The Scientist Who Came in from the Cold: Interfacing Science and Policy

Ian Ferguson Departmental Science Advisor

www.mpi.govt.nz

Plant & Food Research
Plant & Food Research’s mission is to provide the research that drives the growth, profitability and sustainability of plant and seafood-based food industries in New Zealand

The New Zealand Institute for Plant & Food Research Limited

Plant & Food Research
• Operate under the NZ Companies Act • Corporate Structure • Shareholders – New Zealand Government

Auckland, NZ – Head Office

• Annual revenue $115 million

~50% private contracts and royalties ~50% NZ Government contracts and core funding

Locations • NZ (15 sites) • Australia • USA

The New Zealand Institute for Plant & Food Research Limited

potatoes ..ornamentals . The New Zealand Institute for Plant & Food Research Limited .hops .apricots .cereals .peas .blueberries .forage crops .peaches & nectarines .kiwifruit ..raspberry .pears .Breeding programmes .apples .

Crop and fruit cultivars »Booster™ Broccoli » High levels of cancer fighting compounds » Joint Australia-NZ project. launch in second half of 2009 »Purple Heart potato » Purple skin and purple flesh tones » High in antioxidants and loved by gourmets The New Zealand Institute for Plant & Food Research Limited .

juicy apples with flavour » Rated by consumers in Europe and US as outstanding » Excellent shelf life The New Zealand Institute for Plant & Food Research Limited . yellow-fleshed kiwifruit » Annual returns predicted to reach NZ$1 billion by 2009 »JAZZ™ apples » Tangy. crunchy.Crop and fruit cultivars »ZESPRI™ GOLD Kiwifruit » Sweet.

» bite-sized fruit. » ready-to-eat. arguta) » Premium-priced.New crops grown internationally under licence » Kiwiberry (A. » convenience. » appeals to consumers The New Zealand Institute for Plant & Food Research Limited .

Potatoes » High fibre / low glycaemic potency » Diverse colour and shape range with excellent agronomic characters » Resistant to cold-sweetening The New Zealand Institute for Plant & Food Research Limited .New Vegetable Crops .

The genomics pipeline Bioinformatics DNA based homology Microarrays Gene over-expression Testing in plants Thousands of genes Hundreds of leads Function tested candidates New cultivars from market assisted selection High value Functional Foods Gene discovery Function discovery Trait discovery The New Zealand Institute for Plant & Food Research Limited Product development .

Fruit sequences gene databases available Genome Apple* Kiwifruit* * Grape Papaya Citrus Peach Strawberry* Tomato Potato * Pear** Blueberry Avocado genome 2010 genome 2012 genome 2007 genome 2008 genome 2012 genome 2009 genome 2011 genome 2012 genome 2011 genome 2012 … … The New Zealand Institute for Plant & Food Research Limited .

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melanandra .Actinidia chinensis x A.

and we can use its high quality draft sequence to explain the origin of the crop. Draft genome sequence of the apple ‗Golden Delicious‘ Whole genome shotgun (WGS) approach was used 603. anchored 71.524 .3%.643 markers Total number of genes predicted is 57.9 Mb covers about 81.the highest reported among plants so far… .The Whole Genome The genome of apple (Malus x domestica) has been described.2 % of metacontigs using a high quality genetic map with 1.

The pear genome Pear diversity – courtesy of J. Postman. USDA-NCGR-Corvallis .

25% less DNA than apple Apple and pear had a common ancestor 35 million years ago The New Zealand Institute for Plant & Food Research Limited . 51.The pear genome Sequenced with collaborators in IASMA. Italy 600 million base pairs.000 genes.

Provides thousands of sequence variants on every gene/locus.g. . heritage against domesticated. So we can compare two cvs with the same trait and look for what is the same. Provides an immediate marker or gene to select for – doesn‘t have to be predetermined – is an association.The Genomics revolution and breeding and selection The genomics revolution and breeding and selection Genome wide selection: Whole genome sequence Re-sequence (using next gen sequencing) specific cultivars and compare against the whole genome sequence – e.

But need lots of computer power. The problem is computer power.The genomics revolution and breeding and selection This leads to a major modern problem: Information Deep sequencing = next gen sequencing (NGS) Cheap short reads. . Is a challenge to assemble into the whole genome.g. Then assemble them. RNA-seq is same thing with RNA which provides the expression differences. NGS advantage is cheapness. but millions of them e. 15 nucleotides.

they have the same gene and we can then look for that gene in the population and find people with that gene.The genomics revolution and breeding and selection Have the human sequence. wouldn‘t work. since they share too may sequences. the association is too powerful not to be a a a strong selective marker. Even though not related. Lay the genomes of the SLT members on the reference human genome Get an association of a particular gene across all SLT members. Re-sequence each SLT member. . If SLT members related. Because unrelated.

Sustainable Production Protecting and restoring the environment while maintaining profitability The New Zealand Institute for Plant & Food Research Limited .

Quantifying the environmental impact of growing: Sustainable approaches Food miles Carbon costs Transport Grape Growing Harvest Juicing CO2 emission Materials Transport Wastes energy fertilisers rain Grape to Glass Energy Fermenting drainage leachate prunings Emissions Transport CO2 consumption Local & Overseas Drinking Transport Bottling/ Packaging The New Zealand Institute for Plant & Food Research Limited .

Where have we exceed our planet‘s limits? United Nations Department of Economic and Social Affairs:Building a Sustainable and Desirable Economy-inSociety-in-Nature .

or stocks & humans .Nature‘s Blessing: Capital & Interest Natural Capital: Our stocks of natural materials & energy Ecosystem Services: The beneficial flows of goods between natural capital stocks.

The 17 Ecosystem Services – many involve soil • Gas regulation • Climate regulation • Disturbance regulation • Water regulation • Water supply • Erosion control • Soil formation • Nutrient cycling • Waste treatment • Pollination • Biological control • Refugia • Food production • Raw material • Genetic resources • Recreation • Cultural Stocks Costanza et al. Services . (Nature. 1997) .17 ecosystem services across 16 biomes.

7 JUNE 201 2 | VOL 486 | NATURE | 105 . Further species loss will accelerate change in ecosystem processes. but it is unclear how these effects compare to the direct effects of other forms of environmental change that are both driving diversity loss and altering ecosystem function.Biodiversity A global synthesis reveals biodiversity loss as a major driver of ecosystem change Evidence is mounting that extinctions are altering key processes important to the productivity and sustainability of Earth‘s ecosystems.

It hopes to gain similar global scientific authority and policy influence for biodiversity to what the Intergovernmental Panel on Climate Change (IPCC) has for climate change — although not the same opposition and controversies. 454 | NATURE | VOL 488 | 23 AUGUST 2012 .In April this year. the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) was born in Panama City.

Biodiversity matters Not only in wild places… .

…but also on farms and in orchards… where biodiversity provides Ecosystem services Pollination Pest control Decomposition .

Compelling NZ story Pest control Export markets Disease control $ return to growers Biodiversity Decomposition & nutrient release Orchard or orchard Pollination Orchard management practices .

Efficient and Innovative Crop Production Canopy management High Efficency Production Better Cropping Dwarfing The New Zealand Institute for Plant & Food Research Limited .

Biosecurity Protecting our borders Controlling invasions Ensuring market access The New Zealand Institute for Plant & Food Research Limited .

Safety and Sustainability Food Safety Chemicals in food High integrity food The New Zealand Institute for Plant & Food Research Limited .

Food research: Breeding & Biotechnology for Healthy Foods Red-fleshed apples: • • Anthocyanins for health Consumer appeal The New Zealand Institute for Plant & Food Research Limited .

Physical Performance and Fitness » Satiety and Weight Management Foods for Health The New Zealand Institute for Plant & Food Research Limited .Food products and functionality » Digestive Health » Immune Function » Mental Acuity and Brain Health » Energy.

....We Gut microbiota and plants.. (Juliet Ansell) .what they produce ..Gut microbiota and plant foods...... . are what we can digest and what our microbes can ferment. Phytochemicals and non-digestible carbohydrates both interact with the microbial population in our colon and impact on our metabolism It isn’t just who is there that is important.how they produce it Ability to proliferate and succeed in the colon is dependent on the flexibility and responsiveness of microbiota to diverse substrates ..

. Co-metabolism The GI tract and gut microbiotic environment are linked RNA sequencing advances means we can get global snapshot of microbiome Metagenomics means we can measure the global host response Functional metabolomics (urine. faeces) means we can understand the interface ....Gut microbiota and plant foods.

..Gut microbiota and plant foods.. •Research with kiwifruit : in vitro and using an animal model •Then human clinical trials •In vitro kiwifruit fermentation •Specific beneficial bacteria and associated products increase ..

Human gene response to foods Nutritional genomics and personalised nutrition and foods Gastronomics: human gene differences to aromas Consumer preference The New Zealand Institute for Plant & Food Research Limited .

Postharvest Storage and Transport Storage technology to:  Maintain optimal quality  Get fruit to distant markets The New Zealand Institute for Plant & Food Research Limited .

receptor activity reduced CTR1 negatively regulates ethylene response by repressing EIN2 + ethylene reduces CTR1 activity leading to reduced ubiquitin-based EIN3/EIL protein degradation EIN2 relays ethylene response through to TFs in EIN3/EIL family and the ERFs Kendrik & Chang. Curr Op Plant Biol 11. 479. 2008 .Ethylene receptor genes in kiwifruit Receptors are negative regulators active in repressing downstream response + ethylene.

Ethylene receptor genes in kiwifruit Thousands of genes Hundreds of leads Function tested candidates High value Foods Gene discovery .

Fruit ripening 0ºC 20ºC + 1-MCP Thousands of genes Hundreds of leads Function tested candidates High value Foods Gene discovery .

Receptor gene expression Kiwifruit ripening at 20ºC High value Foods Thousands of genes Hundreds of leads Function tested candidates Gene discovery .

Chinese Red Bayberry (Yangmei) The New Zealand Institute for Plant & Food Research Limited .

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640-1280. respectively. respectively. (C) GO classification for upregulated and downregulated UniGenes. (A) Overall expression profiles for the UniGenes expressed in fruit libraries of three different maturity stages. . 40-80. with I and IV indicating UniGenes with up-regulated and downregulated expression. 1280-2560. with the RPKM values 0-10.UniGene expression profiles during bayberry fruit ripening. 80-160. respectively. The lines with 10 different colors from blue to red show the absolute expression magnitude at 75 DAF. and over 2560 represented by colors 1 to 10. 160320. 1020. 20-40. and II and III indicating those with irregular expression. with * and ** indicating significant difference at 5% and 1%. (B) Four expression profiles are shown. 320-640.

(B) Expression analysis of anthocyanin biosynthesis genes as well as MrMYB1 in ripe SJ. (A) Difference in fruit color and anthocyanin content in ripe SJ. DK and BQ fruit by qPCR. 1. The vertical bars represent S. 0 45 30 15 0 20 10 0 MrDFR1 MrDFR2 0 45 30 15 0 MrANS MrUFGT 4 2 MrMYB1 0.02 0. DK and BQ fruit.E. MrACT gene was used to normalize expression of the genes under identical conditions.00 SJ DK BQ SJ DK BQ 0 .Total anthocyanins(mg/100 gFW) 100 80 60 40 20 0 SJ MrCHS DK MrCHI BQ 45 30 15 0 2 1 0 120 80 40 MrF3H 20 10 Relative intensity MrF3'H Fig.01 0. of three replicates.

Old Crops but New Markets? .

Loquat Fruit .

Low temperature damage

Succesful postharvest treatments

Postharvest science to ensure quality in the supply chain

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Expression of DkETRs, DkCTR1, DkEIL1 and DkERF genes during ripening of ‗Yangfeng‘ persimmon fruit at 20 oC. Fruit at day 0 was set as the calibrator (set as 1) for relative expression. Error bars on each column indicate S.E. from three biological replicates

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0 0.5 0.Soluble Tannin (tannin acid equivalent FW%) 1. For the relative mRNA abundance. CO2 (~95%.h) 0 2. v/v) was applied for 2 days.8 0. .0 0 1 2 3 4 Days in storage 5 0 1 2 3 4 5 Days in storage Effects of CO2 treatment on DkERF gene expression in ‗Mopan‘ persimmon fruit.5 1.4 0.2 0. day 0 fruit was set as 1.6 1. Eight ERF genes were choosen to analyze changes in transcripts level in response to the CO2 treatment.0 45 12 8 4 Control 2d CO2 DkERS1 DkEIL1 3 2 1 Relative intensity Relative intensity Relative intensity Relative intensity 0 3 2 1 0 DkETR2 DkETR1 0 4 2 0 8 6 4 2 0 8 6 4 2 0 12 8 4 0 60 40 20 DkERF3 DkERF6 12 8 4 DkERF4 0 3 2 1 0 15 10 5 DkERF1 DkERF7 DkERF2 DkERF5 DkERF8 60 40 Firmness (N) 30 Control 2d CO2 20 0 6 3 0 DkCTR1 0 1 2 3 4 5 Days in storage 0 0 1 2 3 4 5 Days in storage 0 0 1 2 3 4 5 Days in storage 15 Ethylene production (nl/g.0 1.

All these data and information lead to the need for: A systems approach .

8 0.0 120 100 1.0 0 2.0 120 100 AdETR2 AdETR2 AdETR2 40 40 40 20 20 20 0 2.5 0.0 0.5 1.2 0.5 0.8 0.4 0.0 0.2 0.6 AdETR1 1.6 AdERS1b Relative intensity Relative intensity AdETR1 3 2 1 0 1.0 AdETR3 1.0 0 2.6 AdERS1a 6 AdERS1a 6 AdERS1a 4 4 4 2 2 2 0 4 0 4 0 4 Relative intensity AdERS1b AdERS1b 3 2 1 0 1.5 1.0 1.6 3 2 1 0 1.4 0.2 0.4 0.5 1.0 AdETR3 0 1 2 6 12 19 21 25 0 1 2 5 6 8 9 12 0 1 2 6 12 19 21 25 Days after harvest Days after harvest Days after harvest .0 0.0 AdETR3 1.8 0.0 120 100 AdETR1 1.5 0.

5 receptor genes in 2 subfamilies 2 CTR genes 4 EIL genes – transcription factors 14 ERF genes – transcription factors X ripening in air 20C ripening with ethylene at 20C 1-MCP at 20C ripening at 0C plus 20C .

2009 . 41. TF binding sites. metabolic pathways.A systems approach What do we require? Data Drosophila • 6 phenotypes •10096 genetically variable transcripts • intercorrelated resulting in 241 transcriptional modules •Modules of biologically meaningful correlated transcripts e. tissue specificity etc •Transcriptional connectivity = genetic networks Ayroles et al Nature Genetics.g. 299.

but develop valid models which can be tested and . Bayesian networks … Aim is not to develop true models. neural networks.A systems approach What do we need to develop? Predictive models Most common approach for transcriptome analysis is reverse engineering: assumes that causality of transcriptional regulation can be inferred from changes in mRNA expression profiles – is the way we routinely look at transcript patterns Modelling of gene regulatory networks (GRN) uses statistical models.

. rather than very simplistic unidimensional flows of information.to use for experimental testing by disruptive approaches • better ways of analysing large datasets • an appreciation that even if we can‘t measure everything (and probably don‘t want to).A systems approach Just thinking about this alerts us to: • the deficiencies in our datasets • over-interpretation of transcript patterns • the need for models – even at the most conceptual . we need to think in terms of networks and connectivity.

The Scientist Who Went out from the Warm: Interfacing Science and Policy Ian Ferguson The New Zealand Institute for Plant & Food Research Limited .

House of Lords Select Committee on Science and Technology.What is a DSA? ―……provide a source of independent challenge which seeks to ensure that policy decisions are informed by the best science advice and evidence available‖ ―…ensuring the scientific evidence is at the core of departmental decision making. 2012 Independence Evidence at the core of decision making .‖ Report . scrutiny and challenge of departmental resources to facilitate this goal. advise on cross-departmental issues.

April 2011 . provision of strategic scientific advice. Towards better use of evidence in policy formation: a discussion paper Office of the Prime Minister’s Science Advisory Committee.What is a DSA? …they must have the skills to transcend disciplinary boundaries and synthesise knowledge across several disciplines. In that role they are not expected to be experts in all that they confer advice upon mediating between the broader scientific community and policy formation. as well as providing public commentary. managing and supervising the purchase of agency required research. ensuring the quality of evidence to support policy formation. and participation in planning.

delivery. and knowledge/technology transfer and uptake .DSA for MPI Be an accomplished and well-respected leader in science and innovation Have a strong and broad understanding of the primary sector and the science required to support MPI's broad range of responsibilities Understand government processes and the role of science and science innovation in informing policy and regulatory systems Understand the challenges of research prioritisation. quality assurance.

DSA for MPI Have strong connections to the New Zealand and international science community as demonstrated by extensive networks Be an excellent written and oral communicator with strong interpersonal skills Be able to effectively manage potential conflicts of interest .

primary production raised to a very high international standard based on science and innovation Science base and success tends to get forgotten? . environmental driven). greenhouse gas agreements. not just have sustainability . or have regulatory or other constraints? Environmental constraints to production – regulatory such as biosecurity (bringing in new plant material). MPI and Science Science-based and science driven biological economy . landuse decisions – need for high level of science input. Need to make growth sustainable.First thoughts: NZ Primary Production.is hard to measure impact Technological challenges to progress – have we stalled? -step changes may be technology-based which are difficult to implement or not attractive. water quality/irrigation. footprints (export market driven.

mean able to access and evaluate latest and best science – an end-user.a little overwhelming –How do we ensure that there is an adequate science base to this? Four focus areas in strategy all science-based Maximise export opportunities Improve sector productivity Increase sustainable resource use Protect from biological risk . How complete and effective is MPI as an enduser? Breadth of activities . but by driven. but science–driven? MPI based on science but is it science driven? Not like a CRI.First thoughts: Role of DSA in MPI MPI is science-based .

and also have science evaluation processes at the highest level – these should be co-ordinated across the organisation. This requires internal science quality assurance systems. 2. MPI is a major science funder and should be driving research priorities. This needs robust strategy and prioritisation. evaluation of science. how do they know that there the whole pipeline is being filled. We must ensure there is robustness and processes across the organisation. and in the right way? So need substantial say in funding at the more fundamental/developmental end of the pipeline? Providers are faced with fragmented funding agencies . MPI is a science leader and innovator and major end-user.Role of DSA in MPI MPI science – two major aspects: 1. Regulation and standards – requires the most rigorous science information and access and processes to stand up to challenge. So to this extent. and of outcomes and impact – are all these in place at the same level? If MPI funding at the implementation/applied end of the spectrum.

2011/ 2012 . MPI is now working to partner with and enable the primary industries to achieve the maximum benefit for New Zealand” Wayne Mcnee MPI Annual report. MPI’s role is no longer the regulatory compliance role of its predecessor organisations.Role of DSA in MPI “We are making a fundamental shift in the way we work.

Links to research providers – how good are the linkages re science? Patchy probably? Acting at the interface of MPI and science providers and stakeholders partnership models Profiling science culture – internally and externally Accessing external science advice – external verification/audit? International (plus MFAT. MBIE) Internal integration. robust and consistent processes. Quality science used in MPI strategy development Science quality .Role of DSA in MPI Some of the high level aspects: .peer review. NZAid. quality assurance. co-ordination and consistency – currently inconsistent? .

Towards better use of evidence in policy formation: a discussion paper Office of the Prime Minister’s Science Advisory Committee. April 2011 . And the use of scientific approaches to the monitoring and evaluation of policy initiatives. Separating knowledge and evaluation It is important to separate as far as possible the role of expert knowledge generation and evaluation from the role of those charged with policy formation.Science and Policy The challenge is how to do better in two related domains: the generation and application of knowledge to inform policy making.

Again.‖ . if this was about policy responses to science. this would be reasonable. Deakin University Separation of evidence and policy ―You're not entitled to your opinion‖ ―But this implies an equal right to be heard on a matter in which only one of the two parties has the relevant expertise. but they must produce convincing evidence to back their claims‖ ―…but not all should be accorded equal weight when they must be grounded in the likes of scientific or legal expertise.‖ NZ Herald 9 October: Patrick Stokes.Science and Policy (1) everyone must have their say NZ Herald October 20: ―Opinions of the ignorant can‘t beat research Enthusiastic amateurs are entitled to disagree with experts.‖ ―Everyone is free to disagree but ignorance does not have an equal right to be heard.

Towards better use of evidence in policy formation: a discussion paper Office of the Prime Minister’s Science Advisory Committee. The seven were convicted after prosecutors successfully argued that public statements they had contributed to a false sense of security in the Italian city of L‘Aquila ahead of the 2009 earthquake that killed 309 people‖ .Science and Policy (2) We don‘t know everything It is also important to note that there are limits to scientific knowledge and to the scientific approach. April 2011 Hot off the press…… ―Scientists around the world have reacted with dismay to conviction of six Italian scientists and a former government official on manslaughter charges.. governments and their advisors must be aware of such limitations….

Science and Policy Knowledge & evidence Evaluation Policy Science .

Thanks PFR: Andy Allan Brent Clothier Juliet Ansall Louise Malone Zhejiang University: Zhang Bo Yin Xue Ren Chen Kun Song The New Zealand Institute for Plant & Food Research Limited .

govt.mpi.Ian Ferguson www.nz .

The New Zealand Institute for Plant & Food Research Limited www.com The New Zealand Institute for Plant & Food Research Limited .plantandfood.