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United States Department of Agriculture

Agricultural Research Service

Research Project: Plant and Seed Chemistry Genetics
2012 Annual Report


1a.Objectives (from AD-416):
The long-term objective is to develop genetics of plant and seed chemistry useful in developing crops with improved end-use quality. The primary crops studied are barley and maize. The primary targeted end-uses are for feeds, foods, and biofuel production. Over the next five years the main focus will continue to be the genetics of plant and seed phosphorus. There are three specific objectives. The first objective will be to identify and characterize genes perturbed in barley low phytic acid mutants. Second, this project will develop a better understanding of the relationship between seed phosphorus and inositol phosphate chemistry, plant performance, and stress tolerance. The third objective is to identify novel crop genotypes conditioning altered plant or seed phosphorus chemistry or related phenotypes that are of end-use value. This includes the development of genetic tools useful in breeding or engineering crops with normal shoot P but altered levels of seed total P, and the development of genetic approaches useful in engineering reduced shoot total P. This last objective involves developing genotypes that are tolerant to reduced plant total P.


1b.Approach (from AD-416):
For the first objective, the first step is to select target mutant loci as targets. Characterization of phenotypes observed in the barley lpa mutation collection, in combination with chromosomal mapping data, and review of the current knowledge in this field, will be used to identify targets for gene identification. Fine mapping of selected lpa loci will first be conducted. Genomics resources for barley, or comparative mapping data with other species such as rice, will be used to identify candidate genes. Sequencing of candidate genes will confirm if they are in fact the gene perturbed in the target mutant. Definitive proof that a mutant phenotype is the result of a mutation in the identified gene may require additional studies such as “complementation”.

For the second objective, to develop a better understanding of relationship between seed phosphorus, inositol phosphate and plant performance such as stress tolerance, the first step would be to complete “transcription profiling”, using microarray analyses, to identify genes and functions impacted in selected genotypes or in response to selected stress treatments such as heat/drought stress. Genes whose expression or function is greatly impacted will be the focus of more targeted study. Their sequences, map position, and gene family relationships will be obtained. Expression profiles and biochemical/physiological function will be determined.

For the third objective, two types of approaches will be used to develop genotypes with useful alterations in plant or seed phosphorus chemistry. These are “forward genetics” screens and “reverse genetics” approaches. In “Forward genetics”, screens of various types of mutagenized populations will be conducted to identify mutations that impact plant or seed phosphorus. Populations screened will either be chemically mutagenized, or represent collections of transposon insertions. Mutants with interesting phenotypes such as “reduced seed total P” will then be the subject of in depth follow-up study, including chromosomal mapping and agronomic evaluation. Ultimately the gene perturbed in the mutation will be identified, and near-isogenic lines will be developed for use in agronomic and nutritional studies. In the reverse genetics component, mutations such as “single nucleotide polymorphisms” (SNPs) will be isolated in target genes of interest. For example, many genes are already known to be important to phosphorus uptake and transport, but which specific genes or functions are important to seed total phosphorus is not known. Methods such as TILLING will be used to isolate mutations in target genes, which will then be used to determine the effect of such mutations on plant and seed phosphorus.


3.Progress Report:
Progress was made in all three objectives, each of which is important to National Program 301, Component 2, Crop Informatics, Genomics and Genetic Analyses, Problem 2C, Genetic Analyses and Mapping of Important Traits. This project focuses on the genetics of plant and seed phosphorus. Both the total amount of phosphorus and its chemistry are critically important to the end-use quality of grain and legume crops, to the management of phosphorus in agricultural production and to efforts to reduce the impact of agricultural production on the environment. Work continues on Objective 1; studies of low phytic acid mutants and genes. Gene sequencing confirmed the most likely candidate gene perturbed in barley lpa1 appears to be a unique gene that is important to phosphorus levels in cereal grain seed. Substantial progress was made in the study of genetics and epigenetics of maize lpa1. This gene is important to the nutritional quality of maize and to the long-term management of phosphorus in agricultural production. We now know that this gene is subject to a new kind of inheritance called “epigenetics”. Understanding epigenetics is critical to understanding how genes work and how we can insure future success in crop breeding. The identity of genes important to inositol pyrophosphate synthesis was completed and searches began for mutations in these genes. Progress was made in Objective 2, which focuses on the relationship between seed phosphorus and inositol phosphates, plant performance, and stress tolerance. A two-year field trial that evaluated performance of five pairs of barley near-isogenic lines was completed. This study confirmed that we now have at least three different genes in barley that can be used to produce high-yielding nutritionally-enhanced barley. The second generation of recurrent selection for drought stress tolerance and yield within barley lpa lines were completed. These materials will be the basis for studies of the contribution of epigenetics to progress in plant breeding. Substantial progress was made in Objective 3, which focuses on developing new crop genotypes with altered plant or seed total phosphorus. Genetic screens for seed total P mutants are underway using newly developed methods and novel seed P mutants are undergoing more detailed study. Quantitative analyses of a substantial number of maize “seed total P” lines were completed. We also assisted other scientists in developing the first low-phytic acid field pea, an important feed crop. In cooperation with scientists at Stanford University, Harvard University, and the University of California, Davis, we completed an analysis of the effects of global warming on the nutritional quality of basic food crops like wheat, maize, rice, and soybean.


4.Accomplishments
1. Climate change may have little impact on some aspects of crop nutritional quality. There is a great deal of concern that changes in weather patterns associated with climate change may impact both the production and quality of basic food crops. The nutritional health and well being of every American could be impacted. In the first study of its kind, an ARS researcher in Aberdeen, Idaho, working alongside scientists at Harvard University and the University of California Davis, demonstrated that one important component of the nutritional quality of basic foods, their mineral content and mineral nutritional quality, does not appear to be greatly affected by a major contributing factor to climate change, increasing CO2 levels. Nutrients like iron and zinc were not found to be greatly affected, and anti-nutrients like phytic acid were also not greatly affected. With this knowledge, long-term strategies to address the impact of climate change on food production can be more accurately targeted.


Last Modified: 11/20/2014
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