| NSF Org: |
IOS Division Of Integrative Organismal Systems |
| Recipient: |
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| Initial Amendment Date: | September 8, 2016 |
| Latest Amendment Date: | April 21, 2020 |
| Award Number: | 1546825 |
| Award Instrument: | Standard Grant |
| Program Manager: |
Gerald Schoenknecht
gschoenk@nsf.gov (703)292-5076 IOS Division Of Integrative Organismal Systems BIO Directorate for Biological Sciences |
| Start Date: | September 15, 2016 |
| End Date: | August 31, 2022 (Estimated) |
| Total Intended Award Amount: | $2,270,969.00 |
| Total Awarded Amount to Date: | $2,309,969.00 |
| Funds Obligated to Date: |
FY 2018 = $19,500.00 FY 2020 = $19,500.00 |
| History of Investigator: |
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| Recipient Sponsored Research Office: |
845 N PARK AVE RM 538 TUCSON AZ US 85721 (520)626-6000 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
888 N Euclid Ave Tucson AZ US 85721-0001 |
| Primary Place of
Performance Congressional District: |
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| Unique Entity Identifier (UEI): |
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| Parent UEI: |
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| NSF Program(s): | Plant Genome Research Project |
| Primary Program Source: |
01001819DB NSF RESEARCH & RELATED ACTIVIT 01002021DB NSF RESEARCH & RELATED ACTIVIT |
| Program Reference Code(s): |
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| Program Element Code(s): |
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| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.074 |
ABSTRACT
Seeds are the primary source of calories for humans and livestock, and thus one of the most critical aspects of agricultural productivity is seed development. Even small changes in seed development can have profound impacts on productivity with cascading repercussions through the entire food chain. This proposal addresses the role of DNA methylation, a chemical mark placed on DNA, in the development of seeds, particularly those marks that impact seed set, size, and viability. We have recently uncovered three mutations of a DNA methylation pathway in the important oil crop Brassica rapa. Each mutation has severe and specific defects in seed production. Using advanced DNA sequencing technologies, we will identify the genetic, molecular, and genomic consequences of these mutations. These findings will help understand the internal mechanisms that regulate seed development. This project will also provide training opportunities for multiple graduate and undergraduate students. This training will develop their expertise in cutting-edge techniques such as genome editing and high-throughput sequencing.
This work builds on several key observations that link small-RNA directed DNA methylation (RdDM) with proper seed development, likely through establishment and maintenance of: 1) genomic imprinting (parent-of-origin bias in allele expression), and/or 2) genome balance (preferential expression from a dominant subgenome following whole genome duplication). This project will first explore the transcriptional and developmental consequences of RdDM in seed development by profiling small RNAs, transcriptomes, and epigenomes of RNA-directed DNA methylation mutants in Brassica rapa, each of which dramatically reduces seed set. In addition, we will investigate links between genomic imprinting and genome dominance in B. rapa. Finally, we will test the hypothesis that RdDM influences seed set by altering genomic imprinting and/or genome dominance by generating cognate mutations in other members of the Brassicaceae family. Results from this study will provide a better understanding of both imprinting and genome dominance that can be translated to closely related species in the family Brassicaceae, including the seed crop B. napus.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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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.
Seeds are the bedrock of agriculture ? they form the majority of food for humans and livestock and are necessary to grow nearly all of our remaining food. Understanding seed development is therefore a critical component for feeding our growing population with less land, fewer inputs, and diminished environmental impact. This project investigated 24 nucleotide (nt) short interfering (si)RNAs that cause DNA methylation and gene silencing. Developing seeds produce high levels of these 24-nt siRNAs, but the role of these molecules in plant reproduction was unknown because their disruption causes no reproductive defects in the model plant Arabidopsis thaliana. By analyzing other plant species in the Brassicaceae family, this project demonstrated that 24-nt siRNAs are essential for seed development in Brassica rapa and Capsella grandiflora, but are dispensable in Camelina sativa and Capsella rubella, indicating that outbreeding species require these molecules while inbreeding species do not. This project further showed that the abundant 24-nt siRNAs in developing seeds are produced from a small number of genomic regions in the maternal seed coat and that these maternally-derived siRNA might move into the developing endosperm, a fertilized tissue analogous to placenta in mammals. Finally, the project demonstrated that 24-nt siRNAs in seeds can trigger DNA methylation despite mismatches between the siRNA and target DNA, and that that methylation can alter gene expression, providing a feasible hypothesis for how maternally-derived siRNAs influence development of the endosperm. Understanding how 24-nt siRNAs influence seed development could lead to increased yield or improved nutritional composition of seed crops. This project also enabled the training of graduate students and undergraduates in cutting-edge technologies including genome editing and analysis of genome-wide dataset, which prepare these students for careers in advanced biotechnology.
Last Modified: 12/21/2022
Modified by: Rebecca A Mosher
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