Progress 05/28/05 to 05/13/08
Outputs
Progress Report Objectives (from AD-416) Objective 1: Identify and characterize candidate genes and pathways underlying genetic variability for grain amino acid content. Objective 2: Utilize quantitative genetic theory and statistical methods for inbreeding and small population size to enhance breeding methods for biochemical traits. Objective 3: Evaluate improved prediction methods for biochemical traits including NIR Spectroscopy and marker assisted selection to increase efficiency of evaluation and selection. Approach (from AD-416) We will use a recurrent selection approach in which agronomic and biochemical traits are improved concurrently. In order to accomplish this, we propose to develop new methods and tools that will enhance the efficiency of recurrent selection. First, we will identify candidate genes controlling the traits of interest. Second, we will develop novel selection strategies based on small population sizes in order to maximize the gain from selection. Third, we propose to develop methods for predicting the value individuals in the breeding program using Bayesian estimation to develop calibrations for predicting levels of amino acids and to identify molecular markers correlated with the traits to be selected. Significant Activities that Support Special Target Populations This is the final year of this project plan and we are transitioning to our new project plan 3625-21000-055-00D �GENETIC ANALYSIS OF SELECTION RESPONSE IN MAIZE POPULATIONS�. In order to finish the work on this project we continued development of populations that are differentiated for amino acid content. We carried out transcript profiling on the populations selected for high and low methionine content. In addition, we sequenced several candidate genes from these populations to determine the impact of selection on allele frequency. This research fits within NP 301 Action Plan, Component #2, Crop Informatics, Genomics and Genetic Analyses, Problem Statement 2C, Genetic Analysis and Mapping of Important Traits because it is a genetic analysis of grain methionine content, an important trait in maize used for animal feed. Technology Transfer Number of Web Sites managed: 2
Impacts
(N/A)
Publications
- Scott, M.P., Peterson, J.M., Moran, D.L., Sangtong, V., Swain, L., Guillumine, P. 2007. A wheat genomic fragment functions as a gametophytic mutant to reduce pollen transmission of transgenic maize loci. Transgenic Research. 16:629-643.
- Wardyn, B.M., Edwards, J.W., Lamkey, K.R. 2007. The genetic structure of a maize synthetic: the role of dominance. Crop Science. 47:467-476.
- Shepard, C.T., Vignaux, N., Peterson, J.M., Johnson, L.R., Scott, M.P. 2008. Green Fluorescent Protein as a Tissue Marker in Transgenic Maize Seed. Cereal Chemistry. 85:188-195.
- Sheperd, C.T., Vignaux, N., Peterson, J.M., Scott, M.P., Johnson, L.R. 2008. Dry-milling and Fractionation of Transgenic Maize Seed Tissues with Green Fluorescent Protein as a Tissue Marker. Cereal Chemistry. 85:196-201.
- Williams, C.L., Liebman, M., Edwards, J.W., James, D.E., Singer, J.W., Arritt, R.W., Herzmann, D. 2008. Predicting spatial variation of crop yield across a landscape using aggregated environmental data. Crop Science. 48:1545-1559.
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) Objective 1: Identify and characterize candidate genes and pathways underlying genetic variability for grain amino acid content. Objective 2: Utilize quantitative genetic theory and statistical methods for inbreeding and small population size to enhance breeding methods for biochemical traits. Objective 3: Evaluate improved prediction methods for biochemical traits including NIR Spectroscopy and marker assisted selection to increase efficiency of evaluation and selection. Approach (from AD-416) We will use a recurrent selection approach in which agronomic and biochemical traits are improved concurrently. In order to accomplish this, we propose to develop new methods and tools that will enhance the efficiency of recurrent selection. First, we will identify candidate genes controlling the traits of interest. Second, we will develop novel selection strategies based on small population sizes in order to maximize the gain from selection. Third, we propose to develop methods for predicting the value individuals in the breeding program using Bayesian estimation to develop calibrations for predicting levels of amino acids and to identify molecular markers correlated with the traits to be selected. Accomplishments Characterized the mechanism of genetic background-specific pleiotropic effects of the opaque2 gene. The opaque2 (o2) gene improves the nutritional quality of maize, but it is difficult to deploy because in many genetic backgrounds it reduces grain density and hardness. In order to understand the genetic control of these negative effects, we examined whole-genome transcript profiles in grain with severe and mild o2 phenotypes. This allowed us to characterize the genetic mechanisms controlling these effects. This understanding will lead to more efficient strategies for overcoming negative effects in breeding programs that depend on single-gene approaches. This accomplishment addresses National Program 302 Program Component 2 (Functional Utilization of Plant Genomes: Translating Plant Genomics into Crop Improvement), Problem Statement 1B (Applying Genomics to Crop Improvement). Significant Activities that Support Special Target Populations Presentation at Farm-Based Corn Seed Development group meeting, �Amino Acids in Corn� Dubuque, Iowa, March 27, 2007. Technology Transfer Number of Web Sites managed: 1 Number of Non-Peer Reviewed Presentations and Proceedings: 16
Impacts
(N/A)
Publications
- Jia, H., Nettleton, D., Carillo Vazquez, G., Peterson, J., Scott, M.P. 2006. Comparison of transcript profiles in wild-type and 02 maize endosperm in different genetic backgrounds. Crop Sci. (The Plant Genome). 47:S-45-59.
- Scott, M.P., Edwards, J.W., Bell, C.P., Schussler, J.R., Smith, J.S. 2006. Grain composition and amino acid content in maize hybrids representing 80 years of commercial maize varieties. Maydica. 51:417-423.
- Samarah, N., Mullen, R., Cianzio, S., Scott, M.P. 2006. Dehydrin-like proteins in soybean seeds in response to drought stress during seed filling. Crop Science. 46:2141-2150.
- Ji, J., Scott, M.P., Bhattacharyya, M.K. 2006. Light is essential for degradation of ribulose-1,5-biphosphate carboxylase-oxygenase large subunit during sudden death syndrome development in soybean. Plant Biology. 8:597-605.
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Progress 10/01/05 to 09/30/06
Outputs
Progress Report 1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? Why does it matter? This project is aligned with National Program 301, Plant Genetic Resources, Genomics, and Genetics Improvement. Development of commercially produced crop varieties depends on plant breeding. Maize is one of the most important crops produced in the U.S., valued at $20 billion annually. Recent technological advances in genome analysis allow researchers to obtain a wealth of genomic data that has proven valuable to understanding plant biology. Our objective is to determine how to apply this genomic information efficiently to increase the rate of improvement in maize breeding programs. Our focus is to improve agronomic traits and nutritional value of the grain simultaneously. Feed is the greatest expense for U.S. meat producers. Each year approximately $12 billion worth of maize is used
for animal feed in the U.S. Improvements to maize that increase its nutritional quality are therefore among the most important objectives for maize improvement programs. Protein is the nutritionally limiting component of maize, making up about 10% of the kernel. Maize-based animal feed is currently supplemented with protein and essential amino acids to meet the nutritional needs of monogastric animals. Reducing the need for these supplements by increasing the protein and essential amino acid content of maize would substantially reduce the cost of animal feed. For example, increasing quantities of the essential amino acids methionine, tryptophan, and lysine alone could increase the annual value of the maize grain crop by 0. 5 billion dollars annually. Increasing total protein quantity has the potential for an additional increase of up to 3.45 billion dollars. Because the dietary needs of humans are similar to those of other monogastric animals, developing maize germplasm with
improved amino acid quality could impact human nutrition world-wide, potentially opening new export markets for seed, grain and foods. Maize with improved protein nutrition is a value added product. This added value can be captured by maize growers, meat producers, and consumers of meat products. 2. List by year the currently approved milestones (indicators of research progress) Year 1 1. Obtain knock-out mutants of putative transcription factors. 2. Characterization of seed protein levels in knock-out mutants. 3. Transcript profiling of germplasm from breeding program. Year 2 4. Multilocation evaluation of populations selected for amino acid content. 6. Carry out and evaluate selection for agronomic performance and essential amino acids in subdivided populations. Year 3 5. Develop analytical and empirical predictions of the effects of inbreeding on selection response. 7. Develop and optimize NIR calibrations for amino acids. 8. Evaluate IBM lines for amino acid QTL. 4a List
the single most significant research accomplishment during FY 2006. This accomplishment aligns with NP 301 Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties. Grain quality in the era hybrids. We determined that after 70 years of selection in corn belt dent maize germplasm from 1930-2000, protein quantity in maize grain has decreased, but amino acid composition of the protein has not changed significantly. Maize breeders have selected for yield over the last 70 years. It is important to know what impact this approach has had on grain quality so that future efforts can be modified as necessary to maintain or improve grain protein quality. We produced varieties that were widely grown in each decade of the past 70 years and analyzed their grain quality. These results provide guidance to breeders interested in improving both yield and grain nutritional quality. 4b List other significant research accomplishment(s), if any. This accomplishment
aligns with NP 301 Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties. Phytic acid content as a quantitative trait. We established the feasibility of conducting recurrent selection for phytic acid concentration in maize grain. Phytic acid has negative impacts on maize grain nutritional quality and on the environment. We applied quantitative assays and determined that it is possible to select for phytic acid content as a quantitative trait in a breeding program. This result offers a new way of producing maize with reduced phytic acid and improved available phosphorus. Maize produced in this way will allow production of animal feed for less cost and reduce the waste phosphorus produced by livestock and poultry. This accomplishment aligns with NP 301 Problem Statement 3A: Genetic Theory and Methods of Crop Improvement. Modeling heterogeneity of variances. Breeders measure traits in field plot experiments and make selections based on the
mean trait value without considering which of these measurements is more reliable. Using Bayesian statistics, we developed an improved method for modeling heterogeneity of variances that allows breeders to weight their selections based on the reliability of each measurement. This will allow breeders to improve their rate of gain from selection, resulting in more rapid improvement of crop varieties. 5. Describe the major accomplishments to date and their predicted or actual impact. This accomplishment aligns with NP 301 Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties. It is an important component of milestones 4, 6, 7 and 8 of our project plan. It has not been feasible to improve maize nutritional quality by selection for economically important grain components (such as the amino acids lysine, tryptophan, methionine) because reliable, high-throughput assays for these compounds were not available. We have developed methods to measure
these compounds and implemented these methods in breeding programs to develop maize varieties with improved protein quality. As a consequence of this research, four public breeding programs have initiated programs to improve amino acid content. Additionally, we have provided these methods to several companies. 6. What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? Methods for determining levels of economically important grain components have been shared with public and commercial breeders A CRADA is being developed to conduct research on breeding for improved amino acid content. 7. List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications
below). A. Darrigues, Lamkey, K.R., Scott, M.P. 2006. Breeding for grain amino acid composition in maize, p. 335-344, In K. R. Lamkey and M. Lee, eds. Plant Breeding: The Arnel R. Hallauer International Symposium. Blackwell Publishing Professional, Ames, Iowa.
Impacts
(N/A)
Publications
- Darrigues, A., Buffard, C., Lamkey, K.R., Scott, M.P. 2006. Variability and genetic effects for tryptophan and methionine in commercial maize germplasm. Maydica. 50:147-156.
- Edwards, J.W., Jannink, J. 2006. Bayesian modeling of heterogeneous error and genotype by environment interaction variances. Crop Science. 46:820- 833.
- Scott, M.P., Duvick, S.A. 2005. Identification of QTL controlling thermal properties of maize starch. Cereal Chemistry. 82(5):546-553.
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