| NSF Org: |
IOS Division Of Integrative Organismal Systems |
| Recipient: |
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| Initial Amendment Date: | May 31, 2017 |
| Latest Amendment Date: | July 20, 2020 |
| Award Number: | 1732253 |
| Award Instrument: | Continuing Grant |
| Program Manager: |
Diane Jofuku Okamuro
dokamuro@nsf.gov (703)292-4508 IOS Division Of Integrative Organismal Systems BIO Directorate for Biological Sciences |
| Start Date: | July 1, 2017 |
| End Date: | December 31, 2022 (Estimated) |
| Total Intended Award Amount: | $4,608,789.00 |
| Total Awarded Amount to Date: | $4,703,387.00 |
| Funds Obligated to Date: |
FY 2018 = $1,042,102.00 FY 2019 = $94,598.00 FY 2020 = $1,067,408.00 |
| History of Investigator: |
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| Recipient Sponsored Research Office: |
1 BUNGTOWN RD COLD SPG HBR NY US 11724-2202 (516)367-8307 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
1 Bungtown Road Cold Spring Harbor NY US 11724-2209 |
| 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 01001920DB 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
Genome DNA sequences for many crops have been determined in the last two decades, providing the blueprints to discover genes that underlie key agricultural traits. However, a great challenge is identifying the differences in DNA between related varieties of the same crop, which are responsible for the subtle trait variation that plant breeders exploit to improve productivity. A major contributor to this trait variation is 'genome structural variation' where pieces of DNA are deleted, inserted, or rearranged resulting in changes in gene expression. This project will focus on how structural variation contributed to domestication and breeding of tomatoes. A related goal is to expand and develop new molecular tools to create structural variation for crop improvement. This project will improve US agriculture by providing new knowledge and tools to efficiently and predictably enhance crop productivity. A major part of the project will also include training of young scientists in fundamental principles of plant genome research that can be applied to agriculture. This knowledge will also be shared through outreach programs in inner city New York schools that do not have access to research opportunities. Project personnel will develop hands-on teaching activities that will highlight the importance of plant genomics and new genome editing technologies to improve crops and meet the agricultural needs of the 21st century.
Limited knowledge on the extent and diversity of structural variation in plant genomes is hindering the ability to link genes to important crop phenotypes. This project will unite new long-read sequencing technologies, computational biology, developmental and quantitative genetics, and genome editing to elucidate and manipulate structural variation (SV) at a scale never before achieved for a major crop. Tomato provides a powerful system due to its relatively small and high quality reference genome and availability of resequenced genomes. By applying SV-detection algorithms to existing short-read Illumina sequencing data from hundreds of accessions, more than 40 genomes will be selected, capturing the majority of predicted SV diversity, to establish new reference genomes using the latest long-read sequencing technology (PacBio and 10X Genomics). From these data, a compendium of validated SVs will be generated and integrated with ongoing genome-wide association studies. Significant gene-associated SVs, including those affecting gene activity measured by genome-wide transcript profiling, will be characterized using CRISPR/Cas9 gene editing and quantitative phenotypic analyses, focusing on reproductive traits that drive crop productivity. In parallel, CRISPR/Cas9 gene editing will be used to generate a collection of SV mutations in known yield and fruit quality genes in two related wild Solanaceae with agricultural potential, with the goal of achieving major steps towards domestication and for comparative developmental genetics studies. This project will greatly expand our knowledge of genomic diversity in tomato, and provide a road map for dissecting SVs in other crops, where such knowledge can be exploited to improve productivity.
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.
Crop improvement relies on the ongoing selection of natural DNA sequence variations that influence gene functions and the traits they control, such as crop yield. Over the past two decades, scientists have identified key genes and mutations crucial for enhancing economically significant traits in crop plants, including those involved in the earliest stages of crop domestication from their wild counterparts. Recent advances in rapid, high-throughput DNA sequencing technologies have provided genome blueprints for many crop plants. However, a significant portion of the sequence variation that is responsible for crop improvement has remained undiscovered. In particular, more complex DNA sequence variations, such as insertions or deletions of DNA segments within or near genes, are often missed by first generation high-throughput sequencing technologies that only capture short DNA snippets across genomes.
This project addressed this issue by using new technologies that sequence genomes in large, overlapping segments, allowing for the identification and analysis of difficult-to-detect structural DNA mutations. Focusing on tomatoes and their closest wild ancestors as a model, we sequenced 100 varieties and wild species to identify and characterize these structural variants, and investigate how they: i) shape plant genomes and ii) contribute to crop domestication and improvement. By creating and utilizing new computational tools for long-read DNA sequencing, we discovered over 200,000 new mutations in tomatoes, many of which impacted gene function and trait variation. As examples, we found previously undetected mutations responsible for differences in tomato fruit flavor, size and yield. In some instances, we showed that mutations in multiple genes were combined during breeding programs, resulting in complex genetic relationships that ultimately altered productivity traits in quantitative ways.
In a second goal of the project, we explored whether discoveries from major crops, like tomato, could be applied to improve "indigenous crops," which have the potential to become industrialized crops, but have received less attention in both fundamental and applied research. We established blueprints for groundcherries, a close relative of tomatoes that produce edible sweet berries, and used CRISPR genome editing to modify the functions of multiple genes, resulting in increased fruit size and number.
The project trained numerous scientists and also promoted public education in plant biology. Our graduate students and postdocs secured positions in academia and industry, while younger trainees in college pursued further education in biology and education. We also created an outreach program with a Queens, NY elementary school focused on plant engineering curriculum. Finally, we developed a community-science outreach project based on our groundcherry research involving hundreds of participants in dozens of states, which enhanced public understanding and acceptance of the role of leveraging plant genomics and genome editing to improve crops now and in the future.
Last Modified: 04/17/2023
Modified by: Zachary B Lippman
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