Source: QUAIL BOTANICAL GARDENS FOUNDATION, INC. submitted to
CROP DIVERSITY BASELINE: ASSESSING CHANGE IN PLANT GENETIC RESOURCES IN THE PAST, PRESENT, AND FUTURE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1028408
Grant No.
2019-67012-36981
Cumulative Award Amt.
$22,034.38
Proposal No.
2021-13259
Multistate No.
(N/A)
Project Start Date
Jan 1, 2022
Project End Date
Dec 31, 2022
Grant Year
2022
Program Code
[A7201]- AFRI Post Doctoral Fellowships
Project Director
Khoury, C.
Recipient Organization
QUAIL BOTANICAL GARDENS FOUNDATION, INC.
230 QUAIL GARDENS DR
ENCINITAS,CA 920242707
Performing Department
Science and Conservation
Non Technical Summary
Crop genetic resources - seeds and other plant materials conserved in genebanks where they are accessed by plant breeders for crop improvement - are a foundation of agricultural productivity, profitability, and sustainability. These resources enhance the agriculture sector's capacity to respond to changing producer and market demands, and can increase sustainability by enabling producers to reduce their dependence on non-renewable inputs. Some the most important forms of these resources - traditional farmer varieties (landraces) and crop wild relatives (the wild cousins of domesticated crops) - continue to evolve in response to natural and human selection on farms and in wild habitats, and thus represent important founts of useful new traits for plant breeders. Unfortunately, the status of these diverse resources is not well understood despite decades of warnings that they may be disappearing.How much diversity has disappeared from farms and wild habitats over time? Scientists have struggled to answer this question more accurately than with very rough estimates, the most common being that 75 percent of crop diversity was lost over the past century. What are the genetic resources that are of most concern, and where do they occur? Here too the agricultural research community has not yet found clear answers. These persistent information gaps affect the ability for genebanks to assess how complete their collections are in comparison to the full extent of standing crop diversity in farmers' fields and from wild relative populations, to determine how significant their roles are in maintaining crop genetic variation now extinct in these fields and habitats, and to prioritize further collecting activities based on relative urgency.This research proposes to address these knowledge gaps by documenting historical change in the diversity of landraces and wild relatives of important crops such as potatoes and corn, by way of case-study comparisons between current observed diversity in the centers of origin of these crops and historical baseline information compiled from USDA and international public genebank collections. Further, the research will establish a modern dataset for these crops that will enable monitoring of changes in their diversity from the present into the future. Combined, the research, which centrally connects to the AFRI Farm Bill priority area on plant health and production and plant products, will generate important information for present and future genetic resource collecting, conservation, and use. The project includes leadership, training, and career development aspects in tools and methods, communications, teaching, project management, and grant writing; entails international collaboration; incorporates substantive evaluation plans; and involves mentorship from academic, governmental, nonprofit, industry, and international research institutions.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20252401081100%
Knowledge Area
202 - Plant Genetic Resources;

Subject Of Investigation
5240 - Seeds and other plant propagules;

Field Of Science
1081 - Breeding;
Goals / Objectives
The overall goal of this project is to address the critical knowledge gap concerning the degree of historical and projected future change in existing crop diversity in its geographic centers of origin, to inform crop genetic resource collecting and conservation strategies. This will be accomplished by documenting change over time in the in situ diversity of landraces and crop wild relatives of important crops such as potatoes and corn in their primary regions of diversity, by way of case-study comparisons between current observed diversity in the centers of origin of these crops and historical baseline information compiled from USDA and CGIAR genebank collections. Further, the research will establish a modern baseline dataset for these crops that will enable robust monitoring of changes in their diversity from the present to future.The main research objectives include:Assess temporal change in the diversity of exemplar, important crops (e.g. potatoes and corn and their wild relatives) in selected research sites located within their centers of origin, including identifying the key drivers of change as well as the implications of change.Determine the level of representation of existing in situ diversity in selected research sites within the NPGS and CGIAR public genebanks, identify diversity existing in these germplasm collections that no longer persists in situ in the research sites, and recognize novel in situ diversity in the research sites that is not currently represented in germplasm collections which may be considered as priority for further collecting.Establish a robust, repeatable methodology to monitor changes in the diversity of important crops and their wild relatives from the present to the future.Conducting a modern-day assessment of existing diversity for important crops and their wild relatives in their centers of origin, better understanding change in this diversity in these regions from the past to the present, and establishing a baseline methodology enabling better monitoring of changes in this diversity in the future, represent advances in knowledge and in data generation that are tremendously relevant to strategies for genetic resource collecting and conservation. The proposed research will generate critical information that the world's most important public genebanks, including the USDA ARS NPGS and the international collections of the CGIAR, can use to take action toward providing as diverse a genetic resource portfolio as possible to plant breeders. Through crop improvement, these resources can positively impact producers by offering resistance to pests and diseases, enhancing tolerance to abiotic stresses, and increasing yield. The resources ultimately positively impact consumers' access to a stable supply of affordable and nutritious food.The objectives of the research therefore centrally connect to the AFRI Farm Bill priority area on plant health and production and plant products, with additional positive impacts toward food safety, nutrition, and health; bioenergy, natural resources, and environment; agriculture systems and technology; and agriculture economics and rural communities. Research investment in public genebanks is timely, as renewed enthusiasm for international collaboration on collecting and transfer of crop genetic resources has been generated through the facilitated access agreements of the International Treaty on Plant Genetic Resources for Food and Agriculture, under which the CGIAR collections operate, and which the United States recently ratified.
Project Methods
Proposed activities to achieve the goals and objectives can be divided into two main components: a) past to present crop diversity research, and b) present to future research:Past-to-present crop diversity research:Compile and prioritize historical baseline resources on selected crops and their wild relatives from the NPGS and other U.S. institutions and the CGIAR. These resources will be integrated and synthesized via a broad review of genebank database passport data, field notebooks, photographs, and biological materials (herbarium specimens and germplasm accessions), looking for extensive documentation of historical collections of important agricultural crops such as potatoes and corn and their wild relatives in their centers of diversity, from sites that can feasibly be revisited. Important information sources include the NPGS collections, NPGS GRIN Global database and associated Plant Introduction books, the USDA National Agricultural Library, the NPGS Plant Exploration Office, CGIAR genebanks, CGIAR databases databases and field notebooks, university databases and library collections, and herbaria and botanic gardens.Develop a methodology to measure past baselines to present observed diversity. The main components that will be developed are landscape-, community-, and farm- level observations (i.e. are research sites still in agriculture? what crops? what varieties?), and farmer interviews and community surveys to understand the reasons for and implications of change in crop diversity over time. The methodology will also consider field sampling of plant materials, phenotyping, and genotyping, in preparation for research likely to occur after the postdoctoral research is completed.Visit historical baseline collection sites and record current data. The comparative methodology will be tested by revisiting at least two historical case-study collecting sites, and will include the landscape-, community-, and farm- level observations, farmer interviews, community surveys. While opportunities to collect biological materials and to perform collaborative analyses in the target communities will be pursued, the postdoctoral project will focus on observational, interview, and survey data gathering due to the short timeframe and given that acquiring collecting permits and arranging access agreements, as well as performing phenotyping and genotyping, are likely to require more than two years to complete. Further projects will capitalize on the momentum built during this project to complete the collection, phenotyping, and genotyping of biological materials, using the methodology developed during the postdoctoral research, if sufficient comparable biological materials are found in the case-study sites. IRB processes and agricultural community- and household-level approval, will be gained prior to initiating fieldwork.Analyze differences between past and present crop diversity. Case-study historical baseline data and current sampled observation, interview, and survey data will be compared to assess temporal changes in selected crop diversity in targeted research sites. Particular emphasis will be placed on identifying diversity lost in situ but present in germplasm repositories, and on highlighting apparently novel diversity persisting in situ that is not represented in genebanks.Present-to-future crop diversity researchDevelop a methodology to measure present baseline to future diversity. The methodology will include robust quantitative and qualitative sampling methods, based on state-of-art experimental design and sampling strategies, phenotyping, and genotyping research. Components include landscape-, community-, and farm- level observations, farmer interviews and community surveys, field sampling of plant materials, and phenotypic and genotypic analyses. The methodology will aim to be comprehensive while also easily repeatable by future researchers. Documentation of processes in metadata will be emphasized.Record current baseline data to enable future measurements. The current baseline methodology will be performed in at least two sites identified as currently containing considerable species and varietal diversity, being interested in long-term collaborations with researchers, and located in a country that is Party to the International Treaty. Data will include the landscape-, community-, and farm- level observations, farmer interviews, and community surveys. While opportunities to collect biological materials will be pursued, the current data baseline will focus on observational, interview, and survey data gathering due to the short timeframe of the postdoctoral research project. Further projects will capitalize on the momentum built during this project to collect, phenotype, and genotype the biological materials and thus complete the present day baseline. IRB processes and agricultural community- and household-level approval will be gained prior to initiating fieldwork.Preserve for the long-term and make accessible baseline methodologies and data points. Present-to-future methodologies and the current data points will be fully annotated and stored in long-term scientific repositories where they will be accessible to future researchers.

Progress 01/01/22 to 12/30/22

Outputs
Target Audience:The main target audiences for this reporting period are genetic resources conservation professionals, i.e., public genebank and other conservation repository organization curators, managers, administrators, collectors, and technicians. Particular emphasis is placed on national programs in the USA (USDA Agricultural Research Service, National Plant Germplasm System) and and international genebanks of the CGIAR- namely the International Potato Center (headquartered in Peru), the International Center for Tropical Agriculture (headquartered in Colombia with broad Latin America mandate), and the International Maize and Wheat Improvement Center (headquartered in Mexico). The second focal audience is academic and other research organizations, including researchers and students, who are involved in or interested in the preservation, management, and access to crop genetic resources, either in conservation repositories or in farmers' fields and natural habitats. The longer term and wider target audiences are farmers - including both those who manage traditional agricultural biodiversity in Latin America, as well as those in the USA and elsewhere who produce crops whose varieties were bred through the use of crop genetic resources - and consumers, i.e., the general public. Changes/Problems:Since initiation in the fall of 2019 and into early 2020, the project proceeded without major changes or problems. The project was able to complete the institutional IRB, fully engage the advisory board, begin compilation of the historical baseline data and outlining of the diversity comparison methodologies, identify target fieldwork regions and confirm a variety of local collaborators, and arrange for the first major fieldwork trip. The spread of COVID-19 began to impact the project in early March 2020, and within a few weeks the target regions and indeed entire countries were fully shut down to travel/fieldwork, and remained so essentially until 2022. These constraints obviously significantly negatively impacted fieldwork and thus the ability to complete an assessment of the state of crop diversity in these regions, including the comparison of this diversity to historical records. From March 2020 to early 2022, as recommended by and with full support of the project mentors and advisory board, the project adapted to COVID-19 challenges including by: a) collaborating with mentors, the advisory board, and project colleagues and partners virtually, maintaining original activities as much as possible; b) agreeing with target fieldwork region collaborators to maintain frequent communication and look for opportunities to accomplish fieldwork as possible within constraints (generally by further enhancing collaboration with local partners, including by looking for additional funding for these partners); c) contributing to the main overriding goals and objectives of the project as possible with available data and leveraging ongoing related projects; and d) preparing for fieldwork so that when COVID-19 constraints were lifted, fieldwork activities could recommence as soon as possible. The project largely succeeded at the reframed approach to completing the original goals and objectives. Mentors and partners were engaged continuously, with key partners in target regions invested in accomplishing the project as possible. Project collaborators were successful in finding additional funding for fieldwork local partners, which led to a phenomenally productive field season in 2022. In redirecting toward greater investment in conducting analyses of the state of conservation of crop diversity with available data and based on leveraging ongoing projects, we were productive with regard to outputs, publishing 26 scientific articles, including in Science, PNAS, New Phytologist, and Nature journals, as well as technical documents, blogs, posters, and presentations. Further, this redirection opened the opportunity to focus on providing answers to project primary research questions through the largest and most ambitious literature review ever performed on the subject of change over time in crop diversity, the resulting product of which was specially invited by a top-tier plant sciences journal, and was published in 2021. In 2021, we requested a one year extension to complete major project fieldwork and training/capacity building/outreach objectives, to start at the original project end (August 31, 2021). Shortly thereafter this was modified into a PD transfer, as the PD had acquired a long term scientific position. With the remaining project support, in 2022 the project was finally able to initiate fieldwork activities as well as further in person training. With initiation of fieldwork activities in Peru in 2022, the fieldwork team including the project PD as well as collaborators from the International Potato Center (CIP) and local partners succeeded in generating a comprehensive current baseline for the Paucartambo region, including over 350 family interviews as well as community workshops. The productivity of this field season is a direct result of the efforts since 2019 under this project to form extensive partnerships and plan for fieldwork. These data are now being processed and analyzed in preparation for scientific publications. What opportunities for training and professional development has the project provided?The main training and professional development provided by the PD to date has been teaching and mentoring undergraduate and graduate students, as well as conservation practitioner peers, in geographic patterns of crop diversity, genetic resources conservation gap analysis, and other crop conservation topics. Activities have included both in depth training, e.g., a PhD student from Monash University in Australia on the use of ecogeographic tools to perform crop diversity conservation analyses for wild relatives of sorghum (resulting in a peer reviewed publication listed in the publication section) and NASA Develop program student collaborators on wild rice diversity (also resulting in a listed publication), as well as giving dozens of presentations and seminars, both in person and virtually. The PD also participated as an editor in the creation of a special issue in a high quality plant science journal on digital sequence information related to genetic resources, an important emerging topic in the crop diversity conservation field, and also served as a special editor for a journal article on spatial and temporal dimensions of crop diversity, published in PNAS. The articles in this collection are expected to contribute to enhancing the evidence base and general knowledge around these subjects for practitioners, academics, and policy communities. The main training and professional development provided to the PD to date has been increased capacity in both genetic/genomic and phenotypic/phenomic tools as well as in ethnobiological approaches. While originally planned as in person activities, due to COVID-19 these occurred largely through virtual training and journal clubs, mainly provided by Saint Louis University, the Danforth Plant Science Center, and the Missouri Botanical Garden. In the fall of 2019, prior to COVID-19, the PD was also able to gain further capacity in plant conservation by attending two technical/academic conferences. During the summer of 2020, the PD was also able to take the opportunity to train in field surveying and collecting of crop genetic resources through participation in an exploration for a wild relative of potato occurring in southern Colorado. Following the release of major travel constraints in 2022, the PD was able to both train others on the fieldwork team, and to build his own capacity, in fieldwork methodologies and in data processing and analysis. Finally, one of the trips in 2022 was to conduct data processing with a major leader in the field, affording capacity building of the PD in the wider issues around change in crop diversity and effective conservation strategies. How have the results been disseminated to communities of interest?The project has worked to disseminate as widely as possible the main products thus far - research publications - to the main target audiences and to the general public. This has been done through publication as feasible in high quality journals providing open access to the research, through wide distribution of the articles via organizational channels, and through media efforts (i.e., press releases and media engagement) following article publications. A number of the publications have received substantial conventional as well as social media attention and are expected to be widely read and cited. Moreover, the majority of publications have involved diverse collaborations among many authors from different institutions, enabling direct impact for involved authors, and facilitating much wider dissemination through all of their organizational channels. The project also published a number of blogs in widely-read venues, as well as given dozens of presentations in a variety of technical conferences and academic fora, to communicate the results to the target audiences. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The contribution of crop genetic resources to the productivity, sustainability, and adaptability of agriculture is well recognized. Traditional farmer varieties (landraces) and crop wild relatives represent important genetic resources which still occur in fields and wild habitats, with the richest diversity found in the regions of origin of crops, for instance in the highlands of Peru and Bolivia for potatoes, and in central Mexico for corn. Unfortunately, the degree to which these resources are conserved and available for plant breeding from genebanks is not well understood, despite decades of warnings that they may be disappearing from fields and from the wild. This information gap constrains the capacity of genebanks to prioritize their conservation efforts and potentially limits the long term availability of crop diversity for present and future generations. This postdoctoral research project proposes to fill critical knowledge gaps by assessing the comprehensiveness of conservation of crop diversity related to exemplar crops within genebanks, in comparison to diversity still extant in fields and in the wild. The project also aims to improve the methods used to understand how this diversity changes over time so as to better enable monitoring of diversity loss. The findings are intended to be of use to crop genetic resources professionals, academics and other researchers, and members of the public interested in the history and future of food and agriculture, while the long term impacts of the research, via enhanced conservation and availability of crop genetic resources, are intended to benefit farmers and consumers in the United States and around the world. Under this reporting period and up to this date, the project has been successful in establishing the major procedures and relationships needed to accomplish proposed fieldwork preparatory activities, including IRB protocols and engagement of the advisory board; compilation of historical crop diversity baseline data and outlining of sociological, phenotypic, and genotypic comparative methodologies; identification of target fieldwork regions and confirmation of various local collaborators; design of fieldwork travel; completion of one season of fieldwork in Peru; and initiation of field data processing and analysis in preparation for scientific publications. The emergence of COVID-19 in the early months of 2020 prohibited the commencement of travels for fieldwork, with travel and fieldwork in the target regions prohibited until 2022. The project adapted to COVID-19 constraints by a) engaging with mentors, the advisory board, and project colleagues and partners virtually, maintaining progress on original activities as much as possible; b) agreeing with target fieldwork region collaborators to maintain frequent communication and look for opportunities to accomplish fieldwork as possible within constraints (generally by further enhancing collaboration with local partners, including by looking for additional funding for these partners); c) contributing to the overriding goals and objectives of the project as possible through the use of available data and leveraging of ongoing related projects; and d) preparing for fieldwork in terms of data and methods so that when COVID-19 constraints were lifted, fieldwork activities could recommence as soon as possible. The project largely succeeded at contributing to the overriding goals and objectives under these constraints. Using available data and leveraging ongoing related projects, the project contributed to generating knowledge on the state of diversity and its representation in conservation repositories for crop genetic resources relevant to a wide range of crops, including potatoes, beans, maize, carrots, chile peppers, lettuce, mint, sorghum, wildrice, and zucchini and pumpkins. Publications have also identified genetic resource conservation priorities at the national level in the United States, generated an R code for conservation gap analysis, furthered the understanding of geographic origins of crop diversity, proposed improved methodologies for assessing representation of crop diversity in genebanks and in situ, outlined organizational collaborations key to success of crop diversity conservation in the United States, explored novel funding mechanisms for wildlands conservation pertinent to crop diversity, identified genetic resource and crop breeding needs for cover crops, furthered the discussion of use of digital sequence information related to crop genetic resources, and advocated for enhanced conservation of crop genetic resources as well as for wider biodiversity, including by supporting Indigenous and rural agricultural populations worldwide. These total 26 peer-reviewed journal articles, including in Science, PNAS, New Phytologist, and in Nature journals. Adaptation of the project to COVID-19 constraints also enabled a much greater focus than originally envisioned on summarizing the state of knowledge in the field, through a comprehensive review of the scientific literature on change over time in crop diversity (i.e., "crop genetic erosion"), the resulting product of which was published in 2021. The project has written four proposals for further funding, primarily to support collaborators which may be able to accomplish portions of the outlined fieldwork even under some travel constraints. The project also accomplished training and communication activities meant to enhance the capacity of students and the PD in relevant methodologies, and to make project topics and results widely known to genetic resources professionals, academics, and the general public. With initiation of fieldwork activities in Peru in 2022, the fieldwork team including the project PD as well as collaborators from the International Potato Center (CIP) and local partners, succeeded in generating a comprehensive current baseline for the Paucartambo region, including over 350 family interviews as well as community workshops. The productivity of this field season is a direct result of the efforts since 2019 under this project to form extensive partnerships and plan for fieldwork. These data are now being processed and analyzed in preparation for scientific publications.

Publications

  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Fumia N, Pironon S, Rubinoff D, Khoury CK, Gore MA, and Kantar MB (2022) Wild relatives of potato may bolster its adaptation to new niches under future climate scenarios. Food and Energy Security 11(2): e360. doi: 10.1002/fes3.360. https://doi.org/10.1002/fes3.360
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? University of Illinois Department of Crop Sciences & Energy Biosciences Institute, Plant Breeding & Germplasm Resources Lecture, 1 December 2022, Urbana-Champaign, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) The wild future of our food United States Botanic Garden Science Seminar, 23 September 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? New York Botanical Garden Science Seminar, 5 August 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? UCCE San Diego Master Gardener Association's Book Club Seminar, 28 July 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) Crop wild relatives of the United States Denver Botanic Gardens, Global Steppe Symposium, 27 July 2022, Denver, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? California State University San Marcos, Department of Biology, Plants and Society course lecture, 12 April 2022, San Marcos, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? University of Saskatchewan, Department of Plant Sciences, Global Plant Genetic Resources course lecture, 22 March 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) Change over time in potato crop diversity in its region of origin San Diego Botanic Garden Science Seminar Series, 22 July 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? Convolvulaceae Network seminar, 29 April 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? And science and conservation at the San Diego Botanic Garden Escondido Rotary Club, 12 April 2022, Escondido, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Khoury CK (2022) If we are what we eat, then where are we from? University of Hawaii, Department of Tropical Plant and Soil Science Symposium, 11 March 2022, Manoa, USA.