Skip to main content
ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Research Project #425079

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

2016 Annual Report


4. Accomplishments
1. Whole grain rice naturally fortified with higher bioactive compounds. Phenolic compounds have potential in reducing incidence of chronic diseases or their risk factors. Anthocyanins, a major subgroup of phenolic compounds in purple bran rice, have been demonstrated in animal studies and human clinical trials to possess these health beneficial effects. Scientists at Dale Bumpers National Rice Research Center in Stuttgart, Arkansas studied the anthocyanin concentration and antiradical capacity among 25 genetically diverse purple-bran rice cultivars. More than 8.0- and 25-fold variation in antiradical capacity and total anthocyanin concentration, respectively, were found in the bran. The scientists also demonstrated the use of a high throughput analysis method that will enhance the evaluation of these compounds in other varieties as well as selection of this trait in a breeding program. These results will expedite the development of rice varieties having enhanced levels of health beneficial compounds that are commonly found in fruits and vegetables.

2. Sequestration in plant leaves may reduce grain arsenic accumulation in rice. There is public concern over arsenic levels in rice and other food products. The flooded conditions under which most rice is produced makes soil arsenic more bioavailable for uptake, and rice plants transport a portion of the arsenic into the grain. Scientists at Dale Bumpers National Rice Research Center in Stuttgart, Arkansas studied six rice varieties known to produce either high or low in grain arsenic (As) concentrations and asked if they exhibited differences for rates of As uptake, transport, sequestration, and/or detoxification of secondary stress compounds in seedling roots and leaves. The most striking difference was that exposure to high levels of As induced all three varieties low in grain-As, but none of those high in grain-As, to double leaf production of glutathione, a compound necessary for sequestration of As into cell vacuoles. This suggests that one metabolic method of limiting As accumulation in the grain is by trapping it in leaf cell storage areas (i.e. vacuoles). Finding genes that control this sequestration process will help breeders to develop new rice varieties with that exclude As from the grain.

3. Database for rice breeding. Rice breeding can be accelerated by using genomic and genetic diversity data. A database specifically designed for use by rice breeders (Ricebase) was developed by ARS scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas along with researchers at the Boyce Thompson Institute in Ithaca, New York. For the first time the Ricebase program integrates genetic variation, pedigrees, and whole-genome-based data to enable discovery and design of molecular markers. Application of these molecular markers in marker-assisted selection makes rice breeding faster and more efficient.

4. Wild ancestral species improve grain yield in the USA rice cultivar, Jefferson. Increasing diversity by introducing new genes lost during the domestication process is one method of improving yields in crop plants. ARS scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas evaluated eight accessions developed from crossing of the USA cultivar, Jefferson, with O. rufipogon with each having different chromosomal segments of the wild ancestral species. Earlier field studies identified these accessions as having increased yield when compared to the Jefferson parent. Greenhouse studies determined the increased yield was due to a longer growing cycle, more above-ground biomass, longer flag leaves and longer panicles. This demonstrates that DNA from an inferior wild species can contribute variation that increases yield in a commercial rice cultivar. These lines are currently available to the rice breeding community for use in expanding the genetic diversity in their cultivar development program.

5. Improving copper content and the human nutritional value of rice. Rice not only provides more than one fifth of the daily calories for half of the world’s population but is also a major source of mineral nutrients like copper that is important for preventing osteoporosis and anemia. We identified the gene for a protein that transports copper into root vacuoles, and further showed that natural variation in this transporter gene affects how much copper gets transferred to and accumulated in the grains of field cultivated rice. While other copper transporters were previously shown to impact other aspects of copper tissue-to-tissue transfer (such as from roots to the plant vascular system), this is the first copper transporter documented to impact sequestration of copper into cell storage areas (i.e. vacuoles). While most plant metal transporters have been identified using deleterious knock-out mutants, we identified alternative forms of this transporter gene within two high-yielding rice varieties. The identification of natural genetic variation may offer rice breeders the opportunity to fine-tune the copper concentrations in rice grain to improve the diet of the people that rice sustains.

6. Rice with higher resistant starch, a dietary fiber. Resistant starch, a fraction of the starch that resists digestion in the small intestines of healthy humans and is considered part of dietary fiber content, has potential in prevention of colon cancer and inflammatory bowel disease. Resistant starch concentration correlates with grain amylose content in studies using rice varieties with amylose ranging from 0 to 26%. Scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas evaluated resistant starch in cooked rice of 40 cultivars, all with high amylose. More than a 2-fold difference in resistant starch concentration was found and more than three-fourths of the cultivars had higher resistant starch concentration than Dixiebelle, a high amylose US cultivar. The findings of this research indicate that rice cultivars can improved for resistant starch/dietary fiber that will promote colon health.

7. Genetic linkage between kernel fissure resistance and the sd-1 semidwarf gene in rice. Fissures, or cracks, in the rice grain result in reduced milling quality and crop value. An experiment was conducted by researchers at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas to finely map a region on chromosome 1 that was associated with kernel fissure resistance but also included the sd-1 semidwarf locus. Most of the offspring from the fissure resistant x fissure susceptible cross that had high resistance to kernel fissuring were fixed (non-segregating) for the sd-1 allele making them short statured. However, several of the offspring were determined molecularly and phenotypically to contain the Sd-1 allele for taller plant height. This demonstrated that the gene for fissure resistance is linked to but different from the sd-1 gene, and can be used by breeders to improve the fissure resistance of tall as well as semidwarf rice cultivars.


Review Publications
Eizenga, G.C., Neves, P.C., Bryant, R.J., Agrama, H.A., Mackill, D.J. 2015. Evaluation of a M-202x Oryza nivara advanced backcross population for seedling vigor, agronomic traits, yield components, yield and grain quality. Euphytica. 208:157–171. doi: 10.1007/s10681-015-1613-y.
Chen, M., Bergman, C.J. 2016. Vitamin E homologs and y-oryzanol levels in rice (Oryza sativa L.) during seed development. Cereal Chemistry. 93:182-188.
Bryant, R.J., Yeater, K.M., Mcclung, A.M. 2015. Effect of nitrogen rate and the environment on physicochemical properties of selected high amylose rice cultivars. Cereal Chemistry. 92(6):604-610. doi.org/10.1094/CCHEM-02-15-0035-R.
McCouch, S.R., Wright, M.H., Tung, C., Maron, L.G., McNally, K., Fitzgerald, M., Singh, N., DeClerck, G.A., Agosoto Perez, F., Korniliev, P., Greenberg, A., Naredo, M.B., Mercado, S.M., Harrington, S.E., Shi, Y., Branchini, D.A., Kuser-Falcao, P.R., Leung, H., Ebana, K., Yano, M., Eizenga, G.C., McClung, A.M., Mezey, J. 2016. Open access resources for genome wide association studies (GWAS) in rice (Oryza sativa) illustrate the power of population-specific mapping. Nature Communications 7:10532. doi: 10.1038/ncomms10532.
Huang, X., Deng, F., Pinson, S.R., Guerinot, M., Salt, D.E., Ma, J. 2016. A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain. Nature Communications. 7:121138. doi10.138/ncomms12138.
Goodyear, A., Ehrhart, E.J., Swanson, K.S., Grusak, M.A., Leach, J.E., Dow, S.W., McClung, A.M., Ryan, E. 2015. Dietary rice bran supplementation prevents salmonella colonization differentially across varieties and by priming intestinal immunity. Journal of Functional Foods. 18:653-664.
Chen, M., McClung, A.M., Bergman, C.J. 2016. Concentrations of oligomers and polymers of proanthocyanidins in red and purple rice bran and their relationships to total phenolics, flavonoids, antioxidant capacity and whole grain color. Food Chemistry 208:279-287.
Eizenga, G.C., Edwards, J., Yeater, K.M., McCouch, S.R., McClung, A.M. 2016. Transgressive variation for yield components measured throughout the growth cycle of Jefferson rice (Oryza sativa) x O. rufipogon introgression lines. Crop Science 56:1-12. DOI: 10.2135/cropsci2015.10.0603.
Chen, M., McClung, A.M., Bergman, C.J. 2016. Bran data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity, and profiles of proanthocyanidins and whole grain physical traits of 32 red and purple rice varieties. Data in Brief 8:6-13.
Edwards, J., Baldo, A.M., Mueller, L.A. 2016. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data. Database: The Journal of Biological Databases and Curation. 2016:baw107.