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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Identification of Genes That Enhance the Nutritional Value of Rice

Authors
item Pinson, Shannon
item Tarpley, Lee -
item Salt, David -
item Zhang, Min -
item Guerinot, Mary Lou -

Submitted to: Experiment Station Bulletins
Publication Type: Experiment Station
Publication Acceptance Date: June 7, 2012
Publication Date: June 26, 2012
Citation: Pinson, S.R., Tarpley, L., Salt, D.E., Zhang, M., Guerinot, M. 2012. Identification of Genes That Enhance the Nutritional Value of Rice. Texas Rice, July 2012 edition, Special section, pp. VII-IX; http://beaumont.tamu.edu/eLibrary/Newsletter/2012_Highlights_in_Research.pdf Experiment Station Bulletin

Technical Abstract: Consumers in developed countries such as the U.S. are willing to pay premium prices for food products having enhanced nutritional value. Grocery stores contain a myriad of calcium fortified foods ranging from orange juice to margarine to frozen waffles. Cereal aisles and bottled water aisles are lined with products touting their high concentrations of phosphorus, magnesium, zinc, and potassium along with low levels of sodium. Rice is a naturally healthy food low in sodium, but consumer interest could rise if it could be marketed as “Naturally Fortified” for one or more nutritional elements. In a project funded by the National Science Foundation we aimed to identify genes that can be used to enhance the nutritional value of the rice grain. This research includes both increasing the accumulation of nutritional elements such as calcium, zinc, potassium, and iron, and reducing the accumulation of elements that can be detrimental to human and animal health, such as arsenic and cadmium. Also, genes that increase the uptake of elements essential for rice plant health in turn would increase yield potential. A three-pronged approach was selected to maximize ability to identify genes affecting rice grain nutritional value. The first prong involved identifying genes segregating among progeny derived from the U.S. variety ‘Lemont’ crossed with ‘TeQing’ from China, in which mapping populations were grown under two different field conditions — flooded and unflooded. Flooding alters soil chemistry, with some elements more available for plant uptake and others less available. Flooding also alters root structure and ability to contact soil minerals for uptake. Studying rice grains grown under both growing conditions allowed us to study how the grain element genes acted under two very different environments. From the Lemont/TeQing progeny, 127 genes affecting the grain concentration of individual mineral elements were identified. More genes affecting grain concentrations were found when plants were grown under flooded (92 genes) than unflooded field conditions (42 genes). Interestingly, the 127 genes found associated with the various elements often mapped to the same chromosomal location resulting in just 40 genomic regions associated with rice grain element concentration (a.k.a. nutritional value). For example, three elements, cadmium, magnesium, and molybdenum mapped to the bottom region of chromosome 2, whereas higher on the same chromosome, there is a region associated with 11 different elements (including arsenic, potassium, nickel, rubidium, copper, strontium, manganese, phosphorus, zinc, iron, and sulfur). Further research is needed to determine if the 40 grain-element regions are clusters of multiple genes each affecting the uptake or transport a single element, or if they are instead due to a single gene affecting multiple elements. At least some of the regions associated with multiple elements probably contain a single gene that alters a plant mechanism that affects more than one element. For example, a single gene increasing the number of root hairs or affecting how roots exude chemicals to alter the soil surrounding them, could affect the root uptake of multiple elements. In contrast, a few genes were not closely linked to genes for other elements. This is as one would expect if the genes were associated with specific metal transporter mechanisms, such as the copper-transporter gene reported by others in another plant species, Arabidopsis thaliana. The studies using the Lemont/TeQing mapping populations allowed us to fairly quickly and inexpensively map the grain-element genes contained in these two parental lines, but were limited in that they could reveal only the genes that differed between the two parents. In order to study a larger number of genes, the second prong involved a set of 400 rice lines representing important ancestral and modern rice cultivars from all major rice-growing regions of the world. While other researchers were busy characterizing these 400 lines for 1 million genetic markers, we grew them under flooded and unflooded conditions in Beaumont, TX and then analyzed them for grain-element concentrations. To date we have confirmed the location and element-impact of several of the genes first identified in the Lemont/TeQing progeny study, including a gene controlling copper uptake found on chromosome 2. We have also learned that rice varieties that descended from the cold-adapted temperate japonica lineage generally accumulate less detrimental arsenic in their grains than do rice varieties descended from the more tropically adapted indica and tropical japonica lineages. Of particular interest, modern U.S. cultivars including ‘Cybonnet’, ‘Cocodrie’ and ‘Wells’ accumulated, on average, only about half the grain As accumulated by historical U.S. rice varieties such as ‘Carolina Gold’, ‘Blue Rose’, and ‘Saturn’. The third prong of the project involved screening 1640 rice varieties representing both wild and cultivated rice originating from over 100 countries in order to identify rice cultivars that exhibited grain element compositions so different in one or more elements as to suggest that they resulted from a genetic mutation. A set of 50 varieties exhibiting extreme grain elemental concentrations were identified and crossed with a U.S. variety to create segregating cross- progeny in which to map the underlying gene mutations. Cross-progeny seed harvested in 2011 are now being analyzed by collaborators for their grain compositions. Studies to identify the physiological attributes that underlie their extreme nutritional value are also underway. Learning which chromosomal regions contain genes affecting grain element concentrations is a critical first step toward understanding how those genes can be most effectively used to improve grain nutritional value or rice plant nutrition. The fact that the grain-element chromosomal regions identified to date are often associated with more than one element suggests the importance of studying multiple elements at a time as well as the importance of carefully controlling factors such as soil fertility, temperature, and pH that affect the uptake of nutrients by plant roots when conducting further studies.

Last Modified: 12/20/2014
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