Award Abstract # 1545453
NRT-DESE: P3 -- Predictive Phenomics of Plants

NSF Org: DGE
Division Of Graduate Education
Recipient: IOWA STATE UNIVERSITY OF SCIENCE AND TECHNOLOGY
Initial Amendment Date: August 13, 2015
Latest Amendment Date: March 16, 2020
Award Number: 1545453
Award Instrument: Standard Grant
Program Manager: Vinod Lohani
DGE
 Division Of Graduate Education
EDU
 Directorate for STEM Education
Start Date: September 1, 2015
End Date: September 30, 2021 (Estimated)
Total Intended Award Amount: $2,866,938.00
Total Awarded Amount to Date: $2,866,938.00
Funds Obligated to Date: FY 2015 = $2,866,938.00
History of Investigator:
  • Julie Dickerson (Principal Investigator)
    julied@iastate.edu
  • Patrick Schnable (Co-Principal Investigator)
  • Theodore Heindel (Co-Principal Investigator)
  • Carolyn Lawrence-Dill (Co-Principal Investigator)
Recipient Sponsored Research Office: Iowa State University
1350 BEARDSHEAR HALL
AMES
IA  US  50011-2103
(515)294-5225
Sponsor Congressional District: 04
Primary Place of Performance: Iowa State University
IA  US  50011-2207
Primary Place of Performance
Congressional District:
Unique Entity Identifier (UEI): DQDBM7FGJPC5
Parent UEI: DQDBM7FGJPC5
NSF Program(s): NSF Research Traineeship (NRT)
Primary Program Source: 01001516DB NSF RESEARCH & RELATED ACTIVIT
04001516DB NSF Education & Human Resource
Program Reference Code(s): 9150, 9179, SMET
Program Element Code(s): 199700
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.076

ABSTRACT

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.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 43)
Adhikari, P., McNellie, J. & Panthee, D. R. "Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato." Genes , v.11 , 2020 , p.1117
Anderson, S. N., Zhou, P., Higgins, K., Brandvain, Y., & Springer, N. M. "Widespread imprinting of transposable elements and variable genes in the maize endosperm" PLoS genetics , v.17 , 2021 10.1371/journal.pgen.1009491
Baldi, H. D., Foster, T. L., Shen, X., Feagley, S. E., Smeins, F. E., Hays, D. B., Jessup, R. W. "Characterization of Novel Torrefied Biomass and Biochar Amendments" Agricultural Sciences , v.11 , 2020 , p.157 doi: 10.4236/as.2020.112010
Beernink BM*, Holan KL*, Lappe RR, Whitham SA "Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones" Journal of Visualized Experiments , v.168 , 2021 10.3791/62277
Braun I, Lawrence-Dill CJ "Automated methods enable direct computation on phenotypic descriptions for novel candidate gene prediction" Frontiers in Plant Science , v.10 , 2020 , p.1629
Braun IR, Yanarella CF, Lawrence-Dill CJ "Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement" Plant Phenomics , 2020 https://doi.org/10.34133/2020/1963251
Braun IR, Yanarella CF, Lawrence-Dill CJ. "Computing on Phenotypic Descriptionsfor Candidate Gene Discovery and Crop Improvement." Plant Phenomics. , 2020 https://doi.org/10.34133/2020/1963251
Carolyn J. Lawrence-Dill, Theodore J. Heindel, Patrick S. Schnable, Stephanie J. Strong, Jill Wittrock, Mary E. Losch and Julie A. Dickerson "Transdisciplinary Graduate Training in Predictive Plant Phenomics" Agronomy , v.8 , 2018 , p.73 10.3390/agronomy8050073
Carolyn Lawrence-Dill, Patrick Schnable, Nathan Springer "Idea Factory: the Maize Genomes to Fields Initiative" Crop Science , v.59 , 2019 , p.1406 10.2135/cropsci2019.02.0071
Elmore, J.M., Griffin, B.D. and Walley, J.W. "Advances in functional proteomics to study plant-pathogen interactions." Current Opinion in Plant Biology , 2021 https://doi.org/10.1016/j.pbi.2021.102061
Foster, T.L., Baldi, H.D., Shen, X., Burson, B.L., Klein, R.R., Murray, S.C., Jessup, R.W. "Development of Novel Perennial Sorghum bicolor x S. propinquum Hybrids." Crop Science , 2020 doi: 10.1002/csc2.20136.
(Showing: 1 - 10 of 43)

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

A growing global population drives the need to increase agronomic output using less land and agricultural inputs. At the same time, increases in climate variability require crops of the future be more resilient. Integrated research and development efforts that seek to address these needs involve expertise in engineering to develop novel sensing devices that can measure environmental parameters and plant traits; genetics to identify causal genes; and data sciences to predict genetic combinations that will result in crop improvement.

The Predictive Plant Phenomics (P3) NSF Research Traineeship (NRT) created an integrated interdisciplinary training program to fill this gap. The P3 NRT directly trained a diverse group of 30 scientists and engineers to address complex problems in modern agriculture. These ?T-shaped? students differ from most students in STEM graduate programs that produce students with deep disciplinary knowledge in a limited area. This depth represents the vertical bar of the "T". The horizontal bar of the ?T? represents their ability to effectively collaborate across a variety of different disciplines.

The plant phenomics degree specialization draws students from various departments and majors across the campus and involves faculty members working in the Colleges of Agriculture and Life Sciences, Liberal Arts and Sciences, and Engineering. The graduate specialization requires students to complete a set of focused course requirements as part of their existing Ph.D. Program known as the 3-2-1 program. The trainees take 3 courses in their main discipline, 2 in a second and 1 in the third. For example, a student make take three courses in plant breeding, two in data science and statistics, and one in engineering such as image processing. This structure was designed to fit within existing departmental guidelines for electives and minimize any requirements for additional coursework.

A learner-centered training program was created that included: 1) a two-week long immersive Boot Camp to build camaraderie and provide foundational technical and professional skills; 2) a core leveling course in the fundamentals of plant phenomics ranging from plant biology to data science to engineering sensor systems; 3) a graduate learning community; 4) research rotations in labs across different disciplines; 5) team mentoring on interdisciplinary team research projects; 6) support for trainees to present at research conferences; and 7) support for independent research projects in plant phenomics.

Four cohorts of students have now completed two years of training in the graduate program in plant phenomics. The internal evaluation focused on metrics such as student recruitment and retention, program outcomes, and student performance as students take classes in diverse areas.  External evaluation provided quantitative assessments of how well the program developed scientists and engineers with broad skillsets to address the research needs to increase understanding of crop plant and agricultural production.

Evaluations demonstrated increased technical and professional skills for trainees entering research and research-related careers focusing on crop plants and agricultural production: The graduates increased technical skills through Boot Camp training in computational environments, coursework in all three disciplines, unmanned aerial vehicle (UAV) training, and hands-on work in the Fundamentals of Predictive Plant Phenomics course and lab. The most recent cohort used new sensor boxes to perform collaborative work in the course. Students have used technical skills outside their main discipline in their dissertation research.

In addition to broad technical training, the trainees gained competence in key areas including communication and industrial application of concepts/skills:  Communication training occurred in multiple venues (i.e., Boot Camp, presentation practices and workshops in Learning Community meetings, and in the core course). The trainees in all cohorts perceive themselves as highly capable of pursuing careers and applying skills in industrial settings.

Institutional impacts include integration of P3?s novel training activities into courses across the campus, a distance learning version of the P3 core course, and wide dissemination of courses for data analysis and machine learning.

 


Last Modified: 02/15/2022
Modified by: Julie A Dickerson

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