Source: MICHIGAN STATE UNIV submitted to
GENOME-BASED PREDICTION OF ANTIMICROBIAL PEPTIDES FROM POTATO AND ASSESSMENT OF THEIR ROLE IN RESISTANCE TO BACTERIAL, FUNGAL AND OOMYCETE D
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0229754
Grant No.
2012-67012-19820
Project No.
MICL05062
Proposal No.
2012-01276
Multistate No.
(N/A)
Program Code
A7201
Project Start Date
Aug 1, 2012
Project End Date
Jul 31, 2014
Grant Year
2012
Project Director
Adhikari, B. N.
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Plant, Soil and Microbial Science
Non Technical Summary
Potato (Solanum tuberosum L.) is one of the most important food crops in the world. However, a number of diseases caused by bacterial, fungal and oomycete pathogens cause serious economic losses worldwide. Despite the release of new varieties, current control measures for these diseases are not always successful. Development of transgenic plants through incorporation of disease resistance genes encoding antimicrobial peptides (AMP) has shown potential in the development of disease resistant potato cultivars. However, due to lack of genome sequence, a comprehensive genome-wide identification of AMP-encoding genes and subsequent analyses of their efficacy against diverse potato pathogen has not been possible. With the recent release of the potato genome, this proposal seeks to identify the AMP coding potential of the potato genome through bioinformatics analyses. Through the expression of AMP-encoding genes, transgenic plants resistant to a broader spectrum of microbial phytopathogens will be produced and tested against the diseases caused by bacterial, fungal, and oomycete pathogens. Development of transgenic plants capable of producing AMPs may provide broad-spectrum resistance to phytopathogenic microorganisms and complement other resistance genes currently in potato and thus providing a basis for development of novel disease management practices.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
21513101160100%
Knowledge Area
215 - Biological Control of Pests Affecting Plants;

Subject Of Investigation
1310 - Potato;

Field Of Science
1160 - Pathology;
Goals / Objectives
Diseases caused by bacterial, fungal, viral and oomycete pathogens cause serious economic losses for potato growers and processors worldwide. Genetic manipulation to incorporate disease resistance genes encoding AMPs into specific cultivars has shown some potential in the development of disease resistant potato cultivars. This proposal seeks to identify the AMP coding potential of the potato genome and validate through bioinformatics analyses and computational prediction methods for the purpose of developing sustainable pest management method. The specific objectives of this proposal are as follows: 1) Identification and validation of antimicrobial peptides in the potato genome using bioinformatics analyses and computational prediction methods; 2) Development of transgenic potato plants expressing the antimicrobial peptides identified by genome-based analyses; 3) Assessment of the antimicrobial activity of the antimicrobial peptides against bacterial, fungal and oomycete pathogens of potato.
Project Methods
Expression of genes encoding AMPs in transgenic plants represents a powerful tool for creating disease-resistant cultivars to a wide range of bacterial and fungal pathogens. Assessment of the AMP-encoding potential of potato and development of transgenic plants that provide resistance against different phytopathogens are the major goals of this proposal. To accomplish these goals, we will computationally identify and validate antimicrobial peptides in potato. A combination of prediction methods will be used to validate the AMPs encoded by potato which will be identified by genome-wide analyses. We will then develop transgenic potato plants expressing different types of antimicrobial peptides identified in the genome. Potato plants will be transformed by using established Agrobacterium tumefaciens-mediated transformation methods. Finally, a series of transgenic plant lines will be developed and tested for their resistance to Bacterial soft rot (caused by Pectobacterium carotovorum subsp. carotovorum), Fusarium dry rot (caused by Fusarium solani), and late blight of potato (caused by Phytophthora infestans).

Progress 08/01/12 to 07/31/14

Outputs
Target Audience: This project targets the scientific communities working towards development of sustainable pest control measures in potato and working with antimicrobial peptides. It has provided the potato research and plant pathologists with valuable information to formulate future research in the area of application of antimicrobial peptides in potato. The target group of this project also included the undergraduate researchers who were provided the opportunity to learn molecular biology and tissue culture techniques in the lab. Changes/Problems: During the course of the project, the project director was offered Research Geneticist position in USDA, ARS in Tucson, AZ. The project director has already joined the new job and the project funding has been returned. The research activities presented in this project are now being continued by other people in Dr. David Douches's lab at Michigan State University. What opportunities for training and professional development has the project provided? This project has provided an excellent training opportunities for project director both in the fields of bioinformatics, molecular biology and plant pathology. The project has also provided the project director with opportunity to mentor undergraduate students. Project director was also involved in teaching as a teaching assistant to Dr. Douches's class on agriculture biotechnology. In addition to these project director was able to attend a number of meetings and present the findings of the project. This project has provide the project director with the opportunity to interact with people working in different aspects of antimicrobial peptides and networking with different scientists and companies producing antimicrobial peptide based products. How have the results been disseminated to communities of interest? The preliminary findings of this research project has been presented to a number of meetings including Antimicrobial Peptide Gordon Research Conference in Ventura, California, The Potato Association of America's meeting in Quebec City, Canada. The findings has also been presented in the lab meeting in Dr. Douches lab. Manuscript reporting the findings of this project is now under preparation and will be submitted to a potato and pathology related journal. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? As the goal of this project was identification and validation of antimicrobial peptides and their application in potato disease management, the following goals have been accomplished. 1. We have identified over 200 potato genes encoding 22 different antimicrobial peptides. Using a number of different bioinformatics methods, we were able to identify the antimicrobial peptide encoding genes and validate their expression in different potato tissue and growth stages. 2. We have developed a robust bioinformatics protocol for genome wide identification of antimicrobial peptides and their validation. 3. Preliminary work on the development of construct expressing different Antimicrobial Peptides has been initiated and construct development process is underway. 4. The project director was able to utilize his bioinformatics skills on the identification and validation of the antimicrobial peptides. For the first time a genome wide bioinformatics approach has been used to identify the antimicrobial peptide encoding genes from potato. 5. The preliminary findings of this project has been presented in a number of national as well as international meeting. The findings were presented in the Gordon Research Conference in Antimicrobial Peptides: Discovery, Function and Application.

Publications