| NSF Org: |
IOS Division Of Integrative Organismal Systems |
| Recipient: |
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| Initial Amendment Date: | September 8, 2016 |
| Latest Amendment Date: | July 25, 2023 |
| Award Number: | 1546863 |
| Award Instrument: | Continuing 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, 2024 (Estimated) |
| Total Intended Award Amount: | $3,568,549.00 |
| Total Awarded Amount to Date: | $3,568,549.00 |
| Funds Obligated to Date: |
FY 2018 = $1,488,929.00 |
| History of Investigator: |
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| Recipient Sponsored Research Office: |
201 OLD MAIN UNIVERSITY PARK PA US 16802-1503 (814)865-1372 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
422 Life Sciences Building University Park PA US 16802-1503 |
| 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 |
| 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
The human population is projected to grow to 9.6 billion by 2050, requiring a 50% increase in food and fiber production. A major constraint to this goal is crop losses due to microbial plant diseases which destroy approximately 15% of the world's total crop production every year. Advances in the science of plant disease control are needed to reduce crop losses to disease. Plant genomes encode thousands of genes involved in disease resistance, called the plant immune system. For some crops, modern science has made rapid progress in identifying disease resistance genes and using them in plant breeding, but for others such as long-lived tree crops, it is much more difficult to make rapid progress. This project will explore the plant immune system via a comprehensive study of the genes important for disease resistance to key pathogens of an important crop, cacao, which is the source of chocolate, and an important cash crop for millions of farmers in developing countries. The methods, tools and knowledge gained will be directly applicable to discovery of genes underlying important traits in other crops, especially trees and many perennial grasses. In addition to contributing to building a global partnership in reaching the goals of feeding a growing population sustainably, this project will involve students and young scientists in the US and in developing countries though international exchanges and collaborations.
This project will establish a new approach for use with perennial crop plants to identify candidate loci for disease resistance using a model tree crop, Theobroma cacao (the chocolate tree). Whole genome re-sequencing and transcriptome sequencing of a core collection of highly diverse cacao genotypes will provide the genetic information necessary to drive the discovery of genes critical for pathogen resistance. Functional analysis of these genes will test their role in resistance and set the stage for future translation of these basic findings to guiding more efficient breeding programs utilizing a wider array of genetic diversity. Importantly, the methods, tools, and knowledge gained will be directly applicable to discovery of genes underlying important traits in other crops, especially heterozygous perennials such as trees and many grasses which are not particularly amenable to approaches developed for the major annual crops such as corn and soybean. The basic evolutionary and functional principles that will be discovered can be generalized to most if not all crop plants. To promote and build genomics research capacity in developing countries and to promote inter-disciplinary cross-training the project will support scientific exchanges between project members and foreign collaborators, through postdoctoral, graduate and undergraduate student training at multiple institutions and will involve students from minority serving institutions. The results of this study will be made publicly available through electronic resources and publications.
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.
Project Outcomes Report for the General Public (POR)
NSF Plant Genome Research Project: RESEARCH-PGR: Discovery and Functional Characterization of Genes Regulating Plant Immunity in Perennial Crops Federal Award ID: 1546863 PI Mark Guiltinan
Background: By 2050, the human population is expected to reach 9.6 billion, necessitating a 50% increase in food and fiber production on a slightly expanded area of arable land. Modern plant breeding and agricultural technologies have reduced pathogen impact through Integrated Crop and Pest Management, but about 15% of global crop potential is still lost to microbial pathogens. Advances in plant disease control are essential to address changes in disease pressure due to evolving pathogens, climate change, and agricultural practices. This challenge requires integrative approaches and collaboration across various fields of plant science such as genomics, genetics, breeding, cell biology and plant pathogen interactions. This project involved an interdisciplinary team of scientists focused on advancing our understanding of genome evolution with particular focus on the immune system and defense response against pathogen infection of cacao. As part of our broader impact goals to help develop a new generation of plant scientists, members of this team trained participating collaborating students and scientists in modern life sciences research to help address the need for human scientific and technical human capital to meet the future societal challenges outlined in the UN Sustainable Development and USAID Feed the Future Goals.
Key findings of this project include mapping of the significant variations in DNA sequences between multiple cacao varieties from different Amazonian regions. We observe evidence consistent with the hypothesis that genetic variation both facilitates and constrains adaptation to changing environments. We discovered that duplications of specific disease receptor genes have accumulated and contribute to the disease resistance differences seen between varieties. We also identified genes that are turned on or off in response to cacao leaf infection by the pathogen Phytophthora palmivora, providing clues to identify the key defense genes and resistance mechanisms in cacao. These findings contribute to the knowledge of plant genomics and evolution, with applications in breeding disease-resistant cacao and other crops, especially perennials like coffee, nut trees, fruit, and forestry trees. The project included an educational program involving graduate and postdoctoral students in Plant Biology and Genomics, collaborating scientists from developing countries, and undergraduate students interested in sustainability and life sciences. Through traditional educational programs at Penn State, research mentorships, funded collaborations, summer internships, and visiting scholar programs, we provided training in scientific research and career development. We disseminated our findings in scientific publications and engaged the public through presentations, news articles, and a project website.
News Articles for the General Public
https://www.snexplores.org/article/increasingly-chocolate-makers-turn-science
https://upworthyscience.com/would-you-eat-these-futuristic-foods/
Scientific Publications
Local Gene Duplications Drive Extensive NLR Copy Number Variation Across Multiple Genotypes of Theobroma cacaoNoah P. Winters, Eric K. Wafula, Prakash R. Timilsena, Paula E. Ralph, Siela N. Maximova, Claude W. de Pamphilis, Mark J. Guiltinan, James H. Marden doi: https://doi.org/10.1101/2024.09.01.610724 (submitted and posted on BioRIV)
Winters NP, Wafula EK, Knollenberg BJ, Hamala T, Timilsena PR, Perryman M, Zhang D, Sheaffer LL, Praul CA, Ralph PE, Prewitt S, Leandro-Munoz ME, Delgadillo-Duran DA, Altman NS, Tiffin P, Maximova SN, dePamphilis CW, Marden JH, Guiltinan MJ. A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora. BMC Biol. 2024 Feb 16;22(1):38. http://dx.doi.org/10.1186/s12915-024-01831-2. PMID: 38360697; PMCID: PMC10870529.
Tuomas Hamala, Eric K. Wafula, Mark J. Guiltinan, Paula E. Ralph, Claude W. dePamphilis, and Peter Tiffin: Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree. Proc. Natl. Acad Sci. PNAS August 31, 2021 118 (35) e2102914118; https://doi.org/10.1073/pnas.2102914118
Fister AS, Leandro-Munoz ME, Zhang D, Marden JH, Tiffin P, dePamphilis C, Maximova S, Guiltinan MJ: Widely distributed variation in tolerance to Phytophthora palmivora in four genetic groups of cacao. Tree Genetics & Genomes 2020, 16(1). https://doi.org/10.1007/s11295-019-1396-8
Tuomas Hamala, Mark J Guiltinan, James H Marden, Siela N Maximova, Claude W dePamphilis, Peter Tiffin, Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao, Molecular Biology and Evolution, msz206, https://doi.org/10.1093/molbev/msz206
Last Modified: 09/30/2024
Modified by: Mark J Guiltinan
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