 functionally distinct variants at each potentially distinct phenotypes
Don’t underestimate the amount of diversity!
Slide11Diameter of universe
Diameter of smallest particle
What if 99.9999% of haplotypes are lethal?
distinct viable haplotypes
=
number of atoms in universes
10
37,000
???? How many ????
Seconds until the end of the universe
Number of atoms in the universe
Slide12ImplicationsWe have conserved 0% of
the potential diversity of current cropsDon’t even try to do betterAchievable: conserve and document the function of all functional variants of all genesGenebanks’ essential long-term taskExploring 1037,000 combinations of functional variants is an infinite opportunity for invention until the end of timeStatic conservation of genomes from the 1960s is not appropriateGenebanks’ role in accelerating evolution?
Slide1330 years from now:Conserving and delivering the right resources
Slide14Indels and SNPs in coding regionsEpigenetic variantsFunctional variants in non-coding regionsFor all genebank accessions and other known varieties
(so we know what the breeders don’t have)Most functional variants annotated with functionTechnology? [Son of] WGS, GBS …?30 years from now:all variants of all genes known and catalogued
Slide15Future valueNumber of functional variants in the accession absent from breeders’ materials, weighted by rarity in genebanksConserve long-term, regardless of value for current breeding
Current valuePre-breeding materials with important functional variants in useable genetic backgroundsPromote use; discard if not usedHeritage valueFrom a country that considers the variety part of its heritage(and that needs CGIAR to provide security?)30 years from now:accession-specific values for conservation and use estimated
Slide16Small stable conservation-oriented collections Large dynamic use-oriented collectionsOngoing: Acquisition of new accessions with high future, current or heritage valueCreation of new accessions with increased future or current value
Disposal of accessions with low future, current and heritage valueCoordinated among genebanks30 years from now:collection composition optimised
Slide17User =Grower, exploring accessions for use on farmResearcher, exploring diversity and value in genebankPre-breeder, creating novel value in genebankBreeder, creating novel varieties
Users’ changing needs monitoredAlgorithms to convert users’ needs into “ideogenomes”Algorithms to optimise breeding pathway from current materials to ideogenomes30 years from now:delivery well matched to users’ needs
Slide1830 years from now:Conserving and delivering resourcesthe right way
Slide19Acquisition, conservation, delivery and use compliant with all applicable regulationsInternational foraPlant Treaty CBD / Nagoya Protocol / Cartagena ProtocolInternational Plant Protection Convention
Future agreements?Ongoing engagementTo ensure continuing complianceTo devise and offer technically effective and efficient solutions30 years from now:policy in harmony with technology 20 years from now
Slide20(Unchanged) accessions must beviablehealthy
genetically true-to-typeprotected against risks of lossavailable to useAccession management tailored to valuee.g. no viability testing for high current valueManagement targets
Slide21Enhanced quality, increased throughput, reduced costsAutomated seed handlingWithdrawal from and deposit in storageSorting, counting, weighing, labelling, packaging, plantingTesting for viability, health and genetic integrity
Automated phenotyping, genotyping, sequencingStaff retrained for higher throughput21st century genebank, materials and process management
Slide22How should we get there?
Slide23Smart evaluationTo increase knowledge of diversity and genetic control of traitsPartial evaluation of prioritised subsets for prioritised traitsUsed to direct future evaluationAdapt and adopt automated / image-based phenotyping
CharacterizationBasis for monitoring genetic integrityCrop-specific migration to DNA-based fingerprintingImage-based phenotyping for key descriptors e.g. e-seed file for seed sortingGenotyping and sequencingCrop-specific migration towards gene-based methodsSome whole-genome sequencingBuilding knowledge
Slide24Breeder- and researcher-oriented materialsResearch populations optimised for gene discovery & annotationIncluding subsets for whole genome sequencing + GWASNovel genetic resources
Maximise creation of new combinations of genesExpose hidden variationComplementing breeders’ pre-breedingDigital genebanksAccess to info as important as access to materialSearchable info on materials in genebanks and elsewhereDistributed info, in numerous systemsMajor investment required to integrateGLIS is a start
Supporting innovation
Slide25Improvements in each genebank’s efficiency, effectiveness, throughput, qualitySOPsAutomationLarger scale improvementsService provisionCGIAR system
Global integrationR&D for improved effectivenessSeed longevityCryopreservation & tissue cultureCWR, forages, treesPhytosanitary controlsConserving and delivering resources the right way
Slide26Check
Weigh/count
Pack
Label
Check
Equilibrate
Open
Check
Re-dry
Check,
Weigh/countSeal
CheckTestPackLabelCheckShip
Seed withdrawal for distribution:
calling out for automation
Slide27Long-term base conservationDistributionRegeneration / re-culturing PhenotypingHealth & viability testing
Genetic integrity testingPhytosanitary controlGeoreferencing & spatial analysisProviding public access to dataEngaging in policy discussionsService provision:Not every genebank has to do everything in-house
Slide28One CGIAR: should we adopt a USA/India-like model?
Central facilityLTS & MTSOptimised for long-term securityFull testing for viability, health, genetic integrity
Set of regeneration hubs
Optimised for production of
high-quality seed
Replaces seed in distribution hub,
central facility, safety backup,
SGSV
Set of distribution hubs
Optimised for interaction
with users
Slide29Single managementBenefits of scale within crop groups:
automation, specialisation, harmonisation of standardsEasier engagement with international foraInternational transfers for genebank managementPolitically challengingSingle global facility not possible or desirable
2-3 centralised facilities?
One CGIAR: should we adopt a USA/India-like model?
Slide30Global integration: whither the GPA and ABS?
CGIAR genebanksNational genebanks
Community
seedbanks
Private
gene banks
Local
communities
Seed
companies
National
law & policy makers
International
fora
Other
breeders
Researchers
Other
International
genebanks
CGIAR
Breeders
Farmers
Slide31