Division 2: Genetic Resources Conservation and Characterization State of the Genebank

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Division 2 Genetic Resources Conservation and
Characterization- State of the Genebank

• Annual Review - October 2008
• David Tay
• October 28, 2008

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Genebank

• A core work an important social responsibility
• A service unit priority on routine works
  andresearch to support genebanking
• New Div. 2 MTP project title Sustaining potato
  and sweetpotato biodiversity for current and
  future generations

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Functions

• Genebanking
• Research (to support genebanking works)
• Training

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Current Germplasm Collections ( of accessions)
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Germplasm in the Multilateral System of the
Treaty (Annex 1 crops)
Commodity Rank of Taxa of Accs (Total)
Potato
- Cultivated 1 7 4,573 (4,640)
- Wild 1 141 2,106 (2,118)
Sweetpotato
- Cultivated 1 1 4,830 (6,271)
- Wild 1 67 1,135 (1,171)
Total 216 12,644 (14,200)
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Distribution of in-trust potato germplasm
(1979-2007)
3,680/yr
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Figure 1. Distribution of potato accessions
samples to CIP regions (1970-2008) CIP Regions
Central Asia and the Caucasus (CAC), East and
South East Asia and the Pacific (ESEAP), Latin
American and the Caribbean (LAC), Middle East and
North Africa (MENA), South Saharan African (SSA),
South and West Asian (SWA)
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Distribution of sweetpotato accessions samples to
CIP regions (1980-2008) CIP Regions East and
South East Asia and the Pacific (ESEAP), Latin
American and the Caribbean (LAC), Middle East and
North Africa (MENA), South Saharan African (SSA),
South and West Asian (SWA)
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Distribution of in-trust germplasm in 2007
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Recent Achievements

• Barcoding of collections
• ISO 17025 accreditation in Jan 2008
• (for in vitro collection and health quality)
• Black box seed in Svalbard
• Costing of the genebank activities

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Seed inventory system - 1
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The ISO Accreditation Team
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Shipment to Svalbard, Norway
http//www.gs1.org
10,617
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External Review Recommendations - EPMR

• Accelerate the characterization of the remaining
  genotypes in the Centers genebank, and that this
  be completed for all key traits (given top
  priority before working on a core collection)
• 2. Produce a compendium based on passport,
  morphological and molecular data and
  characterization results for key biotic and
  abiotic stresses (finalize germplasm database and
  online)

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External Review Recommendations - EPMR

• Make this information widely available to all
  collaborating NARS to enable them to make choices
  of what may be needed to enhance their genotype
  selection and crossing schemes (online!).
• 5 of budget allocated to ARTCs, 50-60 for
  potato and 40-50 for sweetpotato
• No rationale for reduction of efforts on Division
  2 activities (budget cut) and need a strategy to
  increase and sustain funding for this project

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External Review Recommendations - EC

• 2003
• Acquisition of remaining wild potato (40-50 sp)
• Regeneration of higher quality botanical seed in
  wild potato
• Collaboration with NARS in pathogen cleaning
• More emphasis on safety duplication black box
• Feedback on germplasm distribution impact
• Improved efficiency and cost effective way in
  conservation duplicate elimination, redundancy
• Better objectives for the establishment of core
  collections
• Enhance cooperation with other genebanks in
  potato and sweet potato
• CIP plays an important role in international
  agreements
• CIP accords priority to the public accessibility
  of genebank evaluation data
• (Earmark CP on Genetic Diversity for CIP)

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External Review Recommendations - EC

• 2007
• Apply systematic method in situ conservation
  agro-ecologic and socio-economic consideration,
  and a holistic monitoring system
• Intensify interaction and cooperation with
  European research institutes (and companies)
• Develop more systematic links with international
  development agencies and donors (namely the EC)
  to influence the identification and formulation
  of the development programs
• Use EU standard Logical Framework
• Access real economic value of biodiversity
  conservation a primary importance in the
  implementation of an overall strategy to face the
  consequences of the global climate change.

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My Mission

• To establish an efficient and cost effective
  SYSTEM that will
• ensure the safe and quality conservation and
  distribution of the global in trust potato and
  sweetpotato collections
• enhance utilization through complete
  documentation of passport, characterization, and
  important evaluation information, and making
  online

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State of the Collections

• Two serious issues
• Genetic integrity of the collections
• Germplasm database integrity

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Potato Identity Verification (2001-2006)
26.9
()128 accessions are under process (2007)
Backlog to assess 3,762 accessions Current
capacity 200 accessions/ year
Updated July 26, 2007
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Alberto Salas study 24
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State of the Collections Potato

• Tuber vs. In vitro collection
• Genetic integrity
• Elimination of duplicates
• Elimination of redundant health status entries
• Consolidating breeding line collection
  currently, more breeding lines than germplasm
  collection
• - Lack of original passport and
  characterization information, protein
  fingerprints (1980s), images (1980s), etc.

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In vitro collection backlogs (2003 EC r3)
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Sweetpotato Identity Verification (2001-2006)
21.1
()100 accessions are under process (2007)
Backlog to assess 1,218 accessions Current
capacity 100 accessions/ year
Updated July 26, 2007
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State of the Collections cont.

• Sweetpotato Elimination of duplicates lack of
  original passport and earlier characterization
  information
• Indicators
• 1988 Annual Report 66 of Peru collection are
  duplicates, 726/2,136 accs, i.e. 1,410 duplicates
  for 20 yrs
• LAC collection? 50 duplicates?
• AVRDC and IITA transfers treated as backup
• No original passport information and photos and
  earlier characterization information
• Characterization status 24 (1,631/8,026)

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Database Weaknesses

• Issue accuracy of the data
• Not been checked following data entry
• No or limited original data to check with
• Several people allowed to add/modify data
• Data field states not standardized, e.g.,
  biological status now changing to SINGER
  standard

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CIP database with corrections by Ochoa on Nov 19,
2007
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HR Factors Empowerment

• Curator job description crop, in vitro,
  herbarium
• Committed, accurate and perseverance
• Wanting to ask, discuss, learn and teach
• Sole responsibility for his/her collection
• Only person authorized to add and modify database
  of the collection

• Working norm
• Work hard and smart, i.e. efficiently and
  accurately

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Implementation Plan for Potato

• 2007-2008 Season
• Tuber collection pre-planting tuber
  verification with 1992 (15)
• Tuber collection plant and flower verification
  with 1992 (5)
• Tuber collection digitizing 1974-75 data for
  tuber verification
• Tuber collection tuber verification with 1975
  data (on going)

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Implementation Plan for Potato cont.

• 2008 (La Molina)
• Prepare 1,000 in vitro accessions with redundant
  HSs to produce tubers in greenhouses (Note Also
  aims to eliminate redundant entries of HS0 and
  HS1 when HS2 is available)
• DNA marker comparison between in vitro and tuber
  collection
• Breaking dormancy of in vitro tubers
• 2008-2009
• Field planting in Huancayo tuber and in vitro
  plants of an accession together side by side
• Plant, flower and tuber comparison
• Compare with DNA marker information
• Continue ..

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Risk Management Auditing and Measures

• Loss of information, data, images, etc.
  physical black box and scan save in server
• Securing the facilities keypads, locks, etc.
• Preparing for earthquake, fire, accident, etc.
• Internal auditing
• Control ants in in vitro genebank

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Data Risk Management Measures Data black box
Carlos field books on ARTCs
Albertos field books on wild potato scanned
into server
Keys with CIPs Security Office with user log
book user to return document same day
Albertos field books on wild potato
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Precautions against earthquake
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Potato tuber collection
Will use plastic netting bag for each accession
to prevent tubers from falling and mix up during
earthquake

• 2 sets dirty and clean 4 subsets lack of
  suitable sizeable storage

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Building 7 Biodiversity Complex
Not including office space and post-entry
quarantine issue
In vitro quarantine
Anteroom connecting the building
Move dehumidifier to roof Germinators to wet lab.
Dehumidification
New locks
Preparation shed for tuber storage
Individual backup a/c
Improve ventilation
Convert to tuber storage
Germinators
Repair cold leakage
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State of the Collections cont.

• Germplasm Acquisition Issues
• CBD (Nov. 1993) to 1998 collecting without
  proper national CBD related collecting permits
• 1998 to Jun. 2007 no submission of collecting
  permit application (2003 EC r.1 MTP targets)
• Actions taken to date
• Presenting all collections without proper permits
  to INIA
• First permit application since 1998 approved by
  INIA for final approval by INRENA
• Paying the standard INRENA fees to normalize the
  collected accessions of CIP/USDA wild potato
  collection mission
• Import SP germplasm from Africa (improving the
  Post-entry Quarantine)

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State of the Collections cont.

• Wild potato number of seed in LT storage
• Indicators
• Small number of plants thus many years to produce
  enough seed (2003 EC r.2)
• 1,424 accs with gt5,000 seeds out of 2,448 accs
  (58 done)

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Collection Black box (2003 EC r4)
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Sweet potato evaluation
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Functional Food Evaluation in 2007
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Functional Food Evaluation in 2007
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New Projects

• INCAGRO native potatoes genetics with Agraria,
  La Molina and D3
• ALTAGRO native potatoes and RTAs in Puno
• GCP sweetpotato DNA markers with D3
• CONDESAN in situ conservation in Paramo, Piura
  with the Mountain Institute
• Branstons in situ conservation supporting the
  Potato Park
• Global Trust SP evaluation for salinity
• U Daniel Alcides Carrion/New Mexico
  State/INIA/CIP maca diversity and taxonomy
• Global Trust cryopreservation of sweetpotato

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Coming Projects

• GPG2 new activity study on the implementation
  of IT in Peru

Submitted Proposals

• FONTAGRO with PROINPA and INIA Peru on
  evaluation of native potatoes to climate change
  (approved and moved to 2nd stage application)
• GCP Potato germplasm evaluation against drought
• Global Trust potato germplasm evaluation
  against late blight
• Global Trust potato and SP germplasm evaluation
  for functional food values
• Global Trust SP germplasm evaluation using NIR

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Coming years

• Next few years fixing the critical problems
• Recover the original information
• Protecting the original data
• Concentrating on research to support genebanking
  activities (avoid hobby research)