Partnering on crop wild relative research at three scales: commonalities for success

Partnering on crop wild relative research at three scales: commonalities for success

Colin K. Khoury, Stephanie L. Greene, and Nora P. Castañeda-Álvarez

Symposium: Conserving and Using Crop Wild Relatives: Partnering for SuccessASA, CSSA, SSSA Annual Meeting

16 November 2015Minneapolis, USA

Crop wild relatives (CWR) everywhere

Crop wild relatives are valuable

Aluminium tolerance fromOryza rufipogon

Salinity tolerance from Solanum cheesmaniae

Western corn rootworm resistance

from Tripsacum dactyloides

Salinity tolerance from Helianthus paradoxus

Publications- 2% of citations recorded prior to 1970, 13% in the 1970s, 15% in the 1980s, 32% in the 1990s and 38% 2000-2009 (n=234)Disease resistance 39%, pest and disease resistance 17%, abiotic stress tolerance 13%, quality improvement 11% yield increase 10%, husbandry improvement 6%, cytoplasmic male sterility and fertility restorers 4% (Maxted & Kell 2009)

Improvements in access to CWR taxonomic and relatedness information

http://www.ars-grin.gov/~sbmljw/cgi-bin/taxcwr.pl?language=en

http://www.cwrdiversity.org/checklist/

Improvements in access to CWR distributions information

https://plants.jstor.org/

http://www.gbif.org//

https://www.genesys-pgr.org/welcome

Improvements in methods to assess comprehensiveness of genebank collections

Improvements in methods to assess potential for use of CWR germplasm

http://www.ars-grin.gov/npgs/acc/acc_queries.html

http://www.planttreaty.org/

https://www.cbd.int/abs/

Improvements in tools and mechanisms facilitating access to CWR germplasm (?)

9

Increasing awareness of urgency to adapt agriculture to a more challenging future

2055

Increasing awareness of threats to CWR

11

Wild Pecos sunflower Helianthus paradoxusWild squash Cucurbita okeechobeensis subsp.

okeechobeensis

Scrub plum Prunus geniculataTexas wild rice Zizania texana

Increasing awareness of threats to CWR

CWR at the nexus

Crop Wild Relatives

Food and nutrition security

Agricultural development

Climate change adaptation

Biodiversity conservation

Ecosystem services

Sustainable Development Goals (SDGs)

Convention on Biological Diversity (CBD)

Plant Treaty (ITPGRFA)Sustainable Development

Goals (SDGs)

Sustainable Development Goals (SDGs)

Plant Treaty (ITPGRFA)

Plant Treaty (ITPGRFA)

Challenges in basic CWR research• Who? • Gaps and errors in taxonomic and relatedness information

• Where? • Gaps and errors in species distributions and genebank

holdings data• What? • Underdeveloped and rarely verified predictive

characterization• Very little genotypic and phenotypic information useful to

assess their potential as genetic resources• How? • Difficulties in conservation• Limited access to germplasm• Declining public research funding• Uncertain management authority

Challenges in basic CWR research

Simpson CE (1992) Peanut Science. Photo from Valls JFM (2010) What specific changes in the current way genebanks and breeders do business and interact will be necessary to increase use of Crop Wild Relatives? Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010.

Challenges in using CWR

“It's a bit like crossing a house cat with a wildcat. You don't automatically get a big docile pussycat. What you get is a lot of

wildness that you probably don't want lying on your sofa.”

Challenges in using CWR

Crop Wild Relative Global Occurrence Database

Castañeda-Álvarez et al. 2016. in prep.

13.8 million records with validated coordinates

• 19.4 million total records• 13.8 million records with validated

coordinates• Focused on 193 genera (most important

food crops and their related genera)• Value-added• Taxonomically adjusted/corrected• Geographically cross-checked and geo-

referenced• Records from at least 96% of countries• 98% of records can be openly shared

CWR Global Occurrence Database- summary

• Aim was to gather as much data as possible• Major online biodiversity sources• Major and minor herbaria (H)• Accessible genebanks (G)• Researchers (R)• Published literature (L)

• Method- online download, directly contacting providers, herbarium visits, open requests for data, presentations and posters • Email, email, email, call• Capitalized on partner contacts and personal relationships• Data sharing options• Collaboration opportunities – data repatriation, publications, training

• Resulting in data gathered from:• 16 online resources • Sent to us- 11 G, 33 H, 17 R• 24 herbarium visits- 15,000 records digitized • Data scooped from 5 literature sources• Total- 90 direct providers; ca. 500 total providers

CWR Global Occurrence Database- data gathering

• Only 5 providers signed a data sharing agreement. Only 2 of these did not allow further sharing of data

• 11 total providers requested that data be used only within project, due to:– Potential sensitivity of collection locations– Conflict with other partnership agreements– Data not yet published/threat to intellectual property– Not specified

• By later stages of project, most of these providers decided to permit further use of data

19.1 million records (98.4%) open distribution306,781 records (1.6%) only for use of project

CWR Global Occurrence Database- data arrangements

• Overall overwhelmingly positive about project and sharing data

• The great majority contacted replied (80% responded)• With few exceptions, all who responded and had data,

shared it• Response aided by previous connections and personal

relationships. Although a few providers from closely related organizations did not collaborate, despite extensive attempts at engagement

• Response aided by mutually beneficial agreements (value added data repatriation, publications, training)

• Recognition (attribution) important to providers

CWR Global Occurrence Database- lessons learned about partnering on occurrence data

CWR data and gap analysis training

• PBI/Solanaceae Source/NHM (Solanum)

• ABCIC (African Oryza)

• CIP (Solanum, Ipomoea)

• CGN (Lactuca)• UBC (Helianthus)• EMBRAPA

• Value added data shared back to direct providers (repatriation)

• Creative commons license (Non-commercial, Share-alike; now moving to Attribution 4.0 International)

• Few comments on licensing; all were positive• Data also provided to researchers/organizations by

direct request• Data partly available now through website

(http://www.cwrdiversity.org/checklist/cwr-occurrences.php)

• Will soon provide entire dataset through website and GBIF

• Also providing data processing tools and code (https://github.com/CIAT-DAPA/ cwr_occurrencesvalidation)

CWR Global Occurrence Database- data distribution

CWR gap analyses for crop genepools

potato

sweetpotato

sunflower

pigeonpea

Gather occurrence

data

Make collecting

recommendations

Model distributions

Process data

Determine gaps in

collections

TaxonomicGeographicEcological

Choose species or

area81 crop

genepools 1079 crop wild relative taxa

(close relatives)

Crop wild relative gap analysis method Expert evaluation

Expert evaluation

Expert evaluation

Expert evaluation

Expert evaluation

Distributions of the CWR of pigeonpea

Khoury et al. 2015. Biological Conservation 184: 259-270.

Collecting priorities for the CWR of pigeonpea


Potential adaptive traits in CWR of pigeonpea


Targeted proposed collecting for adaptive traits for the CWR of pigeonpea

Potential distributions of selected CWR in A) south Asia and B) Australia that are not currently represented in germplasm collections and which occur in regions with <500 mm annual precipitation.


Gap analyses for targeted crop genepoolsKantar et al. 2015. Front. Plant Sci. 6: 841.

Castañeda-Álvarez et al. 2015. PLoS One 10(4): e0122599.

Khoury et al. 2015. Biol. Conserv. 184: 259-270.

Khoury et al. 2015. Front. Plant Sci. 6: 251.

Cobben et al. 2015. Plant Gen. Res. 13(2): 153-161.

CWR gap analyses at the national level

Inventory of CWR of the USA• Inventory includes a wide

range of utilized and potentially useful taxa, including both native and naturalized species occurring in the USA

• List peer reviewed by US researchers, curators, breeders

• Inventory contains over 4,600 taxa

• CWR related to major crops prioritized, along with US iconic wild crops (e.g. sugar maple, wild rice, pecan)

• ca. 250 closely related, native taxa related to 38 crops = highest priority

Phaseolus angustissimus. SEINet

Khoury et al. 2013. Crop Science 53(4): 1496.

raspberry 8Ribes 27squash 3star anise 1strawberry 8sugar maple 3sunflower 35sweet potato 9tepary bean 2vanilla 2walnut 5wild rice 5

Associated crop

Number of CWR

apricot 2beet 3blackberry 36blueberry 17cherry 2chestnut 3chives 1cotton 3cranberry 2fig 1garlic 1grape 28guava 1hazelnut 3lettuce 9lingonberry 3maize 3mate 5peach 10pecan 9pepper 1persimmon 2pistachio 1plum 17potato 1ramp 1

Highest priority food CWR of the USA

Khoury et al. 2013. Crop Science 53(4): 1496.

USA CWR distributions

Blac

kber

rySu

nflow

erGr

ape

Ribe

sBl

uebe

rry

Plum

Peac

hLe

ttuce

Peca

nSw

eet p

otat

oRa

spbe

rry

Stra

wber

ryM

ate

Waln

utW

ild ri

ceSq

uash

pep

oCo

tton

Beet

Ches

tnut

Haze

lnut

Lingo

nber

ryM

aize

Suga

r map

leTe

pary

bea

nAp

ricot

Cher

ryCr

anbe

rry

Pers

imm

onVa

nilla

Pota

toCh

ives

FigGa

rlic

Guav

aPe

pper

Pista

chio

Ram

pSt

ar an

ise

0

5

10

15

20

25

30

35

40

83.5%

8.4%

5.5% 2.6%

USA CWR gap analysis priorities

• Collaborations with genebanks, herbaria, researchers, and expert evaluators have overall been overwhelmingly positive, with the great majority very willing to contribute to the projects however they can. Investing in establishing as well as using pre-established personal relationships with partners probably improved response

• Formal data sharing agreement was very rarely used, 98% of occurrence data can be shared with the global community, and open use license (attribution only) seems acceptable. Recognition (attribution) is important

• The CWR data community remains quite some distance from the level of data quality and standardization required to trust in, share, and use taxonomic and occurrence data quickly and easily, although we are making progress

Thoughts and considerations on partnerships 1

• Collaborations involving invested researchers with a wide diversity of skills (taxonomy, distributions, conservation, breeding) were necessary to do our research on CWR, especially when using big datasets

• Iterative evaluations of data and results by collaborators were essential

• Mutually beneficial arrangements (publications, etc.) were highly desired, and resulted in best products

• Open access, open sharing (data, knowledge, tools) is the norm, is appreciated, and becoming expected

• Media appreciates proactivity, or at least willingness, to communicate about CWR

Thoughts and considerations on partnerships 2