Progress 12/01/23 to 11/30/24
Outputs
Target Audience: We have categorized our target audience on the project as short-, medium- and long-term targets. These are described below. Early career researchers, e.g. graduate student and post-doctoral researcher (short-term) Agricultural modeling community (short- and medium-term) Rice breeders (medium- and long-term) During the Year 3 reporting period, we have reached all three categories of target audience. We continued training our graduate students, To-Chia Ting and Sam Schafer. Postdoctoral associate Sajad Jamshidi continued development of a parsimonious plant model, and Luis Vargas, another PhD student at Purdue, developed new open-access tools to aid in data collection on the project with documentation in English and Spanish(see Products). To-Chia and Sam continued to participate in all monthly project meetings, assemble project reports, and help with project management as part of their professional development. We disseminated modeling ideas to the agricultural modeling community through a presentation at North American Plant Phenotyping Network (oral presentation by postdoctoral associate, Sajad Jamshidi) and to modelers and breeders at IRRI at our in-person project meeting held in the Philippines in June 2024 (talks by all three PI/co-PIs, talks by two graduate students in-person, one talk by a graduate student virtually, and one talk by a post-doctoral associate virtually). Changes/Problems:We expected to receive the final genotyping data from collaborators at USDA ARS (Dale Bumpers National Rice Research Center) at the end of September 2024 for graduate student, Sam Schafer, to complete his GWA study on the project (Aim One). However, as of end of Feb 2025, we are still currently waiting for the Data Transfer Agreement to be signed by both parties (Purdue Sponsored Programs and Dale Bumpers Office of Tech Transfer), as of February 2025. This has delayed progress on Sam's manuscript, but unfortunately, the situation is outof the direct hands of PI Wang and co-PI Eizenga (and Dale Bumpers collaborator, Jeremy Edwards, who generated the data). What opportunities for training and professional development has the project provided?During the Year 3reporting period under Aim 3, MS student (who recently switched to our PhD program), Sam Schafer, traveled to IRRI for three weeks to take part in the Rice: Research to Production short-course and an additional week to attend our project meeting. There, he learned about various equipment used to cultivate rice in the field, visited labs studying grain quality, rice pathogens, and breeding, and learned that rice was tightly linked to culture and development of societies. This was the first time Sam had traveled outside the United States and had a major impact on him and his career trajectory. Prior to this year, Sam's career goal was become an industry breeder. His experience on this project, which has included both domestic and international travel, has contributed to his current career goal of staying in research in the public sector (e.g. academia). Sam has provided a testimonial of his experience below: "The time I spent out at the International Rice Research Station (IRRI) for the Rice Research to Production (RR2P) program was among the best experiences in my life. Professionally, I was able to expand my knowledge of rice from the confines of a page or computer screen to something more hands-on and practical, as well as make connections with researchers across numerous research fields. Additionally, I was able to enrich myself in the local culture and observe life through a different lens, especially when chatting with the local rice farmers in the area. Through this experience, I have found that I truly have re-discovered myself in every sense, and am grateful to have been given the opportunity to participate." During this reporting period, asduring Years 1 and 2 on the project, our traineescontinued to beactively involved in monthly Zoom project meetings. To-Chia and Sam, who participated in the in-person project meeting at IRRI in June 2024, were able to presenttheir work to team members and IRRI staff and scientists. Sajad Jamshidi, the post-doc modeler on the project, and Luis Vargas, another PhD student in the Wang Lab, participated virtually in theretreat to share their work with the broader IRRI community. These opportunities to present are critically important in developing these early career scientists. Sajad Jamshidi is now on the job market for faculty positions, and both To-Chia and Luis ar in their final years of their PhD programs. To-Chia is nearing submission of her second lead-author paper supported by this grant. How have the results been disseminated to communities of interest?Results have been disseminated via peer-reviewed manuscripts and presentations at national and international settings (see description in Target Audience). What do you plan to do during the next reporting period to accomplish the goals? During the Year 4 no-cost extension reporting period (i.e. current year), we plan to accomplish the following goals: Publish a review article on high-throughput phenotyping technologies for use in process-based model design and evaluation (led by PhD student, To-Chia Ting). We are currenting awaiting reviews from co-authors and anticipate submitting this review in March 2025. Publish an article on thenew modeling framework we are developing to serve as an easily-adaptable base model across species and genotype diversity. This work is being led by post-doc, Sajad Jamshidi, who is partly supported by this project. We anticipate submitting this around May 2025. Completeassociation analyses of the 200-variety diversity panel as part of Sam Schafer's dissertation work. We are still awaiting about 30% of the genotype data, which we are getting from collaborators at Dale Bumpers. Purdue and Dale Bumpers are currently in negotiations over the Data Transfer Agreement, which has taken significantly longer than expected. Once we have thefinal dataset complete, we anticipate being able to submit the manuscript around six to eight months. All analysis pipelines have been developed using the incomplete dataset so that we are ready. Finalize adaptation of our new model to rice and/or compare with rice-specific parameterization of the existing process-based model, TREES, using datasets collected on the 32-TRJ. This will be completedas thelast chapter of To-Chia Ting's dissertation and we will do our best to have it completed within the final reporting period.
Impacts
What was accomplished under these goals?
Aim One: During this reporting period, the IRRI team completed measurements on the panel of 32-TRJ (2024DS and 2024WS). This completes the Philippines field dataset for the 32-TRJ. IRRI also assembled and shared with Purdue the data from the previous 2023 wet season field experiment (LICOR 6400 readings, canopy temperature, leaf water potential, leaf area, leaf dry weight, stem dry weight, shoot dry weight, specific leaf area, plant height at vegetative stage and maturity, grain yield, straw biomass, and harvest index). Purdue - At Purdue, graduate student, Sam Schafer, has been leading analyses using the data collected by the IRRI team on the panel of 200 diverse tropical japonica during 2022 and 2023 dry seasons. He finished developing a pipeline that uses single nucleotide polymorphism (SNP) data with field-collected data as input files and evaluates genetic population structure, usingthat information to select the most effective GWAS model, and carries out the GWA. At the end of the pipeline, all genes within the region of linkage-disequilibrium (LD) are extracted and filtered by likelihood of candidacy based on frequency of re-occurrence between multiple field traits, gene ontology (GO), or name matching with candidate genes previously identified. For GO term and gene name matching, a pair of meta-analysis search strings were used to retrieve a list of GO terms and gene names to compare against. With the current panel of 112 genotypes, 17 candidate genes have been identified, one of which has GO terms tagged to water transport between cells. We are waiting for the genotype data on the rest of the panel from collaborators at the USDA Dale Bumpers to complete the full study.During Fall 2024, we also recruited a new PhD student, Jairam Danao, who comes with a background in apple genomics. He will becontributing to manuscript preparation for the GWAS work. Aim Two: During the current reporting period, the Purdue team carried out data exploration on Year 2 datasets. We found out that most of the yield component traits at DBNRRC were not significantly different between well-watered (WW) and alternative-wet-and-drying (AWD) treatments, which should provide a contrasting environment from IRRI conditions (where treatments were well-watered and drought) for model evaluation. Additional evaluations on the 32-TRJ panel were carried out under field (IRRI and Dale Bumpers) and controlled-environment (Purdue) conditions. At the Ag Alumni Phenotyping Facility (AAPF, Purdue University, West Lafayette), traits were measured at three time points - before WL treatment, during WL treatment and upon recovery. Those included pre-dawn leaf water potential (LWP), specific leaf area (SLA), and mid-day gas exchange traits. In addition, the number of leaf collars and tillers were counted three times a week, as these represent important growth parameters for the process-based model under development. To understand the predictability of spectral data as proxy for the traits measured, canopy-level red-blue-green images and hyperspectral images were automatically taken three times a week, along with leaf-level spectra, which were manually collected at each time point. During summer 2024, the Purdue team visited DBNRRC during two timepoints, vegetative stage and at the end of vegetative stages, for physiological measurements: pre-dawn LWP, midday gas exchange traits, canopy height, and above-ground biomass in both WW and AWD treatments. The DBNRRC team collected harvest data during the harvest season. In the Philippines, the IRRI team carried out two experiments in field during wet and dry seasons. LWP, SLA, gas exchange traits and above-ground biomass were measured. IRRI additionally assessed root traits (no. of crown roots, root length density, specific root length) and canopy temperature. During the final reporting period, we will analyze the relationship of traits collected between and within the three sites. We will also use data collected at AAPF to parameterize a biophysical growth model and use data at IRRI and DBNRRC to evaluate the model. Aim Three: Our third aim is focused on the professional development of the next generation of agricultural plant scientists. We have described these activities from this reporting period in the following section on professional development and training.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Rojas LV, Ting T, Rainey KM, Reynolds MP, Wang DR. Open-source tools to enhance data collection and
management for plant science research. Frontiers in Plant Science. 20 February 2024. doi: 10.3389/fpls.2024.1265073
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Wang DR, Jamshidi S, Han RK, Edwards J, McClung AM, McCouch SR. Positive effects of public breed-
ing on U.S. rice yields under future climate scenarios. Proceedings of the National Academy of Sciences. 18
March 2024. doi: 10.1073/pnas.2309969121
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Progress 12/01/22 to 11/30/23
Outputs
Target Audience:We have categorized our target audience on the project as short-, medium- and long-term targets. These are described below. 1. Early career researchers, e.g. graduate student and post-doctoral researcher (short-term) 2. Agricultural modeling community (short- and medium-term) 3. Rice breeders (medium- and long-term) During the Year 2 reporting period, we have reached all three categories of target audience. We continued training our PhD student, To-Chia Ting and our newly recruited MS student, Sam Schafer. Additionally, a postdoctoral associate (Sajad Jamshidi) contributed modeling efforts on this project. To-Chia and Sam continued to participate in all project meetings, assemble project reports, and help with project management as part of their professional development. We disseminated modeling ideas to the agricultural modeling community through a presentation at the G x E x M symposium in November 2023 (Wang), at the Tri-Societies meeting (sponsored talk by postdoctoral associate, Sajad Jamshidi) and to rice breeders at the Rice Technical Working Group in February 2023 (Jamshidi). Co-PD Eizenga attended the NIFA-AFRI Plant Breeding Project Directors Session in Greenville, SC July 16, 2023. Changes/Problems:Delays in AAPF experiment: We experienced some delays in carrying out the controlled environment experiment on the 32-variety panel due to scheduling issues as the facility is a shared resource and the growth chambers must accommodate multiple experiments across research groups that are able to share the same growth settings. This was originally scheduled for Year 2. We instead were able to carry out a smaller pilot experiment in Year 2 that will help inform measurements on the final trial, which will be carried out in the next reporting period (Year 3). ? Delays in model development: During this reporting period, in lieu of adapting TREES, we opted to develop a new base plant growth model using object-oriented design, from which a rice specific growth model will derive. The base model development is led by post-doctoral associate Sajad Jamshidi, who was partially supported on this project during this reporting period. Object-oriented design offers several advantages over procedural programming, including making our models more flexible and adaptable for new applications. While this is taking a lot more time up front in development, we believe this will be a good contribution to the modeling community in the long run and we hope will set forth a new standard for more flexible, transparent models that may be adaptable for breeding applications. What opportunities for training and professional development has the project provided?During this reporting period, the new graduate student, Sam Schafer, officially began working as part of the project team. He has been brought up to speed quickly and is already analyzing the IRRI DS2022 and DS2023 data. As described above under Aim 3 accomplishments, To-Chia was able to travel to IRRI to attend RR2P. This May, Sam will attend the same course. These activities were proposed in the original grant and now that travel restrictions have cleared, we are pleased to report that these unique professional development opportunities are available to the project trainees. We are additionally planning an in-person project meeting to be hosted at IRRI during June of the year 3 reporting period. This will include all PI/co-PIs along with the two Purdue graduate students supported on this project (To-Chia Ting and Sam Schafer) as well as IRRI's drought physiology team. Co-PI Eizenga has additionally been invited to present to the greater IRRI community at their seminar series. This strengthens the connections between the national rice research institute in the U.S. with the international research institute. How have the results been disseminated to communities of interest?Results have been disseminated via peer-reviewed manuscripts and presentations at national and international conferences (see description in Target Audience). What do you plan to do during the next reporting period to accomplish the goals?During Year 3 reporting period, we plan to accomplish the following goals: Complete final field evaluations of the 32-variety panel during DS2024 at IRRI and Summer 2024 at DBNRRC Finish yield component measurements from Summer 2023 experiment at DBNRRC Write and publish a review article on high-throughput phenotyping technologies for use in process-based model design and evaluation (led by PhD student, To-Chia Ting) Carry out experiment of the 32-variety panel at Purdue's AAPF Complete association analyses of the 200-variety diversity panel as part of Sam Schafer's M.S. thesis. Design and test new rice process-based growth model Carry out an in-person project retreat at IRRI in June 2024.
Impacts
What was accomplished under these goals?
Aim 1: During the Year 2 reporting period under Aim 1, the IRRI team completed measurements on the panel of 200 tropical japonica (U.S. and global accessions) as proposed. This occurred during Dry Season 2023 (DS2023) and represents the second year field trial on this evaluation (year 1 was completed in the previous reporting period). Traits measured included yield components, leaf water potential, shoot dry weight, crown root number, and canopy temperature. At Purdue, we recruited a new graduate student, Sam Schafer, who has previously worked in the PI's lab as an undergraduate researcher supported by this project. Sam began his M.S. during this reporting period (May 2023). He will lead genetic analyses, including estimating heritabilities on trait responses to vegetative water deficit stress and identifying associated genomic regions using a GWA approach. We anticipate submitting a manuscript that summarizes these results in 2025 as Sam's master's thesis paper. Currently, Sam is QC-ing both DS2022 and DS2023 to ensure all data are ready for downstream analyses and is analyzing relationships between physiological measurements and yield components. Aim 2: During the Year 2 reporting period under Aim 2, the USDA-ARS Dale Bumpers National Rice Research Center (DBNRRC) team carried out their first year evaluation of a down-select set of 32 tropical japonica accessions. These were selected during the previous reporting period and described in that annual report. The Purdue team (PI and the two graduate students supported on this project) traveled to Arkansas to complete one round of phenotyping (traits included leaf area index, leaf water potential, specific leaf area and gas exchange) and the DBNRRC team carried out a second round of gas exchange measurements. The experiment was harvested in September 2023. At the DBNRRC, traits measured were days to 50% heading, flag leaf length and width, culm habit, plant height, no. panicles per plant, seed weight per plant, harvest biomass, and main panicle yield component traits are currently being collected from 648 panicles. We are currently planning the controlled environment experiment at the Ag Alumni Phenotyping Facility (AAPF). This was originally intended to be carried out during this reporting period but we experienced some delays as described below. This experiment will now be carried out in the Year 3 reporting period. Aim 3: During the Year 2 reporting period under Aim 3, PhD student, To-Chia Ting, traveled to IRRI for three weeks to take part in the Rice: Research to Production short-course. There, she learned about various equipment used to cultivate rice in the field, visited labs studying grain quality, rice pathogens, and breeding, and learned that rice was tightly linked to culture and development of societies. This helped contribute to her professional development by "enabling greater understanding of the importance of addressing challenges from multiple perspectives and recognizing the potential impact rice research could have" (from To-Chia). Both To-Chia and Sam are actively involved in monthly project meetings. To-Chia serves as the meeting scribe and each student presents to the group for feedback on alternate months. This has been critical for development in oral and written communication skills especially for To-Chia, who recently passed her PhD prelims. Students are able to receive feedback from the project's co-PI mentors, which will be critical for when they begin to summarize findings in the form of collaborative manuscripts.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Ting T, Souza A, Imel R, Guadagno CR, Hoagland C, Yang Y, Wang DR. Quantifying physiological trait variation with automated hyperspectral imaging in rice. Journal of Experimental Botany. 21 August 2023. doi: 10.3389/fpls.2023.1229161
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Wang DR, Kantar MB, Murugaiyan V, Neyhart J. Where the wild things are: Genetic associations of environmental adaptation in the Oryza rufipogon species complex. Genes Genomes Genetics. 9 June 2023. doi: 10.1093/g3journal/jkad128
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Jamshidi S, Murgia T, Morales-Ona AG, Cerioli T, Famoso AN, Cammarano D, Wang DR. Modeling interactions of planting date and phenology in Louisiana rice under current and future conditions. Crop Science. 8 June 2023. doi: 10.1002/csc2.21036
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Progress 12/01/21 to 11/30/22
Outputs
Target Audience:We have categorized our target audience on the project as short-, medium- and long-term targets. These are described below. -Early career researchers, e.g. graduate student and post-doctoral researcher (short-term) -Agricultural modeling community (short- and medium-term) -Rice breeders (medium- and long-term) During the Year 1 reporting period, we have primarily reached early career researchers. We recruited one PhD student, To-Chia Ting, who has been working as part of the core team. In addition to receiving technical training in data analysis, experimental design, and writing, she has participated in all project meetings, helped to assemble project reports, and has gained skills in project management as part of her professional development. She additionally led outreach to undergraduate audience during a talk she developed for an existing REEU program on Digital Agriculture held at Purdue University in Summer 2022. Changes/Problems:Due to COVID-19-relatedtravel restrictions of USDA employees as well as restrictions imposed on IRRI activities (e.g., hosting visitors), we were not able to have our in-person annual meeting during this reporting period, whichwas originally proposed to take place at IRRI. Additionally, due to an unexpected lengthy sub-contract negotiation process between Purdue and IRRI, IRRI's grants office prevented co-PD Henry from joining project meetings from July 2022 until present. We have just recentlyreceived the signed agreement from IRRI and will re-instate regular project meetings shortly. Despite these major project management challenges, we are still on track with our proposed timeline. Project management has instead depended on email communication rather than correspondence in real-time. COVID-19 travel restrictions have been lifted, and we will plan to schedule an in-person meeting at IRRI likely for late 2023 or early 2024 when we have more results to share (also due to lengthy lead-up paperwork required for co-PD Eizenga). What opportunities for training and professional development has the project provided?The project has recruited two graduate students. The first, To-Chia Ting, is a PhD student who has been involved in all aspects of project management. She has worked closely with PD Wang to learn experimental design, data analysis, as well as soft skills of setting up project meetings, leading meetings, setting agendas, etc. To-Chia will lead modeling efforts on the project in Year 3. The project has also recruited Sam Schafer, who will join in May 2023. Sam is currently an undergraduate senior in the lab and we have used this reporting period to train Sam on various instrumentation that will be used in his graduate program. Sam will be leading up the genetic analyses on the project. As the project provides support for two trainees to attend "Rice: Research to Production" course at IRRI, both To-Chia and Sam will be able to attend. To-Chia will likely attend this year and Sam will attend next year. It was not possible for any our students to attend RR2P and participate in fieldwork at IRRI during Year 1 due to COVID-related restrictions in place at IRRI. How have the results been disseminated to communities of interest?To-Chia has taken several opportunities to talk about her work as related to this project. She has presented at a summer REEU program (catering to undergraduates) and she has been invited to speak at the Phenomics Advisory Board at the end of February. ? What do you plan to do during the next reporting period to accomplish the goals?During the Year 2 reporting period, we plan to accomplish the following goals: Complete second and final evaluation of the large panel of 200 tropical japonica under drought conditions at IRRI Carry out initial evaluation of the down-select set of 32 at Dale Bumpers Carry out extensive phenotyping evaluation of down-select set of 32 at Purdue's phenotyping facility Publish To-Chia's first paper (currently under review) Begin association analyses of the tropical japonica diversity panel (as part of Sam Schafer's M.S. thesis)
Impacts
What was accomplished under these goals?
During Year 1, our group made progress on activities associated with all three aims. Specifically, the team (1) selected a panel of 200 accessions comprise globally-diverse tropical japonica along with varieties developed for U.S. production; (2) conducted a first field trial under well-watered and water-limited conditions (year 2 has been planted and is currently underway); (3) down-selected a set of 32 accessions for further study; (4) conducted a pilot experiment on a subset of accessions from the 200-variety panel under controlled environment phenotyping facility; and (5) recruited personnel on the project. Briefly, the panel of 200 accessions were selected based on having constrained phenology (informed by prior publications) but maximal genetic diversity. Any prior information on performance of these accessions under drought were taken into consideration. Co-PI Amelia Henry successfully carried out the inaugural drought trial under field conditions at the International Rice Research Institute on this diversity panel. Her team collected information on 17 various physiological and yield-related traits, and these data were analyzed by Purdue University PhD student, To-Chia Ting, to shortlist a set of 32 accessions for further study, as proposed on the project. For the down-select set, the 200 genotypes were based on calculated drought indices along with geographical origin, ensuring that U.S. varieties were represented for each drought response category. This set of 32 will be phenotyped at Purdue and Dale Bumpers in 2023.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2023
Citation:
Ting T, Souza A, Imel R, Guadagno CR, Hoagland C, Yang Y, Wang DR. Quantifying physiological trait variation with automated hyperspectral imaging in rice. Under review, Journal of Experimental Botany
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