CGIAR Genebank Accelerator
6 survey modules

Molecular Characterisation Survey

Survey of National Genebank Managers — Strengthening NARS Partner Capacity for Integrated In-situ and Ex-situ Conservation

Module 1 of 6 About You and Your Institution
Module 1 of 6
About You and Your Institution

About You and Your Institution

Seed collections → DNA evidence → data systems → conservation decisions

Note: If this survey is being filled in by a staff member on behalf of the genebank manager, please provide the genebank manager's details in Q1–Q5 where applicable.

Q1. Full name (optional)
* Q2. Email address
* Q3. Institution / Organization
* Q4. Job title / Position
* Q5. Country
* Q6. Years of experience in genetic resources or molecular biology
* Q7. Highest degree obtained
* Q8. Primary area of expertise / professional role (select all that apply)
* Q9. Primary crops or species your genebank holds (select all that apply)
Module 2 of 6
Sequencing Knowledge and Experience

Sequencing Knowledge and Experience

From Molecular Capacity to Applied DSI

Note: Questions Q10 and Q11 are general orientation questions. Q12 onwards covers technical detail — genebank managers may wish to consult technical staff members.

* Q10a. Has your genebank ever been involved in generating DNA/RNA sequence data from plant genetic resources?
If yes, briefly describe the purpose
Only answer this if it applies to your previous answer.
Q10b. If YES, what was your level of involvement? (Select all that apply)
Only answer this if it applies to your previous answer.
* Q11. What are the primary objectives for which your genebank would generate and use Digital Sequence Information (DSI) in its genetic resource management? (Select all that apply)
Note: DSI (Digital Sequence Information) refers to genetic sequence data as discussed under the CBD and ITPGRFA.
* Q12. Rate your familiarity with the following sequencing technologies (1 = never heard of it; 2 = heard of it, no familiarity; 3 = basic understanding; 4 = practical experience; 5 = expert user)
1 2 3 4 5
Sanger sequencing
Illumina (short-read NGS)
Oxford Nanopore (long-read)
PacBio SMRT
Genotyping-by-sequencing (GBS) / DArTseq
SNP arrays
Reduced representation sequencing (RADseq, etc.)
Q13. Which library preparation methods have you used personally? (Select all that apply)
* Q14. Have you ever performed a whole genome sequencing (WGS) experiment?
Species (if plant genome)
Only answer this if it applies to your previous answer.
* Q15. What is the largest number of samples you have processed in a single sequencing run?
Q16. Do you routinely assess DNA / RNA quality before sequencing? (Select all that apply)
Q17a. Which of the following applications has your genebank used sequencing for? (Select all that apply)
Q17b. Has your genebank used sequencing data for any of the following advanced genomic applications? (Select all that apply)
* Q18. Rate your confidence in interpreting the following types of sequencing output (1 = not confident at all; 2 = slightly confident; 3 = moderately confident; 4 = quite confident; 5 = very confident)
1 2 3 4 5
Quality metrics (FastQC / MultiQC reports)
Read alignment statistics (mapping rate, coverage)
Variant call files (VCF format)
Phylogenetic trees / dendrograms
Population structure plots (PCA, ADMIXTURE)
* Q19a. Have you ever received formal training in bioinformatics for NGS data analysis?
* Q19b. Level of practical application after training
* Q20. For the crops your genebank holds, do you know their ploidy levels?
Specify which crops
Only answer this if it applies to your previous answer.
Q21. Which methods has your genebank used to determine ploidy? (Select all that apply)
* Q22. Does your genebank follow standardised protocols (aligned with international guidelines) for collecting passport data and metadata associated with genetic resources?
Q23. What types of metadata does your genebank routinely collect and attach to sequencing projects? (Select all that apply)
Q24a. Which sample types does your genebank typically prepare for sequencing? (Select all that apply)
* Q24b. What molecular material does your genebank use for sequencing?
* Q25. Does your genebank follow standardised SOPs for DNA / RNA extraction?
Module 3 of 6
Infrastructure and Resources

Infrastructure and Resources

Laboratory, Data, and Institutional Readiness

* Q26. Does your genebank laboratory have the following equipment available for routine use? (1 = not available; 2 = available but not functional; 3 = rarely used; 4 = occasionally used; 5 = routinely used)
1 2 3 4 5
PCR thermocycler
Real-time PCR (qPCR) machine
DNA sequencer (any type)
Nanopore MinION / Flongle
Gel electrophoresis system
NanoDrop / spectrophotometer
Qubit / fluorometer
Bioanalyzer / TapeStation
Flow cytometer (for ploidy estimation)
* Q27. Does your genebank have access to a centralised sequencing facility (in-country or regional)?
* Q28. What is the typical turnaround time to receive sequencing data after sending samples?
* Q29a. Does your genebank have computing infrastructure to analyse raw sequencing data (e.g., ≥32 GB RAM, multi-core CPU)?
Q29b. If yes, are these facilities sufficient and functional for analysing raw sequencing data?
Only answer this if it applies to your previous answer.
Q30. Which of the following bioinformatics tools has your genebank installed or used locally? (Select all that apply)
* Q31. Is your genebank able to store large sequencing datasets (≥1 TB) reliably?
* Q32. Does your genebank have a dedicated person or team responsible for bioinformatics support?
* Q33. Does your genebank have a long-term vision / strategy for molecular characterisation?
* Q34. What is the most significant constraint affecting your genebank's sequencing work?
* Q35. What annual budget (approximate) does your genebank allocate for molecular characterisation?
* Q36a. Does your genebank collaborate with external organisations for molecular characterisation of plant genetic resources (PGRs)?
Name of partner organisation(s)
Only answer this if it applies to your previous answer.
Country / region of partner
Only answer this if it applies to your previous answer.
Q36c. Nature of collaboration — Is the molecular characterisation part of a broader research collaboration or project?
Only answer this if it applies to your previous answer.
If yes, briefly describe the broader collaboration
Only answer this if it applies to your previous answer.
Q36d. Roles and contributions — Please describe what your genebank received as part of that partnership to generate DSI. Indicate if your genebank received:
Only answer this if it applies to your previous answer.
Q36e. Frequency of collaboration
Only answer this if it applies to your previous answer.
How are activities and results monitored or coordinated?
Only answer this if it applies to your previous answer.
Module 4 of 6
Data Management and Sharing

Data Management and Sharing

CGIAR Genebank Accelerator Survey Module

Q37. Which public repositories has your genebank submitted sequence data to? (Select all that apply)
* Q38. What are the three most pressing needs for your genebank to enhance its use of sequencing in genetic resource management? (Rank your top 3: write 1 = most pressing, 2 = second most pressing, 3 = third most pressing)
Note: Please select exactly three needs and rank them.

Assign ranks 1, 2, and 3 to your top 3 choices (1 = most important). Leave the rest blank.

Access to sequencing equipment or facilities
Funding for sequencing runs and related laboratory costs
Bioinformatics capacity development (training and staffing)
Standardised protocols and SOPs
Access to reference genomes and genomic databases
Data storage, computing infrastructure and cloud services
Policy guidance on DSI and benefit-sharing
Legal support for data sharing (MTA / SMTA)
Other
Module 5 of 6
Genetic Resources and DSI Policies, Laws and Experiences

Genetic Resources and DSI Policies, Laws and Experiences

Laws and Experiences

This section assesses your genebank's knowledge of, and experience with, the policy and legal frameworks governing Digital Sequence Information (DSI) and genetic resources.

* Q39. Rate your genebank's knowledge of benefit-sharing frameworks related to the use of genetic resources and DSI (1 = no familiarity; 2 = heard of it, no understanding; 3 = basic understanding; 4 = good understanding; 5 = expert knowledge)
1 2 3 4 5
ITPGRFA multilateral system (benefit-sharing for Annex 1 crops)
CBD Nagoya Protocol (access and benefit-sharing)
CBD Decision 15/9 (DSI benefit-sharing framework)
CBD Decision 16/2 (multilateral mechanism for DSI)
SMTA / Standard Material Transfer Agreement
* Q40. Does your genebank, or the organisation that hosts your genebank, have a dedicated legal or policy unit that handles genetic resource intellectual property, MTAs, or benefit-sharing agreements?
* Q41. Are you aware of any national laws or regulations in your country that address (or are under development to address) the access, use, or sharing of DSI?
If yes, briefly name and describe the law and its relevance to DSI
Only answer this if it applies to your previous answer.
* Q42. Does your genebank have a policy or guidelines related to the generation, use, sharing, or publication of DSI from genetic resources?
If yes or under development, please provide a brief description
Only answer this if it applies to your previous answer.
* Q43. Does your genebank experience uncertainty about how international or national laws and policies affect the use of DSI associated with its collections?
If yes, briefly describe the main areas of uncertainty
Only answer this if it applies to your previous answer.
* Q44. Has your genebank generated DSI as part of a research partnership with other organisations?
If yes, were the partnering organisations
Only answer this if it applies to your previous answer.
Q45. If you answered yes to Q44, as part of that partnership to generate DSI, please indicate if your genebank received any of the following benefits from the partnership: (Select all that apply)
Only answer this if it applies to your previous answer.
Q46. Which of the following would most help your genebank address policy-related uncertainties regarding DSI? (Select up to three)
Module 6 of 6
Interest in Future Collaborative DSI Generation for Genebank Use

Interest in Future Collaborative DSI Generation for Genebank Use

Future Collaborative DSI Generation

The following questions explore your genebank's potential interest in developing proposals, together with CGIAR, to generate DSI specifically for genebank management purposes.

* Q47. Would your genebank be interested in developing a proposal with CGIAR centres to generate DSI from genebank accessions for use in breeding programmes?
Comment (if applicable)
Only answer this if it applies to your previous answer.
Q48. If interested, what type of DSI generation would be most relevant for your genebank? (Select all that apply)
Only answer this if it applies to your previous answer.
Q49. What type of agreements would your genebank require to participate in such collaborative DSI generation? (Select all that apply)
* Q50. What support from CGIAR would most help your genebank engage in collaborative DSI generation? (Rank your top 3: 1 = most important)

Assign ranks 1, 2, and 3 to your top 3 choices (1 = most important). Leave the rest blank.

Technical training (bioinformatics / sequencing)
Equipment or infrastructure grants
Legal / MTA template support
Co-funding for sequencing runs
Access to reference databases and pipelines
Policy guidance on DSI benefit-sharing
Other
Q51. What type of long-term collaboration would your genebank prefer with CGIAR? (Select all that apply)
Q52. What major improvements have occurred at your genebank due to molecular characterisation?
Q53. What policy issues would you want to address in the context of a joint DSI initiative with CGIAR?
Q54. Any additional comments or suggestions regarding molecular characterisation capacity at your genebank, especially concerning potential collaborative DSI projects?

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