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United States Department of Agriculture

Agricultural Research Service

Research Project: Plant and Seed Chemistry Genetics

Location: Small Grains and Potato Germplasm Research

2011 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. 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. Genetic analyses led to the identification of the gene perturbed in barley lpa1, and indicate that it encodes a novel phosphorus transporter that represents the first cereal endosperm-specific phosphorus transporter. Progress was also made in the analysis of allelic relationships, epistasis, and dosage effects in our collection of lpa genes. Progress was made in Objective 2- which focuses on the relationship between seed phosphorus and inositol phosphates and plant performance and stress tolerance. Field trials confirm that at least one barley low phytic acid line has yields indistin-guishable from normal barley lines in a wide variety of environments. Ongoing studies of the genetics of inositol pyrophosphates have revealed interesting and useful seed phenotypes in this class of compounds important to metabolic-status sensing and stress tolerance. 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 the recently developed methods and novel seed P mutants are undergoing more detailed study.

4. Accomplishments
1. Genetic and chemical analyses confirm that barley 1pa1 is important to endosperm total phosphorus levels. At all levels of nutrient phosphorus supply, barley 1pa1 endosperms accumulate 30% less phosphorus than do normal endosperms, so that the effect on endosperm total phosphorus is independent of maternal genotype. ARS scientists in Aberdeen, ID, performed chromosomal mapping studies and molecular sequencing to identify the gene perturbed in barley 1pa1 as being a novel P transporter specific to the cereal grain endosperm. This represents a major advance. This gene, in theory, can now be used to engineer endosperm total phosphorus in other cereal crops such as maize.

2. The first study of the nutritional value of a "low phytic acid" rice was completed. One of the major public health problems world-wide concerns micronutrient mineral deficiency, notably iron and zinc deficiency. A contributor to this problem is that staple foods consisting of grains and legumes contain high levels of phytic acid, an antinutrient which negatively impacts iron and zinc nutrition. One approach to developing more nutritious foods would be to develop “low phytic acid” grains and legumes. ARS scientists in Aberdeen, ID, working with scientists at the University of California- Davis, and using the "rat pup" model they developed, compared zinc absorption from a low phytic acid rice with that of normal rice, and with low phytic acid and normal maize and barley. The low phytic acid trait was shown to substantially enhance zinc absorption of rice. This is greatly significant for the nutritional well being of the large numbers of people throughout the world who rely on rice as their staple food.

Review Publications
Lonnerdal, B., Mendoza, C., Brown, K., Rutger, J.N., Raboy, V. 2011. Zinc absorption from low phytic acid genotypes of maize (Zea mays L.), barley (Hordeum vulgare L.) and rice (Oryza sativa L.) assessed in a suckling rat pup model. Journal of Agricultural and Food Chemistry. 59:4755-4762.

Last Modified: 2/23/2016
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