Source: CORNELL UNIVERSITY submitted to
ENHANCING EDUCATION AND RESEARCH IN BREEDING FOR PLANT DISEASE RESISTANCE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
0220914
Grant No.
2010-85117-20551
Project No.
NYC-149568
Proposal No.
2009-04827
Multistate No.
(N/A)
Program Code
91810
Project Start Date
Mar 1, 2010
Project End Date
Feb 28, 2014
Grant Year
2010
Project Director
Mazourek, M.
Recipient Organization
CORNELL UNIVERSITY
(N/A)
ITHACA,NY 14853
Performing Department
Plant Breeding
Non Technical Summary
As we transition to sustainable agricultural systems that focus on local production and prepare for the consequences of global warming, a clear imperative emerges to invest in plant breeding for biotic stress resistance in the northeastern United States. The faculty in the Department of Plant Breeding and Genetics at Cornell University are in a unique position to leverage investments in genomics for crop improvement in this region. We propose to build on our existing programs to train future plant breeders that are able utilize genomic tools, navigate a wealth of data with bioinformatics and synthesize research perspectives from both vegetable and grain breeding as part of their modern skillset. To create this nexus, we have proposed a program that will use student training and curriculum development to bring together fundamental and applied plant breeding research. This project will directly support two graduate students and provide research experiences for sixteen undergraduates. Applied plant resistance breeding programs in fusarium head blight in wheat, Septoria leaf spot in tomato, cyst nematodes in potato, pyramiding Phytophthora blight/virus/bacterial spot in pepper, and northern leaf blight in maize will be used to provide students with summer internships and rotation and thesis projects. The Solanaceae Genome Network and Gramene will offer academic year research projects in genomic databases/bioinformatics. Curriculum will be enhanced by creating new courses and creating learning materials from them. These projects will be advised groups from an institutional education committee, seed producers, growers, processors and private sector plant breeders. Expected Outcomes Sixteen undergraduates will have a better understanding of how the different areas of plant breeding for disease resistance are related. Their experiences will provide informed encouragement to continue their education in Plant Breeding and related fields. Two PhD students will receive state of the art systems training in Plant Breeding for biotic stress resistance. New curricula will be developed and existing courses will be enhanced. Students will advance the progress in the described projects.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011543108010%
2011310108010%
2011461108010%
2011460108010%
2011510108010%
2121543108010%
2121310108010%
2121461108010%
2121460108010%
2121510108010%
Goals / Objectives
This proposal seeks to educate students who can integrate traditional methods of plant breeding with new approaches offered by molecular genetics, genomics, computational biology, and bioinformatics. This new generation of plant breeders will be equipped with the theoretical knowledge and experience to improve resistance to biotic stress. They will also have a background to address other plant breeding needs such as yield, abiotic stress resistance and nutritional quality of existing crops for a healthier food supply and more sustainable agricultural production system and to develop new crops for new purposes such as biofuels. Fellows will learn how fundamental knowledge in molecular, organismal and computational biology contributes to applied plant improvement and will gain proficiency in developing and managing a modern plant breeding program. This project relates directly to FY 2009 Priority 3 by educating students and engaging them in research on plant breeding for disease resistance. Student training that focuses on experiential learning will be supported including: training 2 graduate students in systems approaches for disease resistance breeding, students during rotations through diverse plant breeding projects, providing 8 summer internships for undergraduates to encourage plant breeding careers, mentoring 8 undergraduates during the school year on bioinformatics research projects, promoting opportunities for students to interact with stakeholders and private sector plant breeders. Curriculum will be developed that will be sustained in future years: creation of field practicum, genomics tools and bioinformatics scripting courses; incorporating genetics of disease resistance into undergraduate coursework and labs; creation of a faculty lecture series on the topics of this grant and others as opportunities arise. Professional archiving and processing of Learning Modules will be derived from: PLBR6180 Breeding for Disease Resistance; a faculty lecture series on breeding for disease resistance; QTL Analysis: mapping genotype to phenotype in practice. Research will be conducted on today's disease problems in 5 major US crops: tomato, Introgression of Septoria Leaf Spot resistance; pepper, Pyramiding Phytophthora, Bacterial Spot and Viral resistance; wheat, Genomic selection for Fusarium Head Blight resistance; corn: Fine mapping of genome-wide Northern Leaf Blight resistance; potato, Introgression of resistance to Cyst Nematodes.
Project Methods
Two graduate students will be supported from this grant to work in the area of plant breeding for disease resistance. A total of 16 undergraduate research experiences will be provided as part of this proposal. Pairs of undergraduates from Texas A and M Kingsville will be hosted for summer research in yers 2 and 3. Each year a student will spend at least a semester working in independent research with Gramene and at SGN. We will introduce a new course, Practicum in Plant Breeding. Lecture content and complementary lab exercises will be developed to supplement Plant Genetics related to the inheritance of resistance. A second module devoted to the principles and practice of genomic selection will be created for QTL analysis. We will create Bioinformatics Scripting for Biologists course that will focus on a programming language that is widely used in the bioinformatics community (Perl) and how it can be applied to manipulate different important data types also teach some basic SQL skills to query databases, and give a short introduction to the R language, which is widely used to address statistical questions. High quality "Learning Modules will be developed by recording, editing and assembling lectures from a new faculty lecture series on the latest disease resistance breeding research and b) Breeding for Disease Resistance (PLBR6180) and QTL Analysis: mapping genotype to phenotype in practice. The specific research projects include 5 major US crops. A marker will be developed for Septoria leaf spot based on Conserved Ortholog (COSII) markers that allow genetic map alignment among the Solanaceae. The resolution afforded by new approaches should be sufficient to allow marker assisted selection for disease resistance in pepper. One objective in this proposal is to empirically evaluate the potential of genomic or genome-wide selection (GS) to improve quantitative resistance to FHB in a winter wheat breeding program. Students would run extensive field disease (NLB) screening nurseries during the summer, and contribute towards population development and advancement. For student intern projects during the semester, SGN will offer the possibility to acquire and intensify bioinformatics, programming and database skills. At Gramene students could gain or expand their experience with the Perl programming language, UNIX/Linux operating system, and the mySQL relational database system. The Department of Plant Breeding and Genetics Education Committee will provide guidance regarding curriculum building and curriculum and performance evaluation by critically reviewing the curriculum, syllabi and teaching evaluations and making recommendations to the chair. Two existing stakeholder groups with strong interests in the topics of this proposal will be engaged to form the advisory committee for our proposal. Student participants will be asked to evaluate their specific training experiences. We will also track student accomplishments and career paths beyond the termination of the project to assess overall success of the project's educational activities. Much of the research will be judged by its progress toward indentifying or deploying sources of resistance.

Progress 03/01/11 to 02/28/12

Outputs
OUTPUTS: We continued to enhance our training of graduate and undergraduate students by creating research opportunities that combine bioinformatics, fieldwork, exposure to horticultural and agronomic crops, and by supplementing our curriculum and extend these resources more broadly professionally produced Learning Modules were created that can be distributed on various media. Our project website was created http://plbrgen.cals.cornell.edu/afri. Two graduate students continue there training as part of this project and 6 undergraduate students gained research experience. PARTICIPANTS: William Holdsworth and Anna Levina are PhD student trainees on this project. Bill joined the Mazourek lab after rotations with the Mazourek, Nelson and Sorrells groups. Bill's projects include breeding for oomycete resistance, genotype by sequencing in vegetables and developing SNP markers for gene pyramiding in the Mazourek group breeding program. Anna joined the De Jong lab after three rotations including the De Jong, Sorrells and Mazourek groups. Anna's projects leverage resources developed by the SolCAP project. She had genotyped a tetraploid potato population with 8,000-plus SNP markers and is now working to map loci that confer resistance to common scab. Both students are engaged in both applied breeding programs that release cultivars and utilizing modern genomics. Elena Olsen and Katherine Scheibel are undergraduate students that served as student TAs for Plant Genetics PLBR2250. Katherine designed and lead a lab activity focused on virus resistance in squash. Elena worked on the development of a lab exercise exploring insect resistance in Arabidopsis. Samantha Klasfeld was a Cornell undergraduate summer intern in the Mazourek group. In addition to helping in the field, she assembled a panel of pepper germplasm with contrasting disease resistance and quality traits and co-developed and tested SNP markers linked to those traits. Markers that perform well in diverse backgrounds are highly useful for pyramiding simply inherited traits with Phytophthora capsici resistance in pepper. Undergraduate students worked with the Sol Genomics Network and Gramene. Benjamin Gordon worked at SGN (http://solgenomics.net) curating Solanaceae data for loading into the database, including Solanaceae pathogens. He also wrote Perl scripts to organize the data. Zach Hempstead and Cindy Chen assisted with bioinformatics and programming projects, using Perl and PHP to complete a variety of objectives related to the Gramene project. Programs developed functionality for interacting with relational databases, parsing biological data and creating user interfaces for biologists. A pair of undergraduate students from Texas A&M, Kingsville were hosted as summer interns. Paulo Garcia Jr worked with the Nelson group and in addition to being involved in daily activities managing a maize disease resistance nursery, Paulo individually spearheaded a new project aimed at identifying maize endophytes via the availability of abundant data from the Buckler lab on campus. Omar Vasquez worked with the Mutschler group and also participated in the field program planting and maintaining fields and collecting phenotypic data. Omar was individually responsible for the genotyping of tomato breeding lines to confirm the presence of introgressions. TARGET AUDIENCES: Undergraduate and graduate students formed the target audience at Cornell. The Transnational Learning program made Learning Modules available to its partner institutions in Africa. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Plant breeding for pest and disease resistance is a continual process because pathogens are remarkable for their ability to adapt and evolve to overcome plant resistances. New generations of plant breeders who can utilize state-of-the-art tools and resources must be trained to continue to respond to these needs, protect national food security and agricultural profitability. Our objectives were designed to respond to this need by enhancing our training of graduate and undergraduate students by creating research opportunities that combine bioinformatics, fieldwork, exposure to horticultural and agronomic crops, and by supplementing our curriculum. To extend these resources more broadly professionally produced Learning Modules are being created that can be distributed on various media.

Publications

  • Wisser, W. (2011) Genetics of Disease Resistance and Adaptation in Maize. Learning Module De Jong, W. (2011) Breeding for pest/disease resistance in potato. Learning Module Nelson, R. (2011) Resistance to plant diseases in an agricultural context. Learning Module


Progress 03/01/10 to 02/28/11

Outputs
OUTPUTS: Two PhD graduate students were admitted to be trained in Plant Breeding and Genetics and completed two out of three rotations. An undergraduate gained a summer research experience through an internship that combined field work and molecular biology. New lab exercises for the course "Plant Genetics" were developed by undergraduate student teaching assistants. Numerous seminars were delivered and recorded for learning module creation. A new course PLBR 4092, "Introduction to Scripting and Statistics for Genetics Data Management" was created that provides instruction and hands-on experience with the statistical package "R" as a flexible platform for data analysis, combined with an introduction to perl scripting to manage, mine and organize large datasets. Another new course PLBR 6100, "Practicum in Plant Breeding" was created for practical exposure to applied crop breeding. Students participate in the department's maize, small grains, potato, pepper, squash, forage, tomato, and onion breeding programs to gain hands-on experience in the planning and implementation of crossing, planting, harvesting, selecting, and evaluating disease and quality traits. PARTICIPANTS: Michael Mazourek (PD) oversaw the training aspects and timely completion of objectives. Bill Holdsworth and Anna Levina were PhD graduate students that participated in the project. They attended appropriate courses and completed lab rotations. Chris Mancuso is an undergraduate student at Cornell University who worked with Rebecca Nelson's lab as a summer intern during the summer of 2010. Chris participated in all activities in the lab, which is focussed on dissecting the genetic architecture of disease resistance in maize, with a large emphasis on Northern Leaf Blight and ear rot. His time was equally divided between lab and field work. TARGET AUDIENCES: Undergraduate and graduate students formed the target audience at Cornell. The Transnational Learning program made Learning Modules available to its partner institutions in Africa. Efforts included improving laboratory exercises for Plant Genetics, the development of two new courses and the creation of learning modules that can be shared within and beyond the University. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Plant breeding for pest and disease resistance is a continual process because pathogens are remarkable for their ability to adapt and evolve to overcome plant resistances. New generations of plant breeders who can utilize state-of-the-art tools and resources must be trained to continue to respond to these needs, protect national food security and agricultural profitability. Our objectives were designed to respond to this need by enhancing our training of graduate and undergraduate students by creating research opportunities that combine bioinformatics, fieldwork, exposure to horticultural and agronomic crops, and by supplementing our curriculum. To extend these resources more broadly professionally produced Learning Modules are being created that can be distributed on various media.

Publications

  • Rao, N.C. (2010) Did the Second Green Revolution Start with Bt Cotton in India. Learning Module Presentation. September, 2010.
  • Donofrio, N. (2010) Managing business under pressure: How the rice blast pathogen copes with plant-generated stresses during infection. Learning Module Presentation. September, 2010.
  • Jander, G. (2010) Biosynthesis and defensive function of an Arabidopsis non-protein amino acid. Learning Module Presentation. September, 2010.
  • Griffiths, P.D. (2010) Targeting trait combinations in vegetables adapted for East Africa. Learning Module Presentation. October, 2010.
  • Mazourek, M. (2010) Review and outlook for pepper and cucurbit disease resistance breeding. Learning Module Presentation. November, 2010.
  • Fuchs, M. (2010) Plum pox virus: A threat to the stone fruit industry. Learning Module Presentation. November, 2010.
  • Sorrells, M. E. (2010) Breeding for Disease Resistance in Wheat at Cornell. Learning Module Presentation. November, 2010.