Funded Projects (Sorted by project start date descending order)

Genetic networks regulating structure and function of the maize shoot apical meristem

Award #: 1238142
Michael Scanlon
Patrick Schnable, Marja Timmermans, Jianming Yu, Xiaoyu Zhang
February 1, 2013
January 31, 2018 - Extended thru December 31, 2021

The shoot apical meristem (SAM) is responsible for development of all above ground organs in the plant. SAM structure and function correlates with agronomically-important adult traits in the maize plant, and is also affected by planting density and shade stresses induced by agricultural environments. The ultimate goal of this project is to increase understanding of the regulatory networks controlling SAM structure and function and the responses of these networks to environmental stresses. The specific objectives are to: 1) describe the SAM allometric space in maize and its relatives using nanoscale computer tomographic scanning to provide 3-dimensional images of the phenotypic diversity of SAM structure and identify adult plant traits correlated with SAM structure; 2) identify differentially expressed genes in SAM size/shape outliers and mutants with abnormal SAM structures and generate a co-expression network of key genes implicated during SAM structure and function; 3) perform quantitative genetic analyses to identify specific variations within genes that correlate with variations in SAM structure/function and adult plant traits, and test functions of 40 key genes using reverse genetic aaproaches; 4) analyze the shade avoidance response and its effects on SAM structure and function; and 5) investigate epigenetic changes of SAM functional domains in response to shade avoidance using novel protocols that distinguish the stem cell organizing regions from the organogenic domains in the maize SAM.

These studies will provide the framework for scientific training and the public release of original data. Undergraduates at Truman State University, a small liberal arts institution, will be trained in morphological and LM-RNAseq analyses of maize mutants. REU students and undergraduates enrolled in Plant Physiology courses at Cornell University will participate in physiological experiments. This project will generate extensive transcriptomic data and vector constructs for tissue-specific epigenetic analyses which will be available to the scientific research community. Molecular markers and phenotypic data for diverse maize lines will be supplied to Panzea (http://www.panzea.org/). Genetic mapping associations, physiological shade-avoidance response data, transcriptomic and phenotypic data will be curated at MaizeGDB (http://www.maizegdb.org/), and seed stocks for maize shoot mutants and SAM size variants will be released through the Maize Genetics Cooperation Stock Center (http://maizecoop.cropsci.uiuc.edu/).

NRT-DESE: P3 - Predictive Phenomics of Plants

Award #: 1545453
Julie Dickerson
Patrick Schnable, Theodore Heindel, Carolyn Lawrence-Dill
September 1, 2015
August 31, 2020 -- Extended thru August 31, 2021

NRT- DESE: Predictive Phenomics of Plants (P3)

New methods to increase crop productivity are required to meet anticipated demands for food, feed, fiber, and fuel. Using modern sensors and data analysis techniques, it is now feasible to develop methods to predict plant growth and productivity based on information about their genome and environment. However, doing so requires expertise in plant sciences as well as computational sciences and engineering. This National Science Foundation Research Traineeship (NRT) award to Iowa State University will bring together students with diverse backgrounds, including plant sciences, statistics, and engineering, and provide them with data-enabled science and engineering training. The collaborative spirit required for students to thrive in this unique intellectual environment will be strengthened through the establishment of a community of practice to support collective learning. This traineeship anticipates preparing forty-eight (48) master's and doctoral students, including twenty-eight (28) funded doctoral students, with the understanding and tools to design and construct crops with desired traits that can thrive in a changing environment.

Understanding how particular genetic traits result in given plant characteristics under specific environmental conditions is a core goal of modern biology that will facilitate the efficient development of crops with commercially useful characteristics. Plant characteristics are influenced by genetics and a wide range of environmental factors, including, for example, rainfall, temperature and soil types. Developing methods to effectively integrate these diverse inputs that take advantage of existing biological, statistical, and engineering knowledge will be a key area in this research and training program that will bring together faculty from eight departments. Trainees will engage in cutting-edge research and development areas involving direct data collection and analysis from living plants, including sensor development, high throughput robotic technology, and biological feature extraction through image analysis. This traineeship will use the T-training model to provide students with training across a broad range of disciplines while developing a deep technical expertise in one area. This expertise, in combination with soft skills development, will enable the trainees to work across organizational and cultural boundaries as well as scientific disciplines. To develop understanding of how to share knowledge with diverse groups, the program will provide students with training beyond traditional coursework and research through activities that will develop advanced communication and entrepreneurship skills. Additionally, internship opportunities in industry, national labs, and other settings will equip trainees to choose among the diverse career paths available to scientists and engineers.

The NSF Research Traineeship (NRT) Program is designed to encourage the development and implementation of bold, new, potentially transformative, and scalable models for STEM graduate education training. The Traineeship Track is dedicated to effective training of STEM graduate students in high priority interdisciplinary research areas, through the comprehensive traineeship model that is innovative, evidence-based, and aligned with changing workforce and research needs.

Development of a PhenoNet - an Integrated Robotic Network forĀ Field-basedĀ Studies of Genotype x Environment Interactions

Award #: 1625364
Lie Tang
Patrick Schnable
Srikant Srinivasan
September 15, 2016
August 31, 2019 -- Extended thru August 31, 2021

An award is made to Iowa State University to develop and deploy PhenoNet - an integrated robotic network for field-based studies of genotype crossed with environment (GxE) interactions. The core component of PhenoNet is a set of PhenoBots; lightweight robots that are able to autonomously navigate between crop rows using GPS and local range sensors while employing advanced sensing technologies to phenotype crop plants. The PhenoBots can measure indicators such as stalk size, plant height, leaf angle and tassel/inflorescence properties over time. The robots will be optimized for maize research and can be easily adapted for other row crops. The network (PhenoNet) is a universal platform which enables comprehensive field-based research on genotype and environment interactions. The broader impacts of this project are threefold. First, PhenoNet will have an important impact on society as understanding genome X environment interactions will help address the need for sufficient food, feed, and fiber for the planet's growing population, which is vital in an ever-changing environment. PhenoNet will bring "big data" more deeply into agriculture by cementing connections between plant scientists and engineers in their efforts to reach this goal. Second, this project is synergistic with the NSF-NRT project, "Predictive Phenomics of Plants", recently awarded to Iowa State University. The research and engineering outlined in this Major Research Instrumentation project will provide an outstanding opportunity for students from engineering disciplines, computer science, statistics, and agronomy to collaborate and engage in state-of-the-art interdisciplinary research. This project will also advance the training of current engineers and plant scientists who are experienced with networking, robotics and agronomy. Third, this project will reach out to underrepresented groups by targeting minority-serving institutions for student recruitment and will work with the Society of Women Engineers and other similar groups in seeking women participants to help meet the NSF-NRT award's efforts to broaden participation.

The PhenoBots are an important and essential advancement in the fields of agriculture and technology because they more efficiently characterize tall plants over time to their maturity. Previous technology and platforms are either incapable of, or are greatly hindered by various constraints. The design improvements of the Phenobots enable the robots to be more robust, stable, lightweight, integrated and economical. This creates a pathway for transformative research as it enables in situ, non-invasive monitoring of the traits of tall crops, like maize, over time. PhenoNet will consist of a network of four PhenoBots, which will be deployed by plant scientists in Iowa, Kansas, Minnesota, Nebraska, and Wisconsin. The data generated from high throughput phenotyping will address whether it is possible to predict the phenotype of a given genotype in a specified environment.

Root Genetics in the Field to Understand Drought Adaptation and Carbon Sequestration

Award #: DEAR0000826
John McKay
Parker Antin, Randy A. Bartels, Thomas Borch, Pedro Andrade Sanchez, Francesca Cotrufo, Andrew French, Michael Ottman, Sangmi Palickara, Keith Paustian, Patrick Schnable, Chris Topp, Chris Turner, Matthew Wallenstein, Jianming Yu
July 3, 2017
July 2, 2020 -- Extended thru October 2, 2021

Critical Need: Plants capture atmospheric carbon dioxide (CO2) using photosynthesis, and transfer the carbon to the soil through their roots. Soil organic matter, which is primarily composed of carbon, is a key determinant of soil's overall quality. Even though crop productivity has increased significantly over the past century, soil quality and levels of topsoil have declined during this period. Low levels of soil organic matter affect a plant's productivity, leading to increased fertilizer and water use. Automated tools and methods to accelerate the process of measuring root and soil characteristics and the creation of advanced algorithms for analyzing data can accelerate the development of field crops with deeper and more extensive root systems. Crops with these root systems could increase the amount of carbon stored in soils, leading to improved soil structure, fertilizer use efficiency, water productivity, and crop yield, as well as reduced topsoil erosion. If deployed at scale, these improved crops could passively sequester significant quantities of CO2 from the atmosphere that otherwise cannot be economically captured.

Project Innovation + Advantages: Colorado State University (CSU) will develop a high-throughput ground-based robotic platform that will characterize a plant's root system and the surrounding soil chemistry to better understand how plants cycle carbon and nitrogen in soil. CSU's robotic platform will use a suite of sensor technologies to investigate crop genetic-environment interaction and generate data to improve models of chemical cycling of soil carbon and nitrogen in agricultural environments. The platform will collect information on root structure and depth, and deploy a novel spectroscopic technology to quantify levels of carbon and other key elements in the soil. The technology proposed by the Colorado State team aims to speed the application of genetic and genomic tools for the discovery and deployment of root traits that control plant growth and soil carbon cycling. Crops will be studied at two field sites in Colorado and Arizona with diverse advantages and challenges to crop productivity, and the data collected will be used to develop a sophisticated carbon flux model. The sensing platform will allow characterization of the root systems in the ground and lead to improved quantification of soil health. The collected data will be managed and analyzed through the CyVerse "big data" computational analytics platform, enabling public access to data connecting aboveground plant traits with belowground soil carbon accumulation.

Potential Impact: If successful, developments made under the ROOTS program will produce crops that will greatly increase carbon uptake in soil, helping to remove CO2 from the atmosphere, decrease nitrous oxide (N2O) emissions, and improve agricultural productivity.

  • Security: America's soils are a strategic asset critical to national food and energy security. Improving the quality of soil in America's cropland will enable increased and more efficient production of feedstocks for food, feed, and fuel.
  • Environment: Increased organic matter in soil will help reduce fertilizer use, increase water productivity, reduce emissions of nitrous oxide, and passively sequester carbon dioxide from the atmosphere.
  • Economy: Healthy soil is foundational to the American economy and global trade. Increasing crop productivity will make American farmers more competitive and contribute to U.S. leadership in an emerging bio-economy.

A Scalable Framework for Visual Exploration and Hypotheses Extraction of Phenomics Data using Topological Analytics

Collaborative Research - Iowa State Award #: 1661475 ; Washington State University Award #: 1661348
Anantharaman Kalyanaraman
Bala Krishnamoorthy, Zhiwu Zhang, Bei W. Phillips, Patrick Schnable
August 1, 2017
July 31, 2020 - Extended thru July 31, 2021

Understanding how gene by environment interactions result in specific phenotypes is a core goal of modern biology and has real-world impacts on such things as crop management. Developing and managing successful crop practices is a goal that is fundamentally tied to our national food security. By applying novel computational visual analytical methods, this project seeks to identify and unravel the complex web of interactions linking genotypes, environments and phenotypes. These methods will first need to be designed and developed into usable software applications that can handle large volumes of crop phenomics data. High-throughput sensing technologies collect large volumes of field data for many plant traits, such as flowering time, related to crop development and production. The maize cultivars used here come from multiple genotypes that have been grown under a variety of environmental conditions, in order to give the widest range of conditions for understanding the interactions. The resulting data sets are growing quickly, both in size and complexity, but the analytical tools needed to extract knowledge and catalyze scientific discoveries have significantly lagged behind. The methodologies to be developed in this project represent a systematic attempt at bridging this rapidly widening divide. The project is inherently interdisciplinary, involving close research partnerships among computer scientists, plant scientists, and mathematicians. The research outcomes will be tightly integrated with education using a multipronged approach that includes, among others, postdoctoral and student training (graduates and undergraduates), curriculum development for a new campus-wide interdisciplinary undergraduate degree in Data Analytics, conference tutorials for training phenomics data practitioners, and contribution to the recruitment and retention of underrepresented minorities (particularly women) in STEM fields through the Pacific Northwest Louis Stokes Alliance for Minority Participation.

This project will lead to the design and development of a new, scalable, visual analytics platform suitable for hypothesis extraction and refinement from complex phenomics data sets. Focus on hypothesis extraction is critical in the context of phenomics data sets because much of the high-throughput sensing data being generated in crop fields are generated in the absence of specifically formulated hypotheses. Extracting plausible hypotheses from the data represents an important but tedious task. To this end, this project will apply and develop new capabilities using emerging advanced algorithmic principles, particularly from the branch of mathematics called algebraic topology that studies shapes and structure of complex data. The research objectives are three-fold. First, the project will employ and extend emerging algorithmic techniques from algebraic topology to decode the structure of large, complex phenomics data. Second, an interactive visual analytic platform will be developed to facilitate knowledge discovery using the extracted topological structures. Lastly, the quality and validity of a new visual analytic platform designed by this team will be tested using real-world maize data sets as well as simulated inputs as testbeds. The developed framework will encode functions for scientists to delineate hypotheses of three kinds: i) genetic characterization of single complex traits; ii) genetic characterization of multiple traits that share potentially pleiotropic effects; and iii) decoding and detailed characterization of genotype-by-environmental interactions, in particular, through a collaborative pilot study of maize flowering and growth traits. The expected significance of the proposed work is that biologists will be able to extract different types of testable hypotheses from plant phenomics data sets by employing a new class of visual analytic tools, and thus obtain a deeper understanding of the interactions among genotypes, environments and phenotypes. The project is potentially transformative in two ways: i) it will introduce advanced mathematical and computational principles into mainstream phenomic data analysis; and ii) it will usher in a new era where biologists spearhead data-driven hypothesis extraction and discovery with the aid of interactive, informative, and intuitive tools. The project will have a direct impact on the state of software in phenomics for fundamental data-driven discovery. To facilitate broader community adoption, the project will integrate the tools into the CyVerse Institute, and to a community phenomics software outlet. It will also lead to the development of automated scientific workflows. Project website: http://tdaphenomics.eecs.wsu.edu/

NIFA FACT Workshop: High Throughput, Field-Based Phenotyping Technologies for the Genomes to Fields (G2F) Initiative

Award #: 2018-67013-27389
Patrick Schnable
January 1, 2018
December 31, 2019 -- Extended thru December 31, 2021

G2F is an umbrella initiative to support translation of maize genomic information for the benefit of growers, consumers and society. This initiative will promote projects that advance integrated research and technologies, combining fields such as genetics, genomics, plant physiology, agronomy, climatology and crop modeling, with computation and informatics, statistics and engineering. The G2F conference will focus on exposing the field-based G2F collaborators, many of whom are plant breeders, to novel tools (such as robots, UAVs and sensors) and approaches for analyzing data. Talks will be geared to the needs of the data generators and the group will discuss strategies to integrate these new technologies into G2F. Participants will discuss, together with International Agroinformatics Alliance (IAA), how to clean up, store and share multi-year geocoded field trial data. The Plant Sciences Institute at Iowa State University has been successful at creating an environment that fosters the development of collaborations among plant scientist, engineers and computational scientists. One of the goals of the proposed conference is to encourage participants to replicate this approach on their own campuses, which if successful will expand the pool of engineers and computational scientists who can contribute the G2F-related research in all crops and bring new ideas and approaches to bear on the challenges facing US agriculture. In addition, by encouraging students who are being mentored by the G2F collaborators (many of whom are public sector plant breeders) to attend the conference we will enrich the population of attendees for students with an interest in plant breeding.

Miniature, Low-cost, Field-deployable Sensors to Advance High-throughput Phenotyping for Water Use Dynamics

Award #: 2018-67021-27845
Michael Castellano
Patrick Schnable, Liang Dong
April 15, 2018
April 14, 2021 - Extended thru April 14, 2022

NON-TECHNICAL SUMMARY: This proposal will develop and deploy "wearable" (i.e., non-destructive, leaf-mountable) sensors for the measurement of water transport dynamics in maize. The sensors will be used to enable a high-throughput phenotyping platform that demonstrates the sensors' ability to discriminate among maize genotypes for plant water transport dynamics. The new sensors will advance plant sciences and agricultural research in a manner similar to how wearable human body sensors have advanced human health and biomedical sciences.Two types of sensors to be developed and deployed in field research plots: a relative humidity (RH) sensor and leaf water content sensor. The RH sensor will measure humidity and temperature at the leaf surface, and can self-adjust its size and shape to adapt to the growth of leaves. The leaf water content sensor will be developed using advanced Micro-Electro-Mechanical Systems technology, and will measure leaf thickness and water content. In years one and two, the sensors will be calibrated and validated. In years two and three, 400 of each type of sensor will be deployed across 50 maize hybrids in replicated plots. Each hybrid, selected from the Genomes to Fields Initiative (G2F), includes 24+ site-years of yield, weather and phenotype data from locations spanning Arizona to NY. Using sensor and grain yield data generated during the project in combination with yield and weather data from the G2F site-years, we will test the association of variation in water transport dynamics with variation of yield and yield stability among hybrids and in relation to environmental parameters.

OBJECTIVES: Water is generally the greatest limitation on crop production. Our goal is to develop and deploy "wearable" (i.e., non-destructive, leaf-mountable) sensors for the measurement of water transport dynamics in maize. The sensors will be used to enable a high-throughput plant breeding platform that demonstrates the sensors' ability to discriminate among maize genotypes for plant water transport dynamics. The new sensors will advance plant sciences and agricultural research in a manner similar to how wearable human body sensors have advancedhuman health and biomedical sciences. We have three objectives:Develop, calibrate, and optimize two types of low-cost, leaf-mounted, wearable plant sensors for accurate measurements of plant water dynamics.Use the sensors to develop a water use phenotyping platform that demonstrates the ability of sensors to discriminate among maize genotypes according to plant water dynamics.Test whether differences in plant water dynamics are predictive of yield or stability of yield across environments. Using sensor and grain yield data generated during the project in combination with yield and weather data from the Genomes To Fields project, we will test the association of variation in water transport dynamics with variation of yield and yield stability among hybrids and in relation to environmental parameters.

APPROACH: Two 'wearable' (i.e., non-destructive, leaf-mountable) sensors developed in this project will advance plant sciences and agricultural research in a manner similar to how wearable human body sensors have advanced human health and biomedical sciences. One sensor will measure relative humidity at the leaf surface using an adhesive tape-based sensor technology. The device is a patent-pending gas and vapor permeable tape patterned with graphine and graphine oxide. The graphine serves as an electrical resistor whose resistance changes with varying moisture levels. The second sensor will measure leaf water content and thickness using advanced Micro-Electro-Mechanical Systems (MEMS) technology. Using the two new sensors, we will develop a phenotyping platform that will characterize maize water use efficiency across different weather and soil environments. This will be accomplished by leveraging the Genomes to Fields maize phenotyping program that spans multiple locations from Arizona to New York.

CC* Integration: End-to-End Software-Defined Cyberinfrastruture for Smart Agriculture and Transportation

Award #: 1827211
Hongwei Zhang
Anuj Sharma, Patrick Schnable, Arun Somani, Ahmed Kamal
October 1, 2018
September 30, 2020 - Extended thru September 30, 2021

Imaging and other sensor-based understanding of plant behavior is becoming key to new discoveries in plant genotypes leading to more productive and environment-friendly farming.

Similarly, distributed sensing is seen as a key component of a safe, efficient, and sustainable autonomous transportation systems.

Existing research and education in agriculture and transportation systems are constrained by the lack of connectivity between field-deployed testbed equipment and computing infrastructure. To realize that connectivity, this project proposes to deploy CyNet wireless networks to connect experimental science testbeds to high-performance cloud computing infrastructures.

The CyNet project will:

  1. Deploy Predictable, Reliable, Real-time, and high-Throughput (PRRT) wireless networking solutions using the standards-compliant, open-source Open Air Interface software framework and commodity Universal Software Radio Peripheral (USRP) hardware
  2. Integrate these wireless networks with software defined networks to seamlessly integrate outdoor cameras, sensors, and autonomous vehicles, and connect these components to high performance cloud computing systems
  3. Implement an infrastructure virtualization system that partitions CyNet into programmable, isolated experiments
  4. Create an infrastructure management system that performs admission and access control and establishes specified resource allocation policies

BTT EAGER: Improving crop yield prediction by integrating machine learning with process-based crop models

Award #: 1842097
Lizhi Wang
Sotirios V. Archontoulis, Baskar Ganapathysubramanian, Guiping Hu, Patrick S. Schnable
March 1, 2019
February 28, 2021 - Extended thru February 28, 2022

Predicting crop yield is central to addressing emerging challenges in food security, particularly in an era of global climate change. Currently, machine learning and crop modeling are among the most commonly used approaches for yield prediction. This award supports fundamental research to combine the strengths of machine learning and crop models. Machine learning algorithms will be used to predict intermediate plant traits, which will then be fed into a crop model to predict grain yields across different environment and field management practices. Both conception and execution of this EAGER project depend on collaborations across multiple disciplines, including high-throughput phenotyping, object recognition, machine learning, optimization, computer simulation, and crop modeling. If successful, this research is expected to improve not only accuracy but also interpretability of yield prediction models, which will open numerous opportunities for downstream research and discoveries. The interdisciplinary effort will enhance the impact of science and engineering education across disciplines, while providing a collaborative and inclusive environment for all students to engage in cutting edge research activities.

Underlying yield prediction is one of the grand challenges of biology: understanding how phenotype is determined by genotype, environment, and their interactions. Machine learning algorithms are able to predict crop phenotype to reasonable accuracy based on genotype information, but most models have a black box structure and their results are hard to interpret. On the other hand, crop models offer biological insights into causes of phenotypic variation by providing explicit explanations of the interactions between traits and environmental conditions in different phases of the crop growth cycle, but the collection of trait measurement data and calibration of model coefficients are labor intensive, time consuming, and costly. The proposed approach is a nested model. Deep learning algorithms will be trained to predict leaf appearance rate from genotype and empirically measured trait data. Training data will be extracted from images of plant leaves obtained via field experiments that employ novel phenotyping technique. Next, the resulting predicted traits and environment data will be fed into the crop model to predict yield. If proven effective, this approach can be applied to study other plant traits to improve crop yield prediction.

BTT EAGER: A Wearable Plant Sensor for Real-Time Monitoring of Sap Flow and Stem Diameter to Accelerate Breeding for Water Use Efficiency

Award #: 1844563
Liang Dong
Michael J. Castellano, Patrick S. Schnable
May 15, 2019
April 30, 2021 - Extended thru April 30, 2022

Breeding plants for increased drought resistance without sacrificing yield is a major goal of breeding efforts around the world. However, drought resistance and yield tend to be inversely correlated. The rate that water flows through the stalk of plants on its way to the leaves is a critical variable in explaining differences in drought tolerance between different varieties of plants. However, current technologies for measuring the rate of this flow are bulky and can damage the plant when they remain applied for long time periods; thus they are not able to monitor plants throughout a growing season. In addition, the data collected from current sensors requires measurements of stem size in order to accurately measure flow rates. If stems grow over the course of the experiment, these measurements can introduce error is. This project develops a wearable plant sensor that enables accurate long-term quantification of flow rates across many environments and genotypes. Large numbers of low-cost sensors can be deployed in breeding programs enabling direct evaluation of lines. From these lines specific genetic loci controlling variation in sap flow rates under different environmental conditions can be identified. Likewise data from these sensors can be used in genomic prediction models that prioritize new breeding lines prior to the investment of resources field trials. This research will enhance workforce development by providing research opportunities to next-generation researchers at the intersection of engineering and plant science.

This collaborative project will integrate advances in sensors, microsystems, nanomaterials, and plant sciences to realize a novel sap flow measurement method that ultimately advances functional genomics research and the breeding of drought tolerant crops. The objective is to develop a wearable plant sensor for long-term, accurate, and affordable monitoring of sap flow over an entire growing season. The sensor design allows efficient thermal insulation of the microscale sap flow sensing unit from external environments, thus eliminating the traditional need of additional bulky thermal insulation setup and increasing the response to sap flow. Spatial averaging of multiple sap flow measurements around the stem enhances measurement accuracy. By using stretchability of the sensor materials and structures, physical constraints of the sensor on plant growth is minimized for long-term monitoring. The proposed wearable sensors can be manufactured at large scale and low cost, allowing it to be incorporated into breeding programs tolerating drought tolerance. Lastly, the sensors are characterized, calibrated and validated over time using gravimetric measures of plant water use in the greenhouse. Initial pilot field measurements are performed, where the sensors are applied to several maize hybrids grown under irrigated and non-irrigated conditions as part of the Nebraska contribution to Genomes to Fields (an existing public-private partnership).

High intensity phenotyping sites: a multi-scale, multi-modal sensing and sense-making cyber-ecosystem for genomes to fields

Award #: 2020-68013-30934
Patrick Schnable
Michael J. Castellano, Liang Dong, Baskar Ganapathysubramanian, Carolyn J. Lawrence-Dill, Lie Tang
June 1, 2020
May 31, 2023

To date much of the focus of agricultural research has been on increasing yield rather than ensuring the stability of yields within and across regions and years. It is of course important to develop higher yielding crop varieties. However, increasingly variable weather patterns have already begun to negatively impact agriculture. We currently lack the knowledge and tools necessary to efficiently develop resilient crop varieties that will provide stable and economically viable yields across increasingly variable environments. This problem is exacerbated by the fact that breeding new crop varieties takes 7-10 years, and at many locations today's weather may not be an accurate representation of the spectrum of weather new varieties will experience at that same locations 10 years from now. To address the challenge of breeding next generation resilient crop varieties we require accurate and mechanistically based models that can predict phenotypic outcomes based on genetic, environmental, and crop management data. Fortunately, advances in the plant sciences, computational and data sciences, and engineering offer the potential to help us address this challenge and thereby create a more sustainable, resilient and profitable US agricultural system.Developing accurate predictive crop models requires an enhanced understanding of the combined effect of crop variety (G) and environment (9), GxE. This in turn requires large collections of plant traits and environmental data gathered from common sets of crop varieties grown in diverse environments. With support from state and national Corn Growers, the Genomes to Fields (G2F) initiative has been conducting community-based experiments to do just that. Since 2014, G2F participants have been generating and analyzing genotypic, environmental, and crop management data from commercially relevant maize germplasm to learn how GxE interactions influence plant traits.The proposed project, G2F-HIPS, will support and intensify G2F by deploying, evaluating and validating a combination of established, image-based sensing technologies and promising new field-based agricultural sensors, generating and sharing reference data to foster community innovation, developing and democratizing analysis pipelines for phenotypic data, conducting proof-of-principle research projects to identify genes responsible for crop responses to environmental variation, and contributing in a substantial manner to the training of current and future agricultural researchers to make use of these innovations. As such, G2F-HIPS will promote the widespread adoption of new sensing technologies, methods of data analysis and thinking across the many G2F sites. In combination, these activities have the potential to facilitate a more mechanistic understanding of how phenotypes respond to genotypic and environmental variation, thereby facilitating the development of more resilient crop varieties that make more efficient use of agricultural inputs such as nitrogen and water, with corresponding environmental benefits.

NIFA AG2PI Collaborative: Creating a shared vision across crop and livestock communities

Award #: 2020-70412-32615
Patrick Schnable
Jack Dekkers, Chris Tuggle, Eric Lyons, Brenda Murdoch, Jennifer Clarke, Carolyn Lawrence-Dill
September 1, 2020
August 31, 2023

To address the challenges and opportunities of achieving sustainable genetic improvement of agricultural species, thereby enhancing the sustainability and profitability of US agriculture, the expertise of a broad community of agricultural genome to phenome (AG2P) researchers must be engaged, drawing from both crop and livestock communities, as well as integrative disciplines (e.g., engineers, data scientists, economists, and social scientists). The overall objective of this AG2PI is to assemble and prepare a transdisciplinary community to conduct AG2P research. The project will: Develop a vision for AG2P research by identifying research gaps and opportunities; foster first steps towards the development of community solutions to these challenges and gaps; and rapidly disseminate findings to the broader community. Towards these ends, AG2PI will sponsor and coordinate field days, conferences, training workshops, and seed grants. AG2PI features a robust project management plan, involving leaders with the requisite experience managing large complex projects, implementation plans based on best practices and the science of team science, coupled with a robust assessment plan to refine best practices. A comprehensive and inclusive group of scientific partner organizations (including those serving the global community), a renowned scientific advisory board, and an external stakeholder group will assist the AG2PI in meeting its objectives and ensuring that its activities coordinate and complement existing programs in plant and livestock G2P. Development of a cross-kingdom community prepared to tackle AG2P research offers opportunities to develop novel and creative solutions to enhance our understanding of both kingdoms, for the benefit of US agriculture and society.

NIFA AG2PI Collaborative: seeding the future of agricultural genome to phenome research for crops and livestock

Award #: 2021-70412-35233
Patrick Schnable
Jack Dekkers, Chris Tuggle, Eric Lyons, Brenda Murdoch, Jennifer Clarke, Carolyn Lawrence-Dill
September 1, 2021
August 31, 2023

To achieve sustainable genetic improvement of agricultural species and thereby mitigate environmental impacts and enhance the sustainability and profitability of US agriculture, the expertise of a broad community of agricultural genome to phenome (AG2P) researchers must be engaged, drawing from both crop and livestock communities, as well as integrative disciplines (e.g., engineers, data scientists, economists, and social scientists). Towards this end an existing NIFA-funded project (2020-70412-32615) is assembling and preparing a transdisciplinary community to conduct AG2P research. This project is: Developing a vision for AG2P research by identifying research gaps and opportunities; fostering first steps towards the development of community solutions to these challenges and gaps; and rapidly disseminating findings to the broader community. The current project will leverage these activities by using a competitive process in coordination with NIFA to provide additional seed grants to the AG2PI community. These seed grants will identify bottlenecks and explore novel solutions to community challenges to AG2P research. The project features a robust project management plan, involving leaders with the requisite experience managing large complex projects, implementation plans based on best practices and the science of team science, coupled with a robust assessment plan to refine best practices. A comprehensive and inclusive group of scientific partner organizations (including those serving the global community), a renowned scientific advisory board, and an external stakeholder group will assist the executive team in meeting its objectives and ensuring that its activities coordinate and complement existing programs.