Award Abstract # 1826836
RII Track-2 FEC: Systems Genetics Studies on Rice Genomes for Analysis of Grain Yield and Quality Under Heat Stress

NSF Org: OIA
OIA-Office of Integrative Activities
Recipient: UNIVERSITY OF ARKANSAS
Initial Amendment Date: August 15, 2018
Latest Amendment Date: June 5, 2023
Award Number: 1826836
Award Instrument: Cooperative Agreement
Program Manager: Andrea Johnson
andjohns@nsf.gov
 (703)292-5164
OIA
 OIA-Office of Integrative Activities
O/D
 Office Of The Director
Start Date: August 1, 2018
End Date: July 31, 2024 (Estimated)
Total Intended Award Amount: $4,659,406.00
Total Awarded Amount to Date: $5,564,316.00
Funds Obligated to Date: FY 2018 = $2,533,502.00
FY 2020 = $2,125,904.00

FY 2021 = $904,910.00
History of Investigator:
  • Andy Pereira (Principal Investigator)
    apereira@uark.edu
  • Vibha Srivastava (Co-Principal Investigator)
  • Ramanjulu Sunkar (Co-Principal Investigator)
  • Mariya Khodakovskaya (Co-Principal Investigator)
  • Adam famoso (Co-Principal Investigator)
Recipient Sponsored Research Office: University of Arkansas
1125 W MAPLE ST STE 316
FAYETTEVILLE
AR  US  72701-3124
(479)575-3845
Sponsor Congressional District: 03
Primary Place of Performance: University of Arkansas
115 Plant Sciences Building
Fayetteville
AR  US  72701-1201
Primary Place of Performance
Congressional District:
03
Unique Entity Identifier (UEI): MECEHTM8DB17
Parent UEI:
NSF Program(s): EPSCoR Research Infrastructure
Primary Program Source: 01001819DB NSF RESEARCH & RELATED ACTIVIT
01002021DB NSF RESEARCH & RELATED ACTIVIT

01002122DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 075Z, 097Z, 102Z, 7217, 8038, 9150
Program Element Code(s): 721700
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.083

ABSTRACT

Non-technical Description
The basic knowledge and understanding of how environmental stressors, such as high temperatures, affect cereal crop production is important for global food security. Rice, a model cereal plant and a major world staple crop, is grown in the southern United States, and is threatened by increased night temperatures that contribute to unstable production, resulting in lower grain yield and quality, which result in decreased market value. This project will identify individual rice lines that are tolerant to high nighttime temperatures and will use a variety of genetic and biochemical techniques to identify potential mechanisms that underlie the ability of these plants to be high temperature tolerant. These mechanisms will be tested in the plant using gene editing technologies to confirm that these mechanisms and thus the underling causative alleles are responsible for the plant's resistance to high nighttime temperatures. Knowing the actual mechanisms will aid breeders to develop new lines that can help decrease the risk of major crop losses due to high temperatures in the future. This project will be a collaborative effort among the University of Arkansas campuses at Fayetteville and Little Rock, Louisiana State University, and Oklahoma State University and will help develop the careers of six early career research faculty, train undergraduate and graduate students, and postdocs. In addition, the projects will build educational resources for STEM at the undergraduate level as well as K-12.

Technical description
The japonica rice subspecies is the basis of most US varieties currently in production and have been used in US breeding efforts with other rice introductions from all over the world to select varieties that are tolerant to high night temperature. In this project, a diverse collection of rice lines critical to U.S. production will be screened in the field, including environments differing in night temperature, and replicated under controlled greenhouse conditions, to identify heat tolerant genotypes with contributing genes and novel mechanisms that are of interest to use in improvement of rice and other cereals for their resilience to high night temperatures. The genetic changes or identification of alleles ascribed to the desired phenotypes will be characterized at multi-systems levels: the transcriptome, metabolome, proteome, and the physiological response. Information from these analyses will be integrated into gene regulatory networks that can provide a biological understanding of plant adaptations to the changing environment documented in independent genotypes. Wildtype or mutant alleles identified from the population studies will be validated by transformation and CRISPR/Cas9 mediated allele engineering, followed by phenotypic validation to identify alleles associated with heat tolerance, as proof of concept for use in cultivar development. This Research Infrastructure Improvement Track-2 Focused EPSCoR Collaboration (RII Track-2 FEC) project brings together complementary expertise comprising senior and junior faculty from the University of Arkansas campuses at Fayetteville and Little Rock, Louisiana State University, and Oklahoma State University, to address this complex challenge in an interdisciplinary manner. The participants include six early career faculty from different institutions, who will be integrated into the interdisciplinary program to develop expertise in cross-disciplinary research projects. The project will include training of postdocs, graduate and undergraduate students, participation of 10-12th grade students in STEM girl's leadership events, and of High School teachers and students for training in Plant Genetics and Physiology.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 33)
Addison, Christopher K. and Angira, Brijesh and Cerioli, Tommaso and Groth, Donald E. and Richards, Jonathan K. and Linscombe, Steven D. and Famoso, Adam N. "Identification and mapping of a novel resistance gene to the rice pathogen, Cercospora janseana" Theoretical and Applied Genetics , v.134 , 2021 https://doi.org/10.1007/s00122-021-03821-2 Citation Details
Baisakh, Niranjan and Yabes, Jonalyn and Gutierrez, Andres and Mangu, Venkata and Ma, Peiyong and Famoso, Adam and Pereira, Andy "Genetic Mapping Identifies Consistent Quantitative Trait Loci for Yield Traits of Rice under Greenhouse Drought Conditions" Genes , v.11 , 2020 10.3390/genes11010062 Citation Details
Berchembrock, Yasmin Vasques and Botelho, Flávia Barbosa and Srivastava, Vibha "Suppression of ERECTA Signaling Impacts Agronomic Performance of Soybean (Glycine max (L) Merril) in the Greenhouse" Frontiers in Plant Science , v.12 , 2021 https://doi.org/10.3389/fpls.2021.667825 Citation Details
de Freitas, Gabriela Moraes and Thomas, Julie and Liyanage, Rohana and Lay, Jackson O. and Basu, Supratim and Ramegowda, Venkategowda and do Amaral, Marcelo Nogueira and Benitez, Letícia Carvalho and Bolacel Braga, Eugenia Jacira and Pereira, Andy and Bai "Cold tolerance response mechanisms revealed through comparative analysis of gene and protein expression in multiple rice genotypes" PLOS ONE , v.14 , 2019 10.1371/journal.pone.0218019 Citation Details
de Freitas GM, Thomas J "Cold tolerance response mechanisms revealed through comparative analysis of gene and protein expression in multiple rice genotypes" PloS one , v.14 , 2019 Citation Details
Gann, Peter James and Esguerra, Manuel and Counce, Paul Allen and Srivastava, Vibha "Genotypedependent and heatinduced grain chalkiness in rice correlates with the expression patterns of starch biosynthesis genes" Plant-Environment Interactions , 2021 https://doi.org/10.1002/pei3.10054 Citation Details
Gann, Peter James Icalia and Dharwadker, Dominic and Cherati, Sajedeh Rezaei and Vinzant, Kari and Khodakovskaya, Mariya and Srivastava, Vibha "Targeted mutagenesis of the vacuolar H <sup>+</sup> translocating pyrophosphatase gene reduces grain chalkiness in rice" The Plant Journal , v.115 , 2023 https://doi.org/10.1111/tpj.16317 Citation Details
Gupta, Chirag and Pereira, Andy "Recent advances in gene function prediction using context-specific coexpression networks in plants" F1000Research , v.8 , 2019 10.12688/f1000research.17207.1 Citation Details
Gupta, Chirag and Ramegowda, Vankategowda and Basu, Supratim and Pereira, Andy "Prediction and characterization of transcription factors involved in drought stress response" bioRxiv , 2020 https://doi.org/10.1101/2020.04.29.068379 Citation Details
Gupta, Chirag and Ramegowda, Venkategowda and Basu, Supratim and Pereira, Andy "Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance" Frontiers in Genetics , v.12 , 2021 https://doi.org/10.3389/fgene.2021.652189 Citation Details
Harb, Amal and Simpson, Craig and Guo, Wenbin and Govindan, Ganesan and Kakani, Vijaya Gopal and Sunkar, Ramanjulu "The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance" Frontiers in Plant Science , v.11 , 2020 https://doi.org/10.3389/fpls.2020.618491 Citation Details
(Showing: 1 - 10 of 33)

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.

The AR-OK-LA Rice Consortium (AOLRC) was funded to understand “Systems Genetics Studies on Rice Genomes for Analysis of Grain Yield and Quality Under Heat Stress," employing an integrated, multi-disciplinary strategy to address the challenges posed by high night temperatures (HNT) in rice. The consortium has implemented an integrated, multi-disciplinary approach to tackling the challenges of high night temperatures (HNT) in rice, and the work is a great example of how combining various biological layers—genomics, transcriptomics, miRNA omics, proteomics, and metabolomics—can lead to a more comprehensive understanding of complex traits like grain quality under heat stress. By integrating genomic data from genomic studies with gene expression, we have identified significant genetic variants associated with HNT responses. The integration of miRNA omics has added depth by showing how miRNAs regulate genes involved in starch biosynthesis, grain filling, and nutrient transport in both caryopsis and flag leaves. This is particularly interesting because non-chalky genotypes show miRNA-mediated regulation that helps mitigate the negative effects of heat stress. The proteomics and metabolomics studies has also been invaluable in identifying stress-responsive proteins involved in starch metabolism, stress adaptation, and antioxidant defense. This comprehensive approach helps pinpoint the molecular mechanisms that differentiate heat-tolerant and heat-sensitive rice varieties, facilitating the selection of genotypes with more rice crop resilience under HNT. Moreover, the incorporation of CRISPR technology offered a precise tool for editing genes that could reduce grain chalkiness, one of the key challenges under HNT. With the help of AI/ML algorithms analyzing all this data, we can predict and model gene regulation in starch biosynthesis, helping develop rice varieties with better heat tolerance. Broader impacts: The project actively facilitated collaborations both among the participating institutions and within each individual institution, fostering a dynamic and interdisciplinary research environment. Through these partnerships, it provided extensive training opportunities for a diverse group of undergraduate and graduate students, including those from underrepresented backgrounds. Additionally, the initiative supported postdoctoral researchers by equipping them with valuable skills and experience while also creating meaningful research opportunities for early-career faculty. Beyond research, the project emphasized professional development, offering mentorship, workshops, and networking opportunities to help emerging scholars advance in their academic and professional trajectories. These collective efforts contributed to strengthening the research community, promoting inclusivity, and preparing the next generation of scientists and scholars for impactful careers. The AR-OK-LA Rice Consortium’s focus on training early-career faculty, graduate students, undergraduates, and high school students—along with its commitment to involving minority institutions—is not just about tackling the immediate challenges of high night temperatures and grain quality in rice but also about shaping the future of agricultural and environmental sciences.

 


Last Modified: 02/17/2025
Modified by: Andy Pereira

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