Biotechnology & Forest Health: An Industry Perspective - - PowerPoint PPT Presentation

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Biotechnology & Forest Health: An Industry Perspective - - PowerPoint PPT Presentation

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Biotechnology & Forest Health: An Industry Perspective Christine Dean, PhD Anna Leon, PhD NASEM February 8, 2018 Why Now is the Right Time - Forest Genomics comes of age! 1980s Discovery of Polymerase Chain Reaction technique (PCR)

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Biotechnology & Forest Health: An Industry Perspective

Christine Dean, PhD Anna Leon, PhD NASEM February 8, 2018

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Why Now is the Right Time - Forest Genomics comes of age!

  • 1980s – Discovery of Polymerase Chain Reaction technique (PCR)
  • 1990s – Development of DNA sequencing methods
  • 1993 CRISPR locus identified leading to Gene Editing possibilities
  • 2000s – Human Genome sequenced 2003
  • Poplar 2006, first forest tree sequenced
  • Gene Editing, Genomic Selection, Association Genetics
  • 2010s – Next Generation high throughput Sequencing (NGS)
  • Norway Spruce 2013, first conifer sequenced
  • Eucalyptus 2014
  • Loblolly Pine 2014, Douglas Fir 2017

Key Themes: Time Scale, Technology Bundle, Cross Sector

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Selection, Breeding & Testing Orchard & Propagation Systems Plantation Management Harvest, Transport, Processing, & Products Biotech tools and applications all the way through the value chain

Consider Applications across Life Cycle of Industrial Plantation

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Selection & Improvement Propagation

Novel genes

Selected material

Transformation

Genomics Traditional Tree Improvement Clonal techniques Orchard techniques Propagation & Nursery Growing Systems

Gene Editing

Forest Genetics, Biotechnology & Propagation Alternatives

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Loblolly Pine Example – Differential between genetics &/or propagation stock types in Fusiform Rust performance Cassava Example – Plants regenerated by somatic embryogenesis lose disease resistance

Beyene etal (2016) Molecular Plant Pathology [Published by WILEY] http://onlinelibrary.wiley.com/doi/10.1111/mpp.12353/full#mpp12353-fig-0001 Burkhart (2015) Forest insight Conference. Valdosta, GA. http://internationalforest.co/wp-content/uploads/2015/12/BurkhartForIn2015-10-21.pdf

Unknown Unknowns - Genetics, Epigenetics & Other Effects?

  • Propagation Example - Still so much to learn!
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READINESS: Technology Awareness & Rapid Adoption

  • Be ready to take advantage of crossover applications from

Agriculture, Horticulture and other crops (just as we have in sequencing…)

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  • Risk Awareness
  • Risk Protection
  • Risk Management

Southern Pine Beetle Program: See USFS site for photo credits https://www.fs.usda.gov/detail/r8/forest-grasslandhealth/insects-diseases/?cid=fseprd561234 Recently thinned, well managed stand Stand damaged by Southern Pine Beetle Stand ready for thinning

Plantation Management

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Key Problem Area – Drought and Climate Change

Lateral branch damage on Douglas-fir in the Pacific Northwest caused by secondary pathogens during a drought

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Future climate patterns and drought effects on Douglas-fir

Predicted summer precipitation change by the end of the century assuming continued emissions increases. Brown = negative precipitation change (Walsh et al., 2014) Predicted soil moisture change by the end of the century assuming continued emissions increases. Brown = negative soil moisture change (Walsh et al., 2014) Douglas-fir ring width decreases with increasing vapor pressure deficit. (Restaino et al., 2016)

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Pine Beetle Life Cycle in a Changing Climate

Kolb et al., 2016

  • Predicted

probability of adaptive seasonality (left) and cold survival (right)

  • f mountain

pine beetle (Bentz et al. 2010)

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Secondary Pathogens

Kolb et al., 2016

  • Disease and Drought

– Secondary pathogens increase with drought – Few treatment options

  • Breeding focus on

drought tolerance

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Invasive Diseases – Sudden Oak Death as an Example

Photo: Yana Valachovic, UCCE Humboldt County Douglas-fir photos: John Bienapfl, University of California, Davis

  • Early detection

& identification are critical

  • Potential role for

biotechnology in breeding & monitoring

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Invasive diseases: a global problem

Oregon, USA / Tanoak SOD Infections UK / Larch SOD Infections

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Invasive diseases: Issues demonstrated by SOD movement

Symptom Photos: Ken Peek, Alameda County Dept. of Agriculture Nursery Photo: California Oak Mortality Task Force

  • Improved testing for quarantines
  • Improved management of ornamental populations
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Economically Damaging Pests – PNW Industrial Perspective

Swiss Needle Cast

– 2014 Cooperative analysis

  • >190 million board-feet ($78

million) Douglas-fir loss per year

  • Impacted > 2,100 jobs Oregon

Photo: Robin Mulvey Photo: Dave Shaw Swiss Needle Cast Co-op

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Economically Damaging Pests – PNW Industrial Perspective

– Laminated Root Rot

  • 2013 WA Academy of Sciences Report

– 5-15% of Western WA & OR infected – DNR 2009-2011 harvest shows 5% loss (~$10 million shortfall in harvest revenue)

– Other important root rots

  • Annosus root rot
  • Armillaria root rot
  • Black stain root disease
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Harvest, Transport, Processing, Products

– Transport & ‘Product to Market’ Logistics – Certification (covered in earlier session) – Improved Quarantine Testing

  • Logs and Wood Products

– Ensure material is free from pests

  • Invasive Species

– Prevent new pests from entering or leaving the country

Log Photos: Will Littke Pinewood Nematode Photo: http://www.uvm.edu/~dbergdah/pwn/pwn.html

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New Biotechnology Enabled Diagnostic Tools Arising…

Diagram: Caliendo and Hodinka, 2017 based on Gootenberg et. al., 2017

Example: CRISPR Mediated Diagnostics

  • Importance of technology

development & readiness for rapid adoption

  • Faster, cheaper, more

specific than current technology

– qPCR/PCR – LAMP – ELISA

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Framework for Research

  • Focus on multiagency/multidisciplinary teams

– Include private partners – Leverage and expand funding opportunities

  • Disease and tree improvement cooperatives provide a strong

foundation

– Strong relationships between universities, public agencies, and industry

  • Ad hoc working groups
  • Outreach and extension
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Practical Applications are Required

  • Diagnostic tools
  • Breeding Services (especially for non-

commercial species)

– Who will offer these services? – How will the cost structure be defined?

  • Benefit small and large landowners
  • Above all – User Friendly and

Accessible

– End products must be easy to implement by field personnel

Concentrated Basidiospore Spray inoculation system at Resistance Screening Center (from Cowling and Young 2013)

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Summary

  • Biotechnology tools are just beginning to be used for commercial

scale applications in industrial forestry

  • A wide range of applications will apply at different points in the life

cycle of industrial plantations and products as they flow to markets

  • Global changes (biotic and abiotic) will affect all forests; key response

focus will vary by landowner but need to be coordinated

– Climate change, Invasive species, Economically damaging pests

  • Risk Awareness and Risk Management

– Multi-disciplinary and widely applicable tools need to be developed – Multi-stakeholder participation to focus on detection – Clear deployment and outreach

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THANK YOU

Photos: Weyerhaeuser

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Literature Cited

  • Burkhart, H.E., 2015. Adapting conventional growth and yield models for modeling yield and carbon impacts of open-pollinated, control-mass-pollinated and varietal stands being

established today in SE USA. Forest inSight Conference. October 27-28 2015. Valdosta, Georgia USA. http://internationalforest.co/wp-content/uploads/2015/12/BurkhartForIn2015-10-21.pdf Downloaded 2/5/2018

  • Beyene, G., Chauhan, R.D., Wagaba, H., Moll, T., Alicai, T., Miano, D., Carrington, J.C. and Taylor, N.J. 2016. Loss of CMD2-mediated resistance to cassava mosaic disease in plants

regenerated through somatic embryogenesis. Molecular Plant Pathology, 17: 1095–1110. doi:10.1111/mpp.12353

  • Caliendo, A.M. and Hodinka, R.L. 2017. A CRISPR way to diagnose infectious diseases. The New England Journal of Medicine, 377)17): 1685-1687.
  • Cook, R.J., Edmonds, R.L., Klopfenstein, N.B., Littke, W., McDonald, G., Omdahl, D., Ripley, K., Shaw, C.G., Sturrock, R., Zambino, P. 2013. Opportunities for addressing laminated root

rot caused by Phellinus sulphuracens in Washington’s forests: A report from the Washington State Academy of Sciences in cooperation with the Washington State Department of Natural Resources. 110 p.

  • Cowling, E., and Young, C. 2013. Narrative history of the resistance screening center: It’s origins, leadership and partial list of public benefits and scientific contributions. Forests 4:

666-692.

  • Gootenberg, J.S., Abudayyeh, O.O., Lee, J.W., Essletzbichler, P., Dy, A.J., Joung, J., Verdine, V., Donghia, N., Daringer, N.M., Freije, C.A., Myhrvold, C., Bhattacharyya, R.P., Livny, J., Regev,

A., Koonin, E.V., Hung, D.T., Sabeti, P.C., Collins, J.J., and Zhang, F. 2017. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356: 438-442.

  • Jones, B. and Wylder, B. Phytophthora ramorum: Identifying symptomatic larch. 2012 (revised 2017). Phytophthora guidance note. UK Forestry Commission:

https://www.forestry.gov.uk/pdf/PramorumsymptomsguideApril2012RevisedSept2017.pdf/$FILE/PramorumsymptomsguideApril2012RevisedSept2017.pdf

  • Kolb, T.E., Fettig, C.J., Bentz, B.J., Stewart, J.E., Weed, A.S., Hicke, J.A., and Ayres, M.P. 2016. Forest insect and fungal pathogen responses to drought. In: Vose, J.M., Clark, J.S., Luce,

C.H., Patel-Weynand, T., eds. Effects of drought on forests and rangelands in the United States: a comprehensive science synthesis. Gen. Tech. Report WO-93b. Washington, DC: U.S. Department of Agriculture, Forest Service, Washington Office: 113-133. Chapter 6.

  • Restaino, C.M., Peterson, D.L., and Littell, J. 2016. Increased water deficit decreases Douglas fir growth throughout western US forests. Proceedings of the National Academy of

Sciences U.S.A., 113(34): 9557-9562.

  • Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J.J., Qui, J.-L., Gao, C. 2013. Targeted genome modification of crop plants using a CRISPR-Cas system.

Nature Biotechnology 31(8): 686-688.

  • Walsh, J., D. Wuebbles, K. Hayhoe, J. Kossin, K. Kunkel, G. Stephens, P. Thorne, R. Vose, M. Wehner, J. Willis, D. Anderson, S. Doney, R. Feely, P. Hennon, V. Kharin, T. Knutson, F.

Landerer, T. Lenton, J. Kennedy, and R. Somerville, 2014: Ch. 2: Our Changing Climate. Climate Change Impacts in the United States: The Third National Climate Assessment, J. M. Melillo, Terese (T.C.) Richmond, and G. W. Yohe, Eds., U.S. Global Change Research Program, 19-67. doi:10.7930/J0KW5CXT.

  • Wang, Y., Cheng, X., Shan, Q., Zhang, Y., Liu, J., Gao, C., and Qui, J.-L. 2014. Simultaneous editing of three homeoalleles in hexaploidy bread wheat confers heritable resistance to

powdery milder. Nature Biotechnology 32: 947-951.