Source: KANSAS STATE UNIV submitted to
FACT: GEOSPATIAL PLANT BREEDING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
EXTENDED
Funding Source
Reporting Frequency
Annual
Accession No.
1019820
Grant No.
2019-67021-29931
Project No.
KS1016885
Proposal No.
2018-09236
Multistate No.
(N/A)
Program Code
A1541
Project Start Date
Sep 1, 2019
Project End Date
Aug 31, 2022
Grant Year
2019
Project Director
Rife, T.
Recipient Organization
KANSAS STATE UNIV
(N/A)
MANHATTAN,KS 66506
Performing Department
Plant Pathology
Non Technical Summary
Modern plant breeding fundamentally relies on the observation, acquisition, and application of data to make informed decisions about the selection and release of varieties for farmers around the world. Although there have been improvements in both genetics and agronomics, the design and collection of data within modern field experiments has seen minimal advancement over the past decades. Individual plots are still primarily referenced by relative location in a row and column design and data is collected within the constraints and limitations of this layout. With state-of-the-art geo-position systems, we can now understand, collect, and analyze phenotypic data not only in a generic grid pattern, but in the dynamic geospatial context in which it actually exists. We propose a transformative conceptual shift in both the type and means of data collection for plant breeding field trials. To enable the collection, storage, analysis, and interpretation of phenotypic data on a geospatial basis, we will define open geospatial data structures, integrate support and analytical tools into Cassavabase, and create the breeder-friendly tools necessary to collect and utilize geospatial data in the field. Increasing the integrity, accessibility, and amount of data available to breeders will allow for more accurate and specific selection decisions with increased speed. Simplifying data collection and analysis workflows for breeders will enable the increased data integrity on larger population sizes required to produce adequate genetic gain to feed the world. Developing a framework for geospatial data will benefit all life sciences that rely on field studies.
Animal Health Component
0%
Research Effort Categories
Basic
20%
Applied
40%
Developmental
40%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20572991081100%
Goals / Objectives
Goal: We aim to develop the tools and systems necessary to shift phenotypic data collection in plant breeding from an entry-basis to a geospatial-basis. To meet this goal, we will implement the following specific objectives for the project.Specific Objectives:Develop the apps and database structures needed for collection and use of geospatial data in plant breeding field trials.Create geospatial data models, database schema, and analysis tools.Implement 'geo-navigation' into the Field Book app by integrating algorithms that identify plants/plots based on user location.
Project Methods
1. Apps and algorithms for geospatial data collectionSurvey appThe Survey app will be the primary means by which breeders collect coordinate-based data. Collected plot coordinates will have dual purposes: 1) ground truth points for high throughput phenotyping research and 2) plot points for in-field plot navigation. We will finalize Survey development, evaluate its performance in breeding field environments, and release it to the breeding community. The current, unreleased version of Survey utilizes a deprecated method for interacting with external GNSS hardware and will be updated to ensure compatibility with future versions of Android. Survey will be fully-evaluated in regionally disparate breeding environments and distinct crops to ensure broad compatibility with different breeding program organizational styles as well as the diverse Android hardware ecosystem. As the BrAPI standards are updated to implement geospatial data (Objective 2), we will incorporate BrAPI data types into Survey along with the API calls necessary to directly transfer collected coordinate data to BrAPI compatible databases.Plot navigation algorithmsOur impact zone algorithm will be evaluated in active breeding trials to determine any modifications that must be made. A functional interface will be added that allows breeders to adjust the parameters of the algorithm to their specific breeding program. The final impact zone algorithm will be developed and delivered as an Android service which will allow simple integration into other field-based mobile applications.Smart Glasses interfacesTo facilitate the transition from on-device navigation to automatic plot navigation, we will implement our smart glasses interface into Field Book. This interface currently exists in a fork of the Field Book project and thus cannot be used or evaluated by breeders. Introducing this interface will promote the adoption and evaluation of smart glasses, providing us with the critical feedback needed to improve the interface.The current implementation of the smart glasses interface displays information from Field Book and can utilize the user's voice for navigation. We will integrate an additional voice interface that allows users to collect data directly from the glasses. This will require a functional and efficient workflow that is simultaneously protected from accidental data entry. Defining this workflow in such a way that it maintains the current efficiency of data collection on Field Book will be a priority.2. Data models, database schema, visualization, and analyticsGeospatial data modelsTo maximize the utility of geospatial data in breeding, data must be easy to exchange between different clients, whether those are servers or external hardware used for data collection. This will be accomplished by expanding the BrAPI standard with geospatial data types. Most objects in BrAPI don't currently include geospatial information and thus the proper implementation has not been discussed by the broader development community. Adding this metadata will facilitate the spatial identification of various experimental units including plots, plants, and fields. Standard JSON notation does exist for geospatial data, and we will work with the BrAPI coordinator to integrate these standards into BrAPI.Database integration and visualizationBreeding databases need the ability to store and query geospatial data. We will adapt the Cassavabase database system to accommodate these data types by modifying the relational backend. Every entity in the database (plant, plot, field, etc.) has a unique data object associated with a unique identifier. Relational relationships will allow us to add more data to these items including geospatial information. These modifications will make it possible to import data from our geospatial tools, query geospatial information, create dynamic map overlays that utilize the geospatial information to display phenotypic data, and visualize geospatial information based on user queries, such as color scales for certain phenotypic measurements, field conditions, and other patterns of interest. Data will be loaded either directly through BrAPI or via file uploads.Geospatial data analysis for breedingA novel functionality that we will enable by the new geospatial nature of the data within these databases is the analysis and correction of spatial field effects using geographic information rather than on the row-column grid design of the field experiment. As we have already demonstrated the power of these approaches, the geographic weighted regression for correction of spatial effects will be implemented as a user accessible tool for analysis within the database for initial primary analysis of raw data from the field.3. Geo-navigation in Field BookTo effectively increase the accuracy and integrity of data collected by plant breeders, we will develop a system that allows for in-field navigation when collecting phenotypic data in a breeding program.We will integrate the impact zone algorithm from objective 1 into Field Book which will allow for the identification and display of the specific plot a breeder is viewing based on their current location and directional bearing. We will add support for the data models from objective 2 to ensure that data transfer between Field Book and Cassavabase is seamless and incorporates the rich metadata that will be available.Field Book has evolved to be a fundamental component of breeding programs across the world. Since these changes will require major changes to the backend database, we will extensively evaluate the app for performance prior to release to ensure the broad network of breeders who rely on Field Book have no interruption to their phenotyping. Release of the additional features will be evaluated by collaborating breeders first through the Field Book beta versions that are already in place before a wider release to the public.

Progress 09/01/20 to 08/31/21

Outputs
Target Audience:During this reporting period, our efforts directly reached numerous breeders who are utilizing Field Book and BreedBase for their research. We have been able to release several Field Book updates that are currently being used by more than 5000 plant scientists around the world (~660 within the United States). The updates substantially improved the workflow by adding features and fixing bugs that have been identified by both our group and other research groups. Changes/Problems:The SARS-Covid-2 pandemic inhibited the amount of collaboration that was able to be completed in person. A significant portion of our remaining work will be able to be completed either remotely or outside in the field, so we expect minimal roadblocks for the remaining project time. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?Results for the previous reporting period have been primarily disseminated via our public website, phenoapps.org. This site serves as a hub for users to retrieve the latest information about our new apps, sign up for our newsletter, and download manuals for specific apps. What do you plan to do during the next reporting period to accomplish the goals?We are aiming to have a beta version of Field Book GeoNav available before the end of 2021. We have several partners who are ready to rapidly evaluate these tools within their breeding programs. Based on their feedback, we will iterate features in Q1 and Q2 of 2022. The final system that facilitates location-based breeding will be published in a peer-reviewed journal article in 2022.

Impacts
What was accomplished under these goals? 1. Develop apps and database structures: Field Book v5 was released during the previous reporting period and implements new features that target our specific objectives. The most substantial update was related to a total database refactor that aligns more closely with community standards. By investing time in this refactor, we have created an environment that will allow much more rapid and robust development for future Field Book features. Most evident of this has been our work implementing and supporting the Breeding API v2.0. This updated version of BrAPI has significantly optimized data transfer protocols and is being readily adopted by database and research groups. BrAPI allows users of Field Book to connect to external breeding databases, download field and trait information, and send back collected data. As part of this work, we have also assisted in the development of a new OAuth login system for authentication. This system will allow secured connection and communication by diverse projects and research groups. Field Book v5 also includes a new trait data type that enables the overall model of geospatial breeding to be adopted into public breeding programs. The "GNSS" trait is slightly different from other Field Book traits. Whereas all other traits associate a specific phenotype to a single plot, the GNSS trait additionally modifies the actual plot data structure. This approach supersedes our previous approach of relying on an external app (Survey) but reuses a substantial portion of the previous codebase. 2. Geospatial data models, schema, and analysis tools BreedBase has been updated to allow field plots to have associated geospatial data. This is a functional requirement for full geospatial utilization across both platforms. Further, significant efforts have been made to update compatibility of BreedBase with the Breeding API v2 which has expanded support for these models, allowing geospatial data to be both sent and received via BrAPI. 3. Implement geonav into Field Book During the previous reporting period, we defined the development steps necessary for our team to integrate GeoNavigational support into Field Book. To this end, we have begun the integration of previously developed code into a private version of Field Book. These features are under active development but have not been evaluated publicly.

Publications


    Progress 09/01/19 to 08/31/20

    Outputs
    Target Audience:During this reporting period, our efforts directly reached numerous breeders who are utilizing Field Book for their research. We have been able to release several Field Book updates that are currently being used by more than 4000 plant scientists around the world (~550 within the United States). These updates have added features and fixed bugs identified by both our group and other research groups. Changes/Problems: We were successfully able to hire a postdoctoral fellow to work on this project in May 2020. The delay in identifying a suitable candidate limited the progress that was able to be made during the reporting period. However, the new hire has a comprehensive understanding of the project, the requirements, and what needs to be completed. The SARS-Covid-2 pandemic inhibited the amount of work that was able to be completed in person this year. Fortunately, many of our specific objectives are able to be developed remotely, so we don't expect the project to be severely delayed during the upcoming reporting period. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Results for the previous reporting period have been primarily disseminated via our public website, phenoapps.org. This site serves as a hub for users to retrieve the latest information about our new apps, sign up for our newsletter, and download manuals for specific apps. During the previous reporting period, we also held a training session at two sites in Nepal from March 9-12: Khumaltar (17) and Bhairahawa (12). The training covered how to set up and integrate Field Book and other apps into typical plant breeding programs and included a field component to familiarize participants with the overall data collection workflow. The training primarily focused on Field Book, Coordinate, and Inventory but also included general digitization strategies and discussed potential issues when transitioning to digital data collection. The participating breeding programs were given tablets, weigh scales, and barcode scanners after demonstrating they were capable of utilizing them for plant breeding research. What do you plan to do during the next reporting period to accomplish the goals? Our newly hired post-doc is currently developing an understanding of the Field Book code, the database schema, and identifying the changes necessary to implement and incorporate geospatial data models into Field Book. We expect that his development expertise will increase the speed of Field Book development, resulting in significant progress toward our specific objectives. We will further evaluate Survey in different environments and with different fields to verify that it is capable of capturing the data needed. We will add Breeding API support to Survey to allow communication to external databases to send the positional data being collected.

    Impacts
    What was accomplished under these goals? Develop apps and database structures Field Book was updated several times during the previous reporting period to implement new features that target our specific objectives. The most significant update has been the inclusion of the Breeding API v1.3. This feature allows users of Field Book to connect to external breeding databases, download field and trait information, and send back collected data. By creating a closed digital ecosystem, we are fundamentally changing how breeding data is managed. This development streamlines the data handling process which can reduce data errors and lead to more efficient breeding analysis and decisions.. There are current efforts between this and other projects to update Field Book with BrAPI v2 support. Survey was successfully released as a beta during the previous reporting period. We have evaluated this app in what we consider to be a "worst case scenario" at a very high spatial plot resolution of 2ft. and are optimistic about the results. Create geospatial data models/schema/tools BreedBase has been updated to allow field plots to have associated geospatial data. This is a functional requirement for full geospatial utilization across both platforms. Further, significant efforts have been made to update compatibility of BreedBase with the Breeding API v2 which has expanded support for these models, allowing geospatial data to be both sent and received via BrAPI. Implement geo-nav into Field Book Nothing to report

    Publications