Progress 09/01/05 to 08/31/09
Outputs
This project supported one USDA National Needs Graduate Fellow (Elliot Heffner) for 3 years of his Ph.D. studies in the field of plant breeding at Cornell. His fourth and likely final year is being supported by a Cornell Graduate School Diversity Fellowship. His minor fields are International Agriculture and Rural Development and Business Management, both areas that will help him be a more effective plant breeder in the current global environment. After doing several lab rotations, completing his course work with high marks, and passing the Admission to Candidacy Exam, Heffner focused on thesis research on genomic selection as a tool for plant breeders. The concept of marker assisted selection (MAS) for crop improvement has been around for nearly two decades; however, the impact of MAS has been limited to a few, major effect genes. An emerging method called genomic selection aims to use markers for selection of both large and small effect genes by using markers that are distributed throughout the genome. This method is being tested widely in animal breeding and is predicted to revolutionize the cattle breeding industry. The reason for this revolution is that genome-wide markers can be used to predict an individual's net merit without phenotypic evaluation. This not only can avoid the high costs of precision phenotyping, but can also rapidly increase the speed of each cycle of selection. For these reasons, genomic selection should be a significant tool for both animal and plant breeders. The objective of Heffner's project is to investigate how genomic selection can be used in a plant breeding program to increase gains from selection per unit time. Several reports on genomic selection performance in plants have recently been published, but they have all been through simulation. This project has tested genomic selection through simulation and empirical data generated from work with the mastery nursery of the Cornell wheat breeding program directed by his advisor Mark Sorrells. Heffner generated genotypic and phenotypic data for genomic selection through genotyping and extensive field testing for more than 600 wheat lines. The results will provide critical information on genomic selection's performance in dynamic breeding populations and its potential impact on the breeding program structure and gains from selection. Heffner also participated a 3-week trip to India and Thailand as part of an International Agriculture course and spent a month visiting industry breeding stations in Brazil and Argentina. Heffner has demonstrated exceptional leadership skills, which have been recognized by many awards. These include election as President of the Plant Breeding Graduate Student Organization (2007-2008), the Munger/Murphy Outstanding Plant Breeding Graduate Student Award (2008), Cornell's Barbara McClintock Award (2009), and the American Society of Plant Biology-Pioneer Hi-bred International Graduate Student Prize (2009). Among his many service activities, Heffner was co-developer and co-instructor of a 15 week, 3 credit course on Applications and Fundamentals of Genetics taught at the Auburn Maximum Security Correction Facility. PRODUCTS: One product of the project will be addition to the U.S. work force of a highly skilled plant breeder who can integrate modern genomic techniques and applied crop improvement. His research project will provide new approaches to plant breeding. OUTCOMES: This project allowed us to recruit an outstanding Ph.D. candidate, whose performance as a student and researcher has more than exceeded his promise. His training in plant breeding and genomics will make him highly sought after by U.S. seed/biotechnology companies. An additional outcome beyond those already listed above is enhanced interaction between Cornell plant breeding and major plant/breeding seed companies as a result of initiatives taken by the fellow. DISSEMINATION ACTIVITIES: These results are being disseminated to plant breeders, geneticists, and crop producers through publications in refereed journals (including a major one in Crop Science), conference presentations, and project tours during farmer field days. The Department of Plant Breeding & Genetics will inform USDA about his employment and professional activities after he completes his Ph.D. FUTURE INITIATIVES: The 2009 publication on Genomic Selection for Crop Improvement in Crop Science received very positive feedback from plant breeders and geneticist from both the private and public sectors. To follow up this publication, Heffner and his adviser (Mark Sorrells) are currently preparing a publication in which they evaluate through simulation the impacts of genomic selection on breeding program structure and gains from selection. The aim of this publication is to provide breeders with information on what prediction accuracies are needed from genomic selection to justify its use in breeding. Since only one fellowship was awarded, we cannot support additional students on this grant; however, because of the success of this fellowship grant, we submitted two new proposals for similar student training to the USDA National Needs Graduate Fellowship program in 2006 and 2008 and were awarded a total of 6 additional fellowships. Six excellent Ph.D. candidates supported by these fellowships are currently in the first and third years of their programs in the field of plant breeding at Cornell.
Impacts
The project will not only add to the state-of-the-art of genomic selection in plant breeding, but will also lead to the release of improved wheat varieties for New York wheat growers.
Publications
- Heffner, E.L., Sorrells, M.E., and Jannink, J.-L. 2009. Genomic selection for crop improvement. Crop Science 49: 1-12.
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Progress 09/01/07 to 08/31/08
Outputs
This project supports one USDA National Needs Program Graduate Fellow (Elliot Heffner). He had a highly successful second year as a Ph.D. candidate in the field of plant breeding at Cornell University. His minor fields are International Agriculture & Rural Development and Business Management, subjects that will help him be a more effective plant breeder in the current global environment. During the 2007-2008 academic year, he took 8 courses (Perspectives in International Agriculture & Rural Development; Agriculture in Developing Nations I; Negotiations; Leading Teams & Organizations; Statistical Methods II; Statistical Methods IV; Agriculture in Developing Nations II [which included a 3-week trip to India and Thailand in January 2008]; Quantitative Genetics in Plant Breeding) in addition to the weekly Plant Breeding Seminar. His grade point average since entering Cornell is 3.83. Elliot has also made excellent progress on his thesis research conducted under the supervision of small grains breeder and geneticist Prof. Mark Sorrells. Elliot published a first author paper based largely on work he did during an initial rotation in the Sorrells program. His primary project is investigation of the applicability of Genomic Selection to a plant breeding program, using 400 lines in the Master Nursery of the Cornell soft white winter wheat breeding program. During the summer of 2008 he phenotyped and collected DNA from lines planted in 4 locations during the fall of 2007. He began data analysis in the fall of 2008. Materials planted again in the fall of 2008 will be phenotyped the following summer. Elliot presented a poster related to this work at the 2008 Maize Genetics Conference, and a substantial first author paper on 'Genomic Selection for Crop Improvement' is in press in Crop Science. Elliot has also demonstrated exceptional leadership skills, which were recognized by his election as President of the plant breeding graduate student organization in 2007-2008. He conceived and organized a graduate student trip to industry breeding stations in Indiana and Ohio in which 20 grads participated during June 2008 and also organized an industry recruiting trip to the Dept. of Plant Breeding & Genetics. He was one of two recipients of the 2008 Cornell Outstanding Plant Breeding Graduate Student awards. PRODUCTS: One product of the project will be addition to the U.S. work force of a highly skilled plant breeder who can integrate modern genomic techniques and applied crop improvement. His research project will help the wheat breeding program advance to a new level by testing the applicability of genomic selection/association mapping using materials from the entire Cornell master wheat nursery. Future products may be both more efficient breeding methods and improved wheat lines. OUTCOMES: This grant allowed us to recruit an outstanding Ph.D. candidate. An additional outcome beyond those already listed above is enhanced interaction between Cornell plant breeding and major plant breeding/seed companies, as a result of initiatives taken by the fellow. DISSEMINATION ACTIVITIES: The National Needs Fellow has already presented one poster on his work, published one paper from his research and has a second in press. He will continue to publish his results and report them at professional meetings. The Department of Plant Breeding & Genetics will provide progress reports to USDA and will inform USDA about his employment and professional activities after he completes his Ph.D. FUTURE INITIATIVES: Since only one fellowship was awarded, we cannot support additional students on this grant; however, because of the success of this fellowship grant, we submitted two new proposals for similar student training to the USDA National Needs Graduate Fellowship competition in 2006 and 2008 and were awarded a total of 6 additional fellowships. The current fellow will visit industry breeding stations in Brazil and Argentina in January 2009, gaining additional experience in global plant breeding issues and activities.
Impacts
TThe Fellow's research focuses on bridging the gap between genomics and plant breeding. It has long been thought that molecular markets would revolutionize plant breeding, but polygenic traits that determine the usefulness of a variety have not been amenable to current marker assisted selection methods that look to fix only a few beneficial alleles. The research project seeks to utilize dense genome wide marker coverage to predict polygenic trait values to increase plant breeding gains per unit time. It will provide results on the performance of this method termed 'Genomic Selection'. Results produced will provide the Cornell wheat breeding program and other plant breeding programs with cues on how dense molecular marker coverage may be utilized to make rapid gains from selection.
Publications
- Heffner EL, Chomdej O, Williams KR, Sorrells ME. 2008. Dominant male-sterile populations for association mapping and introgression of exotic wheat germplasm. Australian Journal of Agricultural Research 59:470-474
- Heffner EL, Jannink JL, Sorrells ME. 2008. Association mapping and genome-wide breeding value estimation for marker assisted selection of parental and elite inbred lines. 50th Annual Genetics Conference, Washington D.C. Abstract and Poster #177.
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Progress 09/01/06 to 08/31/07
Outputs
National Needs Graduate Fellow Elliot Heffner has had a highly successful first year as a Ph.D. candidate in the field of plant breeding at Cornell University. During the 2006-2007 academic year, He took 13 courses, including Genetic Improvement of Crop Plants, Concepts & Techniques in Plant Molecular Biology, Methods of Plant Breeding Laboratory, Statistical Methods, Plant Genome Organization and Function, Patents, Plants & Profits, Plant Biotechnology, Advanced Plant Genetics, and Perspectives in Plant Breeding Strategies. His grade point average was 3.625. Having completed most of his plant breeding course requirements, he is currently taking courses related to his two minor areas: International Agriculture & Rural Development and Business Management. These minors will help him be a more effective plant breeder in the current global environment. As part of the Int. Ag. Minor, he will be traveling to India and Thailand for 3 weeks in January of 2008. Elliot has also
made excellent progress on planning and initiating his thesis research work conducted under the supervision of Prof. Mark Sorrells. His primary project is investigation of the applicability of association mapping to a plant breeding program, using materials in the Master Nursery of the Cornell soft white winter wheat breeding program. Objectives are 1) to determine the linkage disequilibrium across the genome of wheat lines to estimate marker number needed for QTL discovery; 2) to determine population structure and kinship for implementation of the mixed-model for correction of false positives in association mapping; 3) to use best linear unbiased prediction to determine marker values that can be used to assess the breeding value of possible breeding program parental material. Four hundred lines have been planted in 4 locations this fall and will be phenotyped in the summer of 2008. DNA collection will be done from selected plants in summer 2008 and extraction and marker analysis will
occur in the fall of 2008. These trials will be planted again in 2008 and phenotyped the following summer. Elliot's second project is discovery of milling quality QTL through the use of 3 bi-parental populations. Currently, he has 2 years of phenotypic data and has planted the material this fall for a 3rd year of phenotypic data. He has already extracted DNA and is currently running SSR markers and will use DArT markers this winter. Elliot has also demonstrated excellent leadership skills, which were recognized by his election as President of the graduate student organization.
PRODUCTS: The end product of this project will be a very well trained and highly motivated plant professional who can integrate modern genomic techniques and applied crop improvement. We expect that his work will also help produce improved wheat lines from the Cornel wheat breeding program.
OUTCOMES: The outcome of the project will be addition to the U.S. work force of a skilled plant breeder who can integrate modern genomic techniques and applied crop improvement. His research project will help the wheat breeding program advance to a new level by testing the applicability of association mapping using materials from the entire Cornell master wheat nursery.
DISSEMINATION ACTIVITIES: The National Needs Fellow has already submitted for publication one paper from his research and he will continue to publish his results and report them at professional meetings. The Department of Plant Breeding & Genetics will provide progress reports to USDA and will inform USDA about his employment and professional activities after he completes his Ph.D.
FUTURE INITIATIVES: Since only one fellowship was awarded, we cannot support additional students on this grant; however, we submitted another proposal for similar student training to the USDA National Needs Graduate Fellowship competition in 2006 and were awarded 3 additional fellowships.
Impacts
It is too soon to report substantive impacts of the project beyond those listed above. Having the USDA fellowship funds made it possible for us to recruit an outstanding student in our program. Elliot has worked with his adviser Mark Sorrells in the preparation of grant proposals and has been a leader among the current graduate student cohort. In fact, he was recently selected to participate in a "by invitation only" graduate course in Leadership Development organized by the College of Agriculture and Life Sciences at Cornell.
Publications
- No publications reported this period
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Progress 09/01/05 to 09/01/06
Outputs
In the spring term of 2006, we succcessfully recruited an outstanding Ph.D. candidate (Elliot Heffner) as our USDA National Needs Graduate Fellow. Elliot earned his B.S. from Pennsylvania State University in Agroecology with a plant science option. He was motivated to do graduate work in plant breeding following an internship at Pioneer Hybrid International where he gained experience working with maize both in the field and the laboratory. Elliot spent the summer of 2006 in Ithaca doing an initial lab rotation in the laboratory of USDA Geneticist and Adjunct Associate Professor Ed Buckler. During that time he identified 12 candidate genes for nitrogen transport in maize, designed primers for them, and sequenced. He was a part of the team that collected phenotypic data for 6000 maize lines at two locations (Ithaca, NY and Raleigh, NC) for association mapping. He also assisted in self-pollination of these lines. During the fall term of 2006, he is taking the following
courses: PLBR 403 Genetic Improvement of Crop Plants (3 credits); PLBR 483.3 Plant Genome Organization & Function (1 credit); PLBR 604 Methods of Plant Breeding Laboratory (3 credits); PLBR 622 Plant Breeding Seminar (1 credit); BTRY 601 Statistical Methods I (4 credits). He is also doing a rotation in the laboratory of Prof. Mark Sorrells, who runs a field and laboratory project on small grains improvement. So far in the rotation Elliot has collected seed size data on 220 lines of winter wheat for association mapping and then prepared seeds and planted them in plots for evaluation next year. He is currently working on the 5A chromosome region of wheat that has been identified to have a significant QTL affecting seed size. He plans to saturate this region with 20-30 markers for further analysis. This data will be used to co-author a paper with Dr. Sorrells early next year. In the spring term of 2007, Elliot will take the following courses: CSS 410 The GMO Debate: Environmental Impacts
(3 credits: Audit); PLBR 405 Patents, Plants, and Profits (2 credits); PLBR 606 Advanced Plant Genetics (3 credits); PLBR 622 Plant Breeding Seminar (1 credit); PLBR Perspectives in Plant Breeding Strategies (3 credits; S&TS 407 Law, Science, and Public Values (4 credits). He will also continue his laboratory research. Elliot reports that he has had a very good start to his graduate career here at Cornell. He has been meeting with a number of professors to discuss possible minor fields of study and will most likely be focusing in International Agriculture and Business/Intellectual Property. Faculty who have worked with Elliot are very impressed with his energy and initiative and expect his to have an outstanding graduate career.
PRODUCTS: The end product of this project will be a very well trained and highly motivated plant professional who can integrate modern genomic techniques with applied crop improvement.
OUTCOMES: The outcome of this project will be addition to the U.S. work force of a skilled plant professional who can integrate modern genomic techniques with applied crop improvement. Such graduates are needed to contribute to U.S. agriculture.
DISSEMINATION ACTIVITIES: The National Needs fellow will attend professional meetings and will publish results of his research in a timely way. The Department of Plant Breeding & Genetics will provide progress reports to USDA and will inform USDA about his employment and professional activities after he completes his Ph.D.
FUTURE INITIATIVES: Since only one fellowship was awarded, we cannot support additional students; however, we hope to obtain further support for similar types of graduate training in later USDA National Needs Graduate Fellowship Program competitions.
Impacts
It is too soon to report substantive impacts but having the fellowship funds made it possible to recruit an excellent student into plant breeding. Elliot has also been an active and lively participant in our graduate student group.
Publications
- No publications reported this period
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