Progress 12/01/08 to 08/31/12
Outputs
OUTPUTS: The most significant output (relating to Objective 2) is a new Distance MS program in Plant Breeding at Iowa State University (http://masters.agron.iastate.edu/), offered since fall 2011. This program has been presented at various occasions, most recently at the meeting of the National Association of Plant Breeders in Indianapolis 2012. Meanwhile more than 30 students are enrolled in this program, mostly employees at breeding companies, indicating acceptance of this program by the plant breeding community and companies. Another important educational output has been training of MS and PhD students. Two of the PhD students involved in the research component of this project are meanwhile employees of plant breeding companies, three more PhD students and one MS student (employee at Pioneer) will finalize their thesis within the next year. The research area of Nitrogen Use Efficiency (NUE) was novel to the project co-PIs at project start (Objective 1). Besides actual results obtained from this project (see list of publications below), one major output is that this research area is pursued beyond this USDA project. New students are currently continuing research initiated by the first generation of graduate students. Partnerships have been formed, expressed by collaboration agreements with Pioneer and Sichuan Agricultural University (SAU), as well as interdisciplinary teams, which succeeded in attracting internal funding from the Plant Sciences Institute, and are actively seeking external funding. The IBM Syn10 population has been genotyped by sequencing by SAU, enabling a detailed genetic analysis of NUE related traits (see publication list). The association analysis is currently extended to novel genotype panels including the Ames panel, a panel developed by the GEM project (USDA), and a CIMMYT panel. Objective 3: A method for integrating high resolution sequence and linkage maps was developed, applied to maize sequences and published (Guo and Beavis 2010). Plant breeding simulation software has been evaluated for the following: GENOME, QU-GENE, BCsim, CPSIM, Meiosis, Plabsim, Plabsoft, GREGOR. None fully meets the requirements described in the proposal. Results of the evaluations will be provided through the GFS Sprague Population Genetics Web-site. PARTICIPANTS: Training Shreyartha Mukherjee, graduate student, bioinformatics; Baohong Guo, a post-doctoral fellow, association mapping theory; Bharath K. T. Narayana, graduate student; candidate gene isolation and association mapping; Pedro Jose Gonzalez Portilla, graduate student, QTL mapping; Constantin Jansen, graduate student; fine mapping (financing by this USDA project from 8/2010 on). Kendra A Meade, pre-doctoral Fellow: Lab manager and research on development of functional mapping methods. Reka Howard, graduate student (PhD): Development of non-parametric methods for Genomic Selection in plant breeding population structures. Collaborations: John Sawyer (ISU), Lizhi Wang, (ISU), Plant Introduction Station (USDA), Frank Hochholdinger (University of Tubingen, Germany), Steve Moose and Martin Bohn (University of Illinois), Pioneer, Dow, Syngenta, Richard Johnson, UIUC; Greg May, NCGR; Jenaro Reyes, Research Professor at Benemerita Universidad Autonoma de Puebla, Sabbatical; Adel Abdel-Ghani, Fulbright Postdoctoral Fellow, Mu'tah University, Jordan. TARGET AUDIENCES: 1) Putative students in the Distance MS program in Plant Breeding 2) Maize breeders and geneticists (NUE). PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
A major expected outcome of this integrated project, focusing on and addressing the need of "Training Plant Breeders for Sustainable Maize Production", has been exceeded by far. Whereas the goal of this project was to conduct a survey and to develop a single course for a future Distance MS program in Plant Breeding, a complete Distance MS program in Plant Breeding is meanwhile offered at Iowa State University since fall 2011 (http://msplantbreeding.iastate.edu/). Seven out of 12 courses have been completed, the remaining courses will be available in 2013. The number of students choosing plant breeding as a career path has been diminishing for a number of years. According to personal communication of the project PIs with commercial breeding companies (Pioneer Hi-Bred, Monsanto, Dow AgroSciences), more than 400 plant breeders will be required in the next five years to meet current and expanding breeding activities. To meet this need, innovative methods for recruiting and educating plant breeders are required. As one potential source, professionals currently in the workforce are an untapped resource for meeting this need, which are targeted by this program. Substantial interest in this program is substantiated by the current high enrollment of more than 30 students in this program. This integrated education and research project lead to an increase in knowledge in two areas. In relation to nitrogen use efficiency (NUE) of maize, we were able to show that genes controlling root development affect NUE. Based on this, functional markers can be derived and used to develop germplasm with improved NUE. This means that the same grain yield can be achieved at lower N fertilization levels in varieties carrying alleles with optimal NUE performance. Our results have been and are currently disseminated at conferences, by publications and in project meetings with our primary collaborator in this project, Pioneer Hibred (collaboration agreement has been established). Additional research funding has been received (and is applied for) to strengthen and broaden this research area. The second research area advanced by this project during this project period relates to the application of functional markers in plant breeding. Innovative approaches have been established based on operations research and compared to genomic selection methods, which are based on random markers. With increasing functional marker information accumulating over time, this research paves the way for future efforts to more efficiently optimize plant varieties by genomic reconstruction of plant genomes. Respective research results have been presented at conferences, to breeding companies, and were published in peer-reviewed journals.
Publications
- Abdel-Ghani, A., Kumar, B.T.N., Montomares, J.R., Gonzalez-Portilla, P., Jansen, C., San Martin, J.P., Lee, M., Lubberstedt, T., 2012. Genotypic variation for seedling root traits in maize (Zea mays L.) inbred lines grown under contrasting nitrogen conditions. (Euphytica: DOI10.1007/s10681-012-0759-0)
- Kumar, B.T.N., Abdel-Ghani, A.H., Pace, J.M., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T. (2013) Association analysis of single nucleotide polymorphisms in candidate genes with root development in maize (Zea mays L.) seedlings. (in preparation).
- Abdel-Ghani, A.H., Kumar, B.T.N., Jansen, C., Gonzalez-Portilla, P., Reyes-Matamoros, J., San Martin, J.P., Lee, M.,Lubberstedt, T. (2013). Association and linkage disequilibrium analysis of genes involved in seedling and adult plant traits in maize (Zea mays L.) inbred lines grown under different nitrogen levels. (in preparation).
- Jansen, C., Liu, H., Gonzalez-Portilla, P.J., Lauter, N., Kumar, B.T.N., Trucillo-Silva, I., San Martin, J.P., Lee, M., Lubberstedt, T. (2013) Mapping QTL for cob architecture under low and normal nitrogen management. (in preparation)
- Beavis, W.D., Suza, W.P., Fehr, W.R. (2012) An Online MS in Plant Breeding based on 14 years of evolving technologies and expectations. Presentation at the 2012 Joint Meeting of the National Association of Plant Breeders (NAPB) and the Plant Breeding Coordinating Committee (PBCC), Indianapolis
- Kumar, B.T.N., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., (2012). Genotypic variation for root architecture traits in seedlings of maize (Zea mays L.) inbred lines. Plant Breeding 131:465-478
- PhD thesis Constantin Jansen (to be submitted fall 2012)
- PhD thesis Bharath T.N. Kumar (to be submitted spring 2013)
- PhD thesis Pedro Gonzalez-Portilla (to be submitted spring 2013)
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Progress 12/01/10 to 11/30/11
Outputs
OUTPUTS: Objective 1 - Develop functional markers for NUE in maize using a candidate-gene approach: The IBMSyn10-DH per se population, as well as respective testcross population produced by Pioneer Hibred during winter 2010/2011, was grown under high and low Nitrogen levels at Marion, IA (Pioneer) and Burkey farm, IA (ISU). Grain yield and several yield-related traits were measured. Near-infrared spectrophotometry (NIR) was used for grain analysis. Finally, a N remobilization analysis was performed by measuring the %N in leaf blades 20 days after flowering (DAF) in each doubled haploid (DH) line. All entries were replicated twice within each N level, at each location. 2011 was the second and final growing season for the per se population. Phenotypic data collected in 2010 and 2011 will be used for QTL analysis once the marker data are available from Pioneer. Genotyping by sequencing is currently applied to the IBMSyn10 genotypes by a Chinese collaborator. Genotypic variation for root architecture traits in 74 AS lines was studied using a paper roll method under different levels of N. Various root traits such as primary root length, seminal root length, lateral root length, root dry weight were measured. Significant variation for root architecture was found in the AS panel. Allele re-sequencing of candidate root genes RTCN, RTH3, RUM1 and RUL1 was carried out in 74 maize inbred lines. SNPs, haplotype structure and linkage disequilibrium was studied. Gene based association analysis was carried out between the root genes and root traits. Significant associations were found, however, fewer significant associations were detected between root gene SNPs and root traits under high N levels. Results from Objective 1 were presented in publications and at different meetings (such as the Crops Science Conference), and involved guest scientists. Objective 2 - Develop a curriculum for a distance MS in Plant Breeding program: We continued to modify the initial needs assessment project survey and adapt it for use in similar distance education work. A paper on best practice for distance education graduate courses is in progress. A poster on the new Distance MS program in plant breeding was presented at the Crop Science Meeting. We also made presentations at both the Society for Information Technology in Teacher Education and the American Educational Research Association highlighting the survey work done as a basis for the curriculum development for this project. Objective 3 - Create and implement an in silico breeder's toolbox to assist the research and education components of this project: Non-parametric Genomic Selection methods proposed by Gianola et al (2006) were developed using a reproducing Kernel Hilbert Space with different bandwidth selection techniques (Sheather 2004) for plant population structures. A preliminary assessment of an operations research approach to genetic improvement, which we refer to as genome construction, was compared with genomic selection for efficacy and long term genetic gain. Presentations were made at Gordon Conference for Quantitative Genetics, the Crop Science Society, and to Syngenta. PARTICIPANTS: Training: Shreyartha Mukherjee, graduate student, bioinformatics; Baohong Guo, a post-doctoral fellow, association mapping theory; Bharath K. T. Narayana, graduate student, candidate gene isolation and association mapping; Pedro Jose Gonzalez Portilla, graduate student, QTL mapping; Constantin Jansen, graduate student; fine mapping (financing by this USDA project from 8/2010 on). Kendra A Meade, pre-doctoral Fellow: Lab manager and research on development of functional mapping methods. Reka Howard, graduate student (PhD): Development of non-parametric methods for Genomic Selection in plant breeding population structures. Collaborations: John Sawyer (ISU), Lizhi Wang, (ISU), Plant Introduction Station (USDA), Frank Hochholdinger (University of Tubingen, Germany), Steve Moose and Martin Bohn (University of Illinois), Pioneer, Dow, Syngenta, Richard Johnson, UIUC; Greg May, NCGR; Jenaro Reyes, Research Professor at Benemerita Universidad Autonoma de Puebla, Sabbatical; Adel Abdel-Ghani, Fulbright Postdoctoral Fellow, Mu'tah University, Jordan TARGET AUDIENCES: 1) Putative students in the Distance MS program in Plant Breeding 2) Maize breeders and geneticists (NUE). PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
A major expected outcome of this integrated project, focusing on and addressing the need of "Training Plant Breeders for Sustainable Maize Production", has been exceeded by far. Whereas the goal of this project was to conduct a survey and to develop a single course for a future Distance MS program in Plant Breeding, a complete Distance MS program in Plant Breeding has been offered at Iowa State University since fall 2011 (http://msplantbreeding.iastate.edu/). Six out of 12 courses have been completed, the remaining courses will be available by beginning of 2013. No other Distance MS program in Plant Breeding is available nationally or internationally. The number of students choosing plant breeding as a career path has been diminishing for a number of years. According to personal communication of the project PIs with commercial breeding companies (Pioneer Hi-Bred, Monsanto, Dow AgroSciences), more than 400 plant breeders will be required in the next five years to meet current and expanding breeding activities. To meet this need, innovative methods for recruiting and educating plant breeders are required. As one potential source, professionals currently in the workforce are an untapped resource for meeting this need, which are targeted by this program. Substantial interest in this program is substantiated by the current high enrollment of 21 students in this program, all of which are employees in breeding companies. This integrated education and research project lead to an increase in knowledge in two areas. In relation to nitrogen use efficiency (NUE) of maize, we were able to show that genes controlling root development affect NUE. Based on this, functional markers can be derived and used to develop germplasm with improved NUE. This means that the same grain yield can be achieved at lower N fertilization levels in varieties carrying alleles with optimal NUE performance. Our results have been and are currently disseminated at conferences, by publications and in project meetings with our primary collaborator in this project, Pioneer Hibred (collaboration agreement has been established). Additional research funding has been received (and is applied for) to strengthen and broaden this research area. The second research area advanced by this project during this project period relates to the application of functional markers in plant breeding. Innovative approaches have been established based on operations research and compared to genomic selection methods, which are based on random markers. With increasing functional marker information accumulating over time, this research paves the way for future efforts to more efficiently optimize plant varieties by genomic reconstruction of plant genomes. Respective research results have been presented at conferences, to breeding companies, and were published in peer-reviewed journals.
Publications
- Kumar, B., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., 2012. Association and linkage disequilibrium analysis of genes involved in root growth in maize (Zea mays L.) seedlings grown under different nitrate levels. () (In preparation)
- Asoro, F.G., Newell, M.A., Beavis, W.D., Scott, M.P., Jannink, J.-L., (2011). Accuracy and training population design for genomic selection. Plant Genome 4:132-144.
- Xu, P., Wang, L., Beavis, W.D., (2011). An optimization approach to gene stacking. European Journal of Operational Research 214: 168-178.
- Kumar, B., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., 2011. Association and linkage disequilibrium analysis of genes involved in root growth in maize (Zea mays L.) seedlings grown under different nitrate levels. Plant and Animal Genome Conference XX. San Diego, CA, USA.
- Kumar, B., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., 2011. Response of expired plant variety protection lines and public inbred maize (Zea mays L.) lines to nitrogen at seedling stage. Agronomy Graduate Research Symposium. Iowa State University, Ames, IA, USA.
- Kumar, B., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., 2011. Response of expired plant variety protection lines and public inbred maize (Zea mays L.) lines to nitrogen at seedling stage. ASA International Annual Meetings. San Antonio, TX, USA.
- Gonzalez Portilla, P.J., Kumar, B., Jansen, C., Lee, M., Lubberstedt, T., 2011. Development of Functional Markers for NUE in Maize (Zea mays L.). 4th Annual Plant Breeding Meeting, Pioneer Hi-Bred International, Johnston, IA, USA.
- Gonzalez Portilla, P.J., Jansen, J., Kumar, B., Lee, M., Lubberstedt, T., 2011. Development of Functional Markers for NUE in Maize (Zea mays L.). Plant Breeding Symposium, Iowa State University, Ames, IA, USA.
- Meade, KA, Cooper, M, Beavis, W, 2011. Phenotypic and genotypic analysis of biomass and moisture content in testcrossed double-haploids of Maize. Quantitative Genetics and Genomics, Gordon Research Conference, Galveston, TX, USA.
- Meade, KA, Cooper, M, Beavis, W., 2011 Phenotypic of biomass and moisture contents in testcrossed double-haploids of maize. ASA, CSSA, SSSA International Annual Meetings, October 16-19, 2011, San Antonio, TX, USA.
- Kumar, B., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., (2012). Genotypic variation for root architecture traits in seedlings of maize (Zea mays L.) inbred lines. Plant Breeding (under review)
- Kumar, B., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., 2012. Association analysis of genes controlling root development in maize (Zea mays L.).() (In preparation)
- Kumar, B., Abdel-Ghani, A.H., Gonzalez-Portilla, P.J., Jansen, C., Lee, M., Lubberstedt, T., 2012. Association study between polymorphisms in maize (Zea mays L.) root candidate genes and nitrogen use efficiency. ()(In preparation)
- Kumar, B., Abdel-Ghani, A.H., Reyes-Matamoros, J., Hochholdinger, F., Lubberstedt, T., 2012. Genotypic variation for seedling root traits in maize (Zea mays L.) inbred lines grown under contrasting nitrogen conditions. (Euphytica) (Under review)
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Progress 12/01/09 to 11/30/10
Outputs
OUTPUTS: Identifying genes that impact the nitrogen-use-efficiency (NUE) of maize can lead to advances in developing cultivars that require fewer crop inputs, a benefit to the financial well-being of farmers and to the quality of ground water reserves. Our project seeks to identify these genes using a candidate-gene approach. In summer 2010, association study (AS) lines consisting of expired PVP and diverse public inbred lines were grown on low and normal nitrogen (N) fields created at Marion, IA (Pioneer Hi-Bred Research station) and at Burkey farm (ISU). Lines were grown in two-row plots with two replications. As criteria to measure NUE, grain yield under low and high N was determined. Various yield related traits such as grain moisture, kernel weight, ears per plant, plant height were also measured. NUE field trials will be repeated in 2011 at the above mentioned locations. To study the root characteristics in 6, 10, and 14 day old maize seedlings of AS lines, a paper roll method was used. About 10 different root traits were measured. Data collected on young root characteristics will be used for association analysis, which is carried out for allele-sequenced root genes (ongoing). AS lines were genotyped with 110 ISU-IBM SNP markers spread across the whole maize genome to estimate the population structure in AS panel lines, which is used as a covariate for the association analysis. The IBM2Syn10 population consisting of 243 doubled haploid (DH) lines was grown under low and high N levels at Marion and Burkey farm. As criteria to measure NUE, grain yield and various yield related traits were measured. Furthermore, kernel measurements for protein, starch, and oil content are currently measured using near-infrared spectrophotometry. Testcross seed will be produced this winter by Pioneer Hi Bred for trials in 2011. Posters have been shown at Plant Breeding Conferences in Ames and Johnston 2010. Developing an education system to meet the challenges facing students was one goal of this project. We surveyed curriculum content for other Plant Breeding Masters programs around the world. We organized the list of courses in each program according to four major subject areas; Genetics, Breeding Methods, Statistics, and Synthesis. Then we compared the courses in each area to the ones available in the current Plant Breeding and MS in Agronomy programs at Iowa State University. We created a set of guidelines for the Plant Breeding faculty and personnel engaged in the creation of MS in Plant Breeding. The guideline includes the description of major steps namely design, development, implementation, and evaluation followed in building an online program. We also created a list of factors affecting the success of online programs. We are in the process of writing two journal articles for publication from the project. The first article focuses on needs assessment conducted to analyze a variety of stakeholders' needs and expectations regarding the MS program in Plant Breeding. The second article will be a research review on factors affecting the success of graduate online programs. PARTICIPANTS: Project Director: Thomas Lubberstedt, Iowa State University. Co-PDs: William D. Beavis, Iowa State University; Ann Thompson, Iowa State University; Michael Lee, Iowa State University; Kendall R. Lamkey, Iowa State University. Training opportunities were provided for the following students: Yasemin Demisrsalan, graduate student (PhD), surveys for Distance MS program; Shreyartha Mukherjee, graduate student (PhD), bioinformatics; Baohong Guo, a post-doctoral fellow, association mapping theory; Bharath K. T. Narayana, graduate student (PhD), candidate gene isolation and association mapping; Jenaro Reyes Matamoros (Research Professor at Benemerita Universidad Autonoma de Puebla; Sabbatical); Pedro Jose Gonzalez Portilla (PhD), graduate student, QTL mapping; Constantin Jansen, graduate student (PhD), fine mapping (financing by this USDA project from 8/2010 on). All students contributed to posters presentations to plant breeding professional groups. Collaborations: John Sawyer (ISU), Plant Introduction Station (USDA), Frank Hochholdinger (University of Tubingen, Germany), Steve Moose and Martin Bohn (University of Illinois), Pioneer, Dow, Syngenta. TARGET AUDIENCES: The target audiences of the information generated in this project include plant breeding professionals who will benefit from knowledge of the location of genes that affect the plant use of nitrogen. Plant breeding professionals and plant breeding students will also benefit from the use of the in silico breeder's toolbox, which will assist research in plant breeding. Another target audience is the group of potential plant breeding students who will obtain degrees from the distance education program, as well as professionals who may take individual, isolated courses on particular aspects of plant breeding of interest to them. Finally, a major target audience are private and public employers in plant breeding. The distance MS program in Plant Breeding will enable employers to retain qualified employees, while offering the program as opportunity for qualification. PROJECT MODIFICATIONS: Relative to the original time plan, the genetic mapping experiment is delayed. This had mainly to do with the timing for confirmation of project funding, which did not arrive as anticipated in spring (so that summer 2008 could have been used for seed multiplication) but in late spring 2009 (too late for using a winter nursery). While the experiment will be conducted as planned, the two students involved in the mapping and fine mapping study were hired with delay. Cost neutral extension for this part of the project has been approved by USDA until August 2012.
Impacts
Our project will create and implement an in silico breeder's toolbox to assist the research and education components of other aspects of this project. None of the publicly available sotwares fully meets the requirements described in the proposal. Results of the evaluations will be provided through the GFS Sprague Population Genetics Web-site. Power, precision and accuracy of nested association mapping to identify QTN was investigated using simulation modeling by Baohong Guo and Beavis. Nested mating designs are capable of resolving functional markers with high power and accuracy, even in situations where disequilibrium among functional and non functional markers in the same genomic region has the potential to confound interpretation of results. Community resources generated within this project include a high resolution map of SNPs, available through the GFS Sprague Population Genetics Group web-site. A method for integrating high resolution sequence and linkage maps was developed, applied to maize sequences and published (Guo and Beavis 2010). Our current research activities are expected to provide detailed information on associations of sequence polymorphisms with NUE or any associated traits, and their conversion into functional markers. We expect to identify QTL affecting NUE, and will be able to answer the question, whether or not genes affecting root development also affect NUE at the level as determined by grain yield under high and low N fertilization regimes. Towards establishment of a Distance MS program in Plant Breeding, the following community resources have been generated: 1. The survey and comparison of curriculum content for Plant Breeding Masters programs in six universities. 2. The list of factors affecting the success of online programs. 3. The list of procedures and actions in designing and developing an online program. As a result of the survey, the ISU Agronomy Department committed to develop a distance MS program. Four course development teams have been established and presented their course outlines at a retreat in November 2010. The course sequence has recently been published on a web-site for the Distance MS program in Plant Breeding, which will start fall 2011 (http://msplantbreeding.iastate.edu/). One lecturer (Laura Merrik) has been hired for development of course development, the hire of a second lecturer is pending. The new Distance MS program in Plant Breeding has been announced at the Plant Breeding conference in Johnston 2010, and will be announced at the Plant Animal Genome Conference 2011. Once the 2nd lecturer has been hired, the program will be broadly advertised. The development of this program may lead to an increase in the number of plant breeders entering the public and private sectors. It will initiate new education models requiring a closer interaction of breeding companies and ISU faculty in plant breeding.
Publications
- Guo, B and WD Beavis (2010) In silico Genotyping of the Maize Nested Association Mapping Population. Molecular Breeding DOI 10.1007/s11032-010-9503-4
- Guo, B, SA Sleper, WD Beavis (2010) Nested Association Mapping for Identification of Functional Markers Genetics 186, 373-383
- Demiraslan, Y., Baran, E., Thompson, A. (2010, May). A Theory-based Needs Analysis Approach in the Design of an Online Masters Program. Presented at the Annual Meeting of the American Educational Research Association, Colorado, Denver. (oral presentation)
- Pedro Jose Gonzalez Portilla, Constantin Jansen, Bharath K.T. Narayana, Michael Lee and Thomas Lubberstedt. (2010). Development of functional markers for Nitrogen usage efficiency in maize. 4th Annual Plant Breeding Meeting, Pioneer Hi-Bred International, Johnston, Iowa. (poster)
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Progress 12/01/08 to 11/30/09
Outputs
OUTPUTS: Identifying genes that impact the nitrogen-use-efficiency of maize can lead to advances in developing cultivars that require fewer crop inputs, a benefit to the financial well-being of farmers and to the quality of ground water reserves. Our project seeks to identify these genes using a candidate-gene approach. A high resolution mapping population for nitrogen-use efficiency (NUE) quantitative trait loci (QTL), the IBMSyn10 population consisting of 243 doubled haploid lines, was grown in summer 2009 for seed multiplication. In summer 2010, these lines will be tested at high and low N sites provided by Pioneer Hi Bred and at the Burkey farm, ISU, to identify QTL and candidate genes underlying those QTL. For reverse genetic functional marker (FM) development for NUE, we focused on 5 sequenced maize genes affecting root development. 80 association study (AS) lines consisting of expired PVP and diverse public inbred lines were obtained from the Plant Introduction Station in Ames, IA, and multiplied in summer 2009. DNA was extracted from all AS lines. For each of the genotype-root gene combinations, PCR amplicons are currently produced and sequenced at the DNA facility of ISU. Phenotyping of seedling roots is performed in collaboration with Dr. Hochholdinger (U. Tubingen, Germany), determination of NUE of these lines will be performed at the same sites as for the IBM population in 2010. Poster presentations were given at partnering events with Monsanto and Conoco Phillips, the BioCentury Research Farm opening, and the International Plant Molecular Biology Congress (St. Louis) by researchers investigating this problem. A presentation on Functional Markers was given at the Maize Breeders School meeting, where a meeting with collaborators was organized. Meetings with commercial collaborators were held with Pioneer and Dow. Increasing the number of trained plant breeders has been a goal for public and private research communities. Developing an education system to meet the challenges facing students was one goal of this project. A distance learning on-line model, structured similarly to the successful MS in Agronomy model would address the needs of prospective students and increase the pool of trained plant breeders. Our first steps included conducting a survey to access needs and interest in this program. We completed surveys for potential employers, students and research collaborators. Survey results indicate a high degree of interest in a potential Masters at a Distance in Plant Breeding from potential audiences and also provide information on curriculum for this program. A paper on the needs analysis process for establishing an online Master of Science (MS) program in Plant Breeding was accepted for the Annual Meeting of the American Educational Research Association in 2010. Based on the completed survey, we visited four major breeding companies to present the concept of a Distance MS program in Plant Breeding. A new course on Molecular Plant Breeding has meanwhile been established (Agron 523x, Lubberstedt & Beavis), which would become part of this program. Moreover, Lubberstedt will edit a book on Plant Functional Markers for Springer. PARTICIPANTS: Project Director: Thomas Lubberstedt, Iowa State University. Co-PDs: William D. Beavis, Iowa State University; Ann Thompson, Iowa State University; Michael Lee, Iowa State University; Kendall R. Lamkey, Iowa State University. Training opportunities were provided for the following students: Yasemin Demisrsalan, graduate student (PhD), surveys for Distance MS program; Shreyartha Mukherjee, graduate student (PhD), bioinformatics; Baohong Guo, a post-doctoral fellow, association mapping theory; Bharath K. T. Narayana, graduate student (MSc), candidate gene isolation and association mapping; Pedro Jose Gonzalez Portilla (PhD), graduate student, QTL mapping; Constantin Jansen, graduate student (PhD), fine mapping (financing by this USDA project from 8/2010 on). All students contributed to posters presentations to plant breeding professional groups. Collaborations: John Sawyer (ISU), Plant Introduction Station (USDA), Frank Hochholdinger (University of Tubingen, Germany), Steve Moose and Martin Bohn (University of Illinois), Pioneer, Dow, Syngenta. TARGET AUDIENCES: The target audiences of the information generated in this project include plant breeding professionals who will benefit from knowledge of the location of genes that affect the plant use of nitrogen. Plant breeding professionals and plant breeding students will also benefit from the use of the in silico breeder's toolbox, which will assist research in plant breeding. Another target audience is the group of potential plant breeding students who will obtain degrees from the distance education program, as well as professionals who may take individual, isolated courses on particular aspects of plant breeding of interest to them. Finally, a major target audience are private and public employers in plant breeding. The distance MS program in Plant Breeding will enable employers to retain qualified employees, while offering the program as opportunity for qualification. PROJECT MODIFICATIONS: Relative to the original time plan, the genetic mapping experiment is delayed. This had mainly to do with the timing for confirmation of project funding, which did not arrive as anticipated in spring (so that summer 2008 could have been used for seed multiplication) but in late spring 2009 (too late for using a winter nursery). While the experiment will be conducted as planned, the two students involved in the mapping and fine mapping study were hired with delay. Cost neutral extension for this part of the project will be requested to be able to complete this part of the project.
Impacts
Our project will create and implement an in silico breeder's toolbox to assist the research and education components of other aspects of this project. Power, precision and accuracy of nested association mapping to identify QTN was investigated using simulation modeling by Baohong Guo and Beavis. Results indicate that nested mating designs involving several reference parents are capable of resolving functional markers with high power and accuracy, even in situations where disequilibrium among functional and non functional markers in the same genomic region has the potential to confound interpretation of results. Results will appear in a manuscript accepted and under revision in the journal Genetics. Our current research activities are expected to provide detailed information on genetic diversity of NUE candidate genes in elite and exotic germplasm, associations of sequence polymorphisms with NUE or any associated traits, and their conversion into functional markers. Tertiary protein structures from a few candidates have been modeled using a novel decoy approach. Development of protein decoy models suggests a novel method for understanding variable transport of nitrogen compounds into cells for Nitrogen metabolism. If the models reveal heritable structures, then genetic mechanisms underlying N flux in meeting sink demands may lead to novel methods for increasing NUE. Most advanced at current are the activities related to establishment of a Distance MS program in Plant Breeding. Data for this survey were collected from 16 employers or supervisors (in total more than 100 company employees returned surveys). 87.6% percent of the employer respondents either agreed (56.3%) or strongly agreed (31.3 %) to the need for an online MS in Plant Breeding and 81.3% indicated they had employees who they would recommend involving in such a program if offered, as indicated by a strongly agree or agree response. 87.5% either agreed or strongly agreed that their companies would provide financial support for employees involved in such a program. Furthermore, majority of the employers either agreed or strongly agreed that their companies had a need for PhD (81.3%) or MS (87.6%) graduates in plant breeding. In addition, 62.5% either agreed or strongly agreed that for some employees, they would like the proposed program to lead to a PhD program, and all the employers indicated that a typical student should complete such a program in 3-5 years, as indicated by a strongly agree or agree response. As a result of these findings, the Iowa State University Agronomy Department has committed to developing the distance MS program. We began work on surveying curriculum content for other Plant Breeding Masters programs around the world as our next step in developing objectives, outcomes, and curriculum content for the program. The development of this program may lead to an increase in the number of plant breeders entering the public and private sectors. It will initiate new education models requiring a closer interaction of breeding companies and ISU faculty in plant breeding.
Publications
- Narayana, B.K.T., Jansen, C., Gonzalez Portilla, P.J., Mukherjee, S., Beavis, W., Lee, M., and Lubberstedt, T. 2009. Development of Functional Markers for NUE in Maize using a Candidate-gene Approach. 9th International Plant Molecular Biology Congress, St. Louis.
- Lubberstedt, T., Chen, Y., Brenner, E.A., Zein, I. 2009. Development and application of functional markers. 45th Annual Corn Breeder's School meeting, Urbana-Champaign. p. 23-31.
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