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
EXTENDED
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, 2015
Grant Year
2014
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 02/28/13 to 02/27/14

Outputs
Target Audience: Target audiences for this project include graduate and undergraduate students who participated in the project through on-line and classroom instruction or through experiential learning in research projects focused on breeding for disease resistance in 5 major crops. Stakeholder groups targeted in this project include grain and vegetable seed producers and growers who accessed improved germplasm and varieties as well as technical resources developed in the breeding programs via annual field days and related outreach publications. The research community working in the same or related fields was also targeted through access to publications and other scientific communications that both inform and enhance their own research efforts. Changes/Problems: There were no students participating in the wheat breeding program during this reporting period. However, the number of students training in the project was not affected. What opportunities for training and professional development has the project provided? Three graduate students were actively engaged in their thesis research in cucumbers, pepper and potato. Four Cornell undergraduates were engaged in research experiences in our tomato, cucurbit and tomato breeding programs and 3 interned with Gramene and SGN. Training and professional development are the major goals of this project and opportunities provided by the award are described in more detail under the “Accomplishments” section. How have the results been disseminated to communities of interest? The educational components of this project are reaching the undergraduate and graduate student communities via new curricula offered in the classroom and via Learning Modules available on-line, Faculty Lectures on special topics initially offered in a departmental seminar series and also available on-line, as well as through experiential learning obtained while conducting research in the projects breeding programs. Technical information developed through the project is reaching the scientific community through publications and presentations while genetic resources are reaching seed producers and growers through field days and distribution of new and improved germplasm. What do you plan to do during the next reporting period to accomplish the goals? We will continue to offer the classroom and on-line resources described in the accomplishments section. Our graduate students will continue to pursue their research objectives in the cucumber and potato breeding programs and in summer 2014 an undergraduate student will intern in the tomato breeding program. Our outreach activities are expected to include additional publications, presentations and field days and improved genetic resources that will be distributed to stakeholders in the vegetable industry. Finally, we will follow up on our undergraduate participants to determine how their experiences in this project have affected their career paths.

Impacts
What was accomplished under these goals? Modern plant breeders need to be skilled in the development and management of plant populations in the field, knowledgeable about molecular genetics and laboratory-based inquiry and experienced in the use of bioinformatics to access and utilize genomic information. Graduates with this combination of skills are needed to ensure the long-term productivity and competitiveness of U.S. agriculture as well as the safety and nutritional value of our food supply. During this reporting period 3 graduate students and 7 undergraduate students were actively engaged in research experiences integrating applied and fundamental approaches while working on the development of disease resistance in 5 major food crops. While training in these programs, students utilized crosscutting technologies to generate products and results which advanced the breeding programs towards the practical goal of creating disease resistant lines and cultivars for release to seed producers and growers. A much larger group of graduate and undergraduate students took advantage of the new curricula developed for this project including 3 new courses and a series of 37 learning modules covering disease resistance, genomics and bioinformatics in the classroom setting and on-line. Advancements generated by student research projects were disseminated via presentations and field days to the scientific community and to stakeholders in the vegetable and grain industry. These advancements include technical information and improved germplasm releases and that will be used in research, breeding and/or trialing and production. Objectives 1 and 2: Student training that focuses on experiential learning which integrates applied and fundamental approaches while conducting research on today's disease problems in 5 major US crops. Our 3 graduate students are Bill Holdsworth, Anna Levina and Lindsay Wyatt. Bill Holdsworth attended the 2014 Plant and Animal Genome meeting to network and present his results at the Tucson Plant Breeding Institute for intensive training in advanced statistical genomics. In the past year his research has focused on breeding cucumbers for downy mildew resistance and analyzing the population structure and genomic architecture of the USDA pea core collection. Bill’s downy mildew research resulted in a variety release of the first cucumber with exceptional resistance to the new strain of downy mildew and collaborations with growers and pathologists that are part of an aligned OREI project, “ESO-Cuc”. Bill is extending genotyping by sequencing technology to an array of vegetable crops to study important disease resistance and human nutritional traits. This year Anna evaluated different potato clones for their sensitivity to thaxtomin A, one of the main compounds exuded by bacteria Streptomyces scabies, the causal agent of common scab, during infection of potatoes. The sensitivity was evaluated by potato slice assay, in which paper disks were soaked in thaxtomin A solution, and then placed on potato slices. The potato slices were incubated for five days and necrotic regions were scored on a scale of 1-5. It was discovered that reaction to thaxtomin A was not indicative of the clones resistance or susceptibility to common scab in the field, and thus further testing was needed. The same assay was used to test potato clones with extract solution from Streptomyces scabies. In this case, there was a slight correlation between resistance to common scab in the field and lower level of necrosis. Further testing is still required. Currently the project is focusing on analyzing types and levels of metabolites in the SolCap population, with future analysis linking those metabolites to nutrition and disease resistance markers. Lindsay Wyatt continued her evaluation of our Phytophthora resistant bell peppers and mentored undergraduates John Owens and Nick Biebel. Seven Cornell undergraduates were engaged in research experiences during this reporting period including Jie Yung, Samuel Moijueh, Min Sun Song, Daniel Waizman, Alexander Chin, John Owens and Nick Beibel. Jie Yung worked on improving the SGN database (http://solgenomics.net/). She wrote new software so researchers can easily convert identifiers for genes to other sets of identifiers that were widely used before the genome was sequenced.Samuel Moijueh returned to SGN (http://solgenomics.net/) and analyzed mRNA expression in different tomato tissues and created tracks on the genome browser that reflect the gene expression in each tissue. He used tools such as TopHat, samtools, and other next generation sequencing analysis programs. Min Sun Song was involved with a few different programming and bioinformatics projects related to the Rice Diversity project in the McCouch Lab. Her main focus was the creation of a web-based visualization tool for rice genotyping data using php and javascript. Daniel Waizman interned with the MetaMaize project of Rebecca Nelson's laboratory, which is focused on identifying the endophytic microbiome of aboveground maize tissues. Daniel was involved in all aspects of the MetaMaize project ranging from preparation of samples to identify endophytes by gene sequencing to troubleshooting technical challenges associated with the research and prepared field plants for crossing. Alexander Chin worked with the Mutschler group assisting with an insect resistance project to determine the genetic regulation of both acylsugar level and chemotype of the type IV glandular trichomes of the Solanum pennelliiwild tomatoesand which chemotype (glucose of sucrose) would be most effective against silverleaf whiteflies, a vector of Tomato Yellow Leaf Curl. Alex also aided in inducing plants with jasmonic acid to assess the distinct odors they produceon different leaf positions and ages. While working on this project Alex has the opportunity to be mentored by research associate, Brian Leckie, through the Thrips-Tospovirus Educational Network Mentoring Program. John Owens phenotyped peppers and cucurbits for virus symptoms while another student, Nick Beibel, performed genotyping in pepper using PCR markers and participated in in all aspects of the breeding program. Objectives 3 and 4: Curriculum will be developed and sustained in future years including 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. At this point in the project all of the Learning Modules (total of 37) and course enhancements have been developed and are being offered as part of the Plant Breeding and Genetics curriculum and are also available to the public on the project website http://plbrgen.cals.cornell.edu/research-extension/afri/coursework .

Publications

  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Holdsworth, W. High Throughput Genotyping of the USDA PeaPSP Collection, North American Pulse Improvement Association (NAPIA), Portland, OR; Oct. 30-Nov. 1, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Holdsworth, W., Genotyping by Sequencing of the Pea PSP Collection, Plant and Animal Genome (PAG), San Diego, CA; January 11-15, 2014.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mazourek, M. and L. Wyatt (2013). Candidate Gene Approaches in Capsicum. In Genetics, Genomics and Breeding of Peppers and Eggplants, eds. B.C. Kang and C. Kole. CRC Press, Boca Raton, FL.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wyatt, L., Dunn, A., Falise, M., Reiners, S., Jahn, M., Smart, C., and M. Mazourek (2013). Red Harvest Yield and Fruit Characteristics of Phytophthora capsici-Resistant Bell Pepper Inbred Lines in New York. HortTechnology, 23. 356-363.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Holdsworth, W.L., Summers, C.F., Glos, M., Smart, C.D., Mazourek, M. (2014) Development of Downy Mildew-resistant Cucumbers for Late-season Production in the Northeastern United States. HortScience 49 (1):10-17


Progress 02/29/12 to 02/27/13

Outputs
Target Audience: Target audiences for this project include Cornell graduate and undergraduate students who participated in the project through on-line and classroom instruction and/or through experiential learning in research projects focused on breeding for disease resistance in 5 major crops. Undergraduate students also included minority students from the Texas A&M system who traveled to Cornell University for summer internships with the project. Stakeholder groups targeted in this project include grain and vegetable seed producers and growers who accessed improved germplasm and varieties as well as technical resources developed in the breeding programs via annual field days and related outreach activities and publications. The research community working in the same or related fields was also targeted through access to presentations and other scientific communications that both inform and enhance their own research efforts and create opportunities for collaboration. Changes/Problems: The tomato disease project added enhancing control of insect vectored viruses via modification of acylsugar chemistry. Breeding work on potato Common Scab continues in place of Cyst Nematodes. There were no students participating in the wheat breeding program (Fusarium Head Blight) during this reporting period, however, the number of students training in the project was not affected. What opportunities for training and professional development has the project provided? Three graduate students were actively engaged in their thesis research in cucurbits, pepper and potato. Three Cornell undergraduates were engaged in research experiences and an additional two students from Texas A&M and University of Texas Pan-American were hosted as summer interns. Training and professional development are the major goals of this project and opportunities provided by the award are described in more detail under the “Accomplishments” section. How have the results been disseminated to communities of interest? The results of the project have both an educational and a technical component. The educational components are reaching the graduate and undergraduate student communities via new curricula offered in the classroom and via Learning Modules available on-line, Faculty Lectures on special topics in breeding for disease resistance initially offered in a departmental seminar series and also available on-line, as well as through experiential learning obtained while conducting research in the projects breeding programs. Technical information developed through the project is reaching the scientific community through presentations at conferences while genetic resources are reaching seed producers and growers through field days, outreach publications and distribution of new and improved germplasm. What do you plan to do during the next reporting period to accomplish the goals? We will continue to offer the new and enhanced classroom and on-line resources created for this project as described in the accomplishments section. Our graduate students will continue to pursue their research objectives in the cucumber, pepper and potato breeding programs. We will look forward to hosting another set of undergraduate interns in SGN and Gramene during the 2013-2014 academic year as well as in and one of our applied breeding programs during the summer 2013. Our outreach activities will include additional publications, presentations and field days and improved genetic resources will be distributed to stakeholders in the vegetable and grain industries.

Impacts
What was accomplished under these goals? Modern plant breeders need to be skilled in the development and management of plant populations in the field, knowledgeable about molecular genetics and laboratory-based inquiry and experienced in the use of bioinformatics to access and utilize genomic information. Graduates with this combination of skills are needed to ensure the long-term productivity and competitiveness of U.S. agriculture as well as the safety and nutritional value of our food supply. During this reporting period 3 graduate students and 5 undergraduate students were actively engaged in research experiences integrating applied and fundamental approaches while working on the development of disease resistance in 5 major food crops. While training in these programs, students utilized crosscutting technologies to generate products and results which advanced the breeding programs towards the practical goal of creating disease resistant lines and cultivars for release to seed producers and growers. A much larger group of graduate and undergraduate students took advantage of the new curricula developed for this project including 3 new courses and a series of 37 learning modules covering disease resistance, genomics and bioinformatics in the classroom setting and on-line. Advancements generated by student research projects were disseminated via presentations and field days to the scientific community and to stakeholders in the vegetable and grain industry. These advancements include technical information and improved germplasm releases and that will be used in research, breeding and/or trialing and production. Objectives 1 and 2: Student training that focuses on experiential learning which integrates applied and fundamental approaches while conducting research on today's disease problems in 5 major US crops. Our 3 graduate students are Bill Holdsworth, Anna Levina and Lindsay Wyatt. Bill Holdsworth’s graduate work focused on disease resistance in three vegetable crops. He worked to breed cucumbers for downy mildew resistance, and trialed promising F4 breeding material along with commercial standards and accessions with reported downy mildew resistance. Cornell breeding lines outperformed all commercial comparison, and these lines were subsequently crossed with cucumbers varieties representing diverse market types. In squash, Bill phenotyped a zucchini F2 population for powdery mildew resistance and genotyped individuals in order to map wild species introgressions that contribute to resistance. In pepper, he successfully developed user-friendly markers based on LGC Genomics KASP assay for important disease resistance genes, including Bs3 and pvr1. Anna Levina’s thesis research focused on common scab of potatoes, a bacterial disease with low heritability that causes production losses due to surface lesions. Anna genotyped a tetraploid population that segregates for resistance to common scab with 8303 SNP markers developed through SolCAP. Each individual will be evaluated for reaction to thaxtomin A, a phytotoxin essential for scab infection. In pepper, Lindsay Wyatt used molecular marker approaches to pyramid traits in Phytophthora capsici resistant breeding lines were the emphasis. Use of causal polymorphisms in the gene of interest have been constrained by the nature of the flanking sequences and breeders using diverse germplasm backgrounds have noted a lack of transferability of linked markers. In response, we have pioneered genotyping by sequencing in pepper to tackle these questions. Our undergraduates included Samuel Moijueh, Kathryn Blackley, John Owens, Manuel Romo and Jessica Johnston . Samuel Moijueh worked at SGN (http://solgenomics.net) to improve the website software. He implemented an interface to enable the web-start of a Java application called GenomeView, which allows users to view the structural genome data in more detail; users with the necessary access privileges can also edit the annotations, and store the data back to the database, creating a distributed annotation system for genome features integrated with the SGN database. Kathyrn Blackley worked at Gramene (http://www.gramene.org/) developing a tool which allows inference of gene networks based on normalized gene expression data gathered from many different experiments. She wrote R scripts which allow improved processing of input data, permutation testing on the data for significance and graphical display of the results which depict only the genes of interest and genes to which they are likely to be connected. John Owens worked in the Mazourek group to evaluate and troubleshoot barcode data collection systems for use in vegetable field plots. The bar coding system greatly facilitates data recording and management. Manuel Romo, an undergraduate from Texas A&M International University, worked in the Nelson group focused on an effort to identify genes with quantitative effects on resistance to Northern Corn Leaf Blight (NLB) in maize. NLB, caused by Setosphaeria turcica, is a major fungal foliar pathogen affecting maize (Zea mays) and sorghum (Sorghum bicolor). Utilizing the Nested Association Mapping (NAM) populations, QTL for resistance are being fine mapped. A major finding is that Tasselseed genes, Ts1 and Ts2, appear to have a dual role in sex determination and disease resistance. Manuel was a key researcher on this project and was engaged in all other aspect of the breeding program as well including sample collection, DNA extraction, inoculation and disease scoring. Jessica Johnston, an undergrad from University of Texas – Pan American, worked in the Mutschler group assisting with lab, greenhouse and field work in the tomato breeding program. Septoria leaf spot (SLS), Late Blight (LB) and Early Blight (EB) are the three diseases that singly or in combination cause severe defoliation and fruit loss in tomato in temperate growing regions. Leveraging SolCAP resources, SNP analysis of LB/EB/SLS lines resulted in putative location of SLS resistance within a 6 million base pair region. Progeny of recombinant plants will be used to fine map SLS in the coming year. In addition to helping with the LB/EB/SLS resistance project, Jessica contributed to the insect resistance effort by assessing whitefly oviposition rates on selected lines as well as a special project investigating the relationship between acylsugar production in type IV glandular trichomes, leaf position and plant age. Whitefly resistance is an important factor in preventing spread of the insect vectored virus Tomato Yellow Leaf Curl. Objectives 3 and 4: Curriculum will be developed and sustained in future years including 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. Our curriculum creation goal has been met. Our new current coursework offerings include QTL Analysis: Mapping Genotype to Phenotype in Practice (PLBR4080), Introduction to Scripting and Statistics for Genetic Data Management (PLBR4092),Breeding for Pest Resistance (PLBR6180),Plant Breeding Field Experience Practicum (PLBR6100), expanded lab exercises for Intro to Plant Genetics (PLBR2250) focused on breeding for disease resistance as well as a Faculty Lecture Serieson special topics of interest in breeding for disease resistance. A total of 37 Learning Modules have been professionally archived from this coursework and are being offered as part of the Plant Breeding and Genetics curriculum and are also available to the public on the project website http://plbrgen.cals.cornell.edu/research-extension/afri/coursework

Publications

  • Type: Other Status: Other Year Published: 2010 Citation: Mutschler, M.A. (2010) Combining genetic control of defoliating diseases. Learning Module Presentation
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: Mazourek, M. and L. Wyatt. Update on Phytophthora capsici resistance breeding at Cornell. Empire State Fruit & Vegetable Expo. Syracuse, NY. January, 2012.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: Wyatt, L. and M. Mazourek. Breeding Peppers Resistant to Phytophthora capsici. International Pepper Conference. Naples, FL. November, 2012.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: Holdsworth, W. Developing Improved Resistance to Downy Mildew in Cucumber, Northeast Organic Farming Association-NY (NOFA-NY) Organic Research Symposium, Saratoga Springs, NY. January 19-22, 2012.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: Holdsworth, W. and J. Keach. DIY Plant Breeding: How to Develop Your Own Variety of Vegetable, Mother Earth News Fair, Seven Springs, PA; September 21-23, 2012.


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.