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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

2014 Annual Report


1a. Objectives (from AD-416):
This project will explore existing genetic rice resources and develop new methods of evaluation to elucidate genetic and environmental factors that influence yield and grain quality. Phenotypic information will be combined with genomic scans to identify chromosomal regions and genes that control these traits. 1: Maintain, regenerate, back-up, characterize, and distribute rice genetic stocks and associated information, and genetically and phenotypically characterize accessions in the NSGC rice collection and elite breeding materials for agronomic and grain quality traits to provide new genetic resources for rice research 1A: Expand and phenotypically and genotypically characterize NSGC collection (Core, Mini-Core, GSOR subsets) for traits essential to rice research community and US rice industry 1B: Develop/characterize a tropical japonica Core collection (TRJ-Core) representing US and international tropical japonica rice germplasm for mining genes for US breeding programs 1C: Evaluate cultivars with divergent processing quality for differences in enzyme activity of starch metabolism genes in response to environmental temperature 1D: Evaluate germplasm with pigmented bran using in vitro cell assays for 1) influence of cooking on bioactivity of phenolics having potential health-beneficial properties against cancer, and 2) bioactivity of bran extracts against diabetes 1E: Assess accessions in rice diversity panels for health-beneficial starch fractions 1F: Assess accessions for bran components that impact storage stability of brown rice 2: Use genome wide association studies and QTL mapping techniques to identify alleles that control yield components and grain quality traits in response to environmental variables 2A: Determine location of QTL and allelic variability associated with yield components in bi-parental mapping populations 2B: Identify QTLs and alleles responsible for transgressive variation in selected yield components found in rice wild species using chromosome segment substitution lines 2C: Identify QTLs for rice grain chalkiness in bi-parental mapping populations, and validate the markers in diverse germplasm 2D: Characterize QTLs associated with rice milling yield 2E: Identify/fine-map/further characterize the mode of action of genomic regions affecting rice grain fissure resistance 2F: Identify/further characterize genes affecting grain mineral nutritional value 2G: Evaluate germplasm/RILs that differ for grain arsenic accumulation and resistance to straighthead disease to understand mechanisms of arsenic uptake from soil and association with staighthead 3: Use marker-assisted selection to introgress novel alleles and to stack genes associated with yield, disease resistance, and grain milling, cooking and nutritional quality into new cultivars and improved breeding stocks 3A: Develop marker analysis platform for marker-assisted transfer of traits from various rice germplasm backgrounds into targeted US cultivars 3B: Utilize genetic resources (RIL, genetic fingerprints, and markers linked to QTLs) to introgress improved alleles for agronomic performance, disease resistance, and stress tolerance into southern US adapted cultivars


1b. Approach (from AD-416):
This project will explore genetic resources using phenotypic and genomic tools to identify novel traits that impact rice yield and grain quality. Chromosomal regions that control these traits will be determined though association mapping techniques using germplasm surveys and QTL mapping of bi-parental and backcross mapping populations. Genetic resources ranging from elite US breeding materials and commercial cultivars, to diverse global germplasm, and wild Oryza species accessions will serve as the basis for extensive phenotyping and genotyping studies. In addition, a new diversity panel based upon tropical japonica germplasm, which is the source of US cultivars, will be developed to mine for novel alleles for traits relevant to the US rice industry. Targeted traits will include yield, disease resistance, and agronomic traits, as well as milling, nutritional, and processing quality. Mapping populations will be developed for diverse tropical japonica parents and from crosses with wild species to identify alleles that are associated with yield components. Compounds in rice bran that have been identified in raw rice that reduce cancer cell growth and glucose uptake in in vitro studies will be isolated and evaluated for their health beneficial properties and their bio-activity following cooking. Global rice genetic resources that have high amylose content will be evaluated for resistant starch to identify germplasm that may be beneficial for reducing spikes in blood sugar associated with diabetes. Enzymes that control starch structure and rice parboiling quality will be evaluated in diverse rice germplasm grown under high temperature. Enzymes that are sensitive to temperature stress and negatively impact processing quality will be identified. These will be targets for genetic improvement to develop improved stability in processing quality. In an effort to increase market use for whole grain brown rice, which is more nutritious than milled rice, components in the rice bran that can reduce rancidity during storage will be identified. Mapping populations that are segregating for grain chalk, milling yield, and grain fissure resistance, factors that impact crop value, will be used to finely map QTL and identify candidate genes associated with these traits. In addition, segregating populations will be analyzed for grain mineral content in an effort to develop nutrient-dense germplasm. Grain arsenic accumulation can occur when rice is grown under flooded, anaerobic conditions. The interaction of diverse germplasm and water management techniques will be studied to identify how these two factors can minimize grain arsenic accumulation while sustaining economically viable yields. The long-term objective of this project is to seek a better understanding of the genetic control of yield and grain quality traits, and this information can be translated into superior rice cultivars that will strengthen domestic and export markets for USA rice.


3. Progress Report:
Although progress was made on most milestones, several were not completed due to two on-going scientific vacancies since the inception of the project, along with two new scientific vacancies that occurred early in FY14, and the filling of one other vacancy late in FY14. Over 1800 NPGS rice accessions were rejuvenated and characterized for agronomic traits, data submitted to GRIN, and panicles sent to NPGS for photoarchiving. Plans were delayed to finalize accessions for establishing a Tropical Japonica (TRJ) core collection. However, through collaboration with IRRI, APHIS, and several universities, 1333 rice accessions known as the Rice Diversity Panel 2 (RDP2) were imported and over 900 have completed the USA quarantine growout. TRJ accessions from RDP2 and from a core collection from Brazil will be included in our new TRJ core. The recent hiring of the new Molecular Geneticist and Computational Biologist will facilitate structuring the TRJ core based upon existing genomic information in addition to passport data and agronomic traits. Progress was made on several grain quality traits. Grain chalk was quantified on some 1200 RILs grown in FY13 and used to identify a putative QTL on chromosome 2 related to chalk development. This will be confirmed with data being collected in 2014. We determined the genotypic variation of extractable proanthocyanidins concentration, a health beneficial compound, in bran of a set of pigmented rice accessions and identified genotypes high in proanthocyanidin concentration that can be used by breeders to develop new cultivars with improved bioactive proanthocyanidins. Research was also conducted that improved the throughput for analysis of these health beneficial compounds. A chemically mutated high amylose rice cultivar was determined to have several-fold higher resistant starch concentration than its original source. This line will be evaluated along with other germplasm accessions for resistant and slowly digestible starch using a lab protocol that has now been established. As a service to the US rice breeding community, several hundred breeding lines were characterized for traits associated with grain cooking quality. In addition, the most advanced selections from the breeders were characterized for genetic markers associated with grain cooking quality, blast disease resistance, and smooth leaves. New this year, we added percent grain chalk and a marker for a herbicide resistance gene that will be evaluated for the breeders in the future. As part of a NSF-funded project in collaboration with Cornell University, mapping populations that differ widely in various yield components were advanced and characterized. The first year of yield component data was collected on one mapping population in a replicated field study. Two other populations were advanced to the F7 and F8 generations. Leaf tissue was collected for genotyping by sequencing (GBS) that will occur in FY15. In addition, the final backcrossing was completed for two chromosome segment substitution libraries (sets) that are based on IR64 and different accessions of Oryza rufipogon. Genotyping results are being used to identify the progeny lines that are homozygous for the targeted segments prior to further backcrossing. In addition, BC3 lines between Jefferson and O. rufipogon that were previously shown to have enhanced yield were characterized for specific yield components in the greenhouse. Funding from the Organic Trade Center was used to determine the impact of cultivar and fertility management on grain arsenic accumulation. Preliminary results indicate that cultivars differ significantly in grain arsenic accumulation, with higher yielding varieties having higher grain arsenic. However, it was possible to minimize grain arsenic and maintain economic yields through choice of variety. In collaboration with University of Arkansas, Pine Bluff (1890s institution), research was conducted to ascertain genetic and soil factors associated with straighthead susceptibility. Response of a panel of diverse cultivars grown under straighthead inducing conditions was determined. Collaboration with University of California at Riverside on an NSF-funded project led to the development of a hydroponic salt screening method and evaluation of a mapping population and other germplasm that contain a transposable element, mPing. Preliminary results suggest that mPing insertions diminish tolerance to salt, perhaps by interruption of gene function.


4. Accomplishments
1. Health beneficial compounds in rice bran promote colon health. Having a diet that includes whole grains has been recommended by U.S. Department of Agriculture for many years. Research has shown that whole grain rice contains various antioxidant compounds that have been linked with health beneficial effects. ARS researchers in Stuttgart, Arkansas, and Houston, Texas, in collaboration with researchers at Colorado State University, evaluated the impact of six rice varieties on colon health in an animal study. Varieties differed in their impact on Salmonella infection and other immune response biomarkers. In general, increased immunity to Salmonella infection was associated with rice varieties that had high soluble fiber and vitamin E, among other compounds. A rice variety with purple bran was found to have the most positive impact on activating intestinal immunity. This research indicates that natural compounds in bran of some varieties of rice have potential for use in nutritional therapy.

2. Organic crop management does not change health beneficial compounds in rice. Various antioxidant compounds exist in the rice bran and have been associated with health beneficial effects. The organic food market and consumer interest in healthy foods continues to expand each year. ARS scientists in Stuttgart, Arkansas, evaluated brown and pigmented bran rice varieties grown under organic and conventional production systems to determine the impact on antioxidant compounds in the rice bran. There was little difference in concentrations of these compounds due to field management systems; however, pigmented bran cultivars had a four-fold increase in antioxidant activity as compared to brown bran cultivars. This research supports new market opportunities for pigmented bran rice cultivars grown under organic or conventional systems.

3. Assessment of flavor and texture qualities of cooked whole grain rice. Consumption of whole grain rice is recommended by the U.S. Department of Agriculture because of the health benefits associated with a whole grain diet. However, the key to successful rice commercialization is consumer acceptance of the eating quality of a new variety. ARS scientists at Stuttgart, Arkansas, and New Orleans, Louisiana, identified several physical and chemical traits associated with the texture and flavor of cooked whole grain rice and associated these with specific health beneficial compounds found in rice bran. This knowledge can be used to develop whole grain rice varieties with improved palatability and consumer acceptance.

4. Optimizing the "harvest" of health beneficial compounds in the rice grain for use in functional foods. Vitamin E homologs (tocopherols and tocotrienols) and gamma-oryzanol are antioxidants that are found in rice bran that have garnered significant attention due to potential human health benefits and due to interest by the food industry for use in increasing vegetable oil stability. Understanding the optimum growth stage to harvest rice that will maximize levels of these fat-soluble antioxidants is important for nutraceutical and functional food applications. ARS scientists at Stuttgart, Arkansas, and researchers at University of Nevada, Las Vegas, investigated the accumulation of these antioxidants during development of rice grains. The study identified that the immature rice grain has the highest amount of tocopherols, while the levels of the other antioxidants can be optimized by harvesting grain at maturity. This information will help develop new markets for natural ingredients that can be used in functional foods.

5. Reducing high temperature stress response in rice by blocking ethylene production. High night temperature (HNT) is recognized as a cause of yield loss in rice. The HNT triggers increased production of ethylene, a plant hormone, leading to oxidative stress and resulting in yield loss. ARS scientist at Stuttgart, Arkansas, and scientists at Texas A&M AgriLife Research, Beaumont, Texas, and Texas A&M University, College Station, Texas, treated plants grown under HNT with an ethylene blocker, 1-methylcyclopropene, and found that, as compared to untreated controls, these plants had increased yield, greater photosynthesis, decreased plant respiration and cell membrane damage in leaves, and increased seedhead fertility. The 1-methylcyclopropene has potential to minimize rice yield losses due to environmental stresses that affect oxidative stress in the foliage.

6. Rice varieties packed with nutrition. Biofortification is the process by which the nutritional quality of food crops is improved through conventional plant breeding and/or use of biotechnology. With the aim of identifying germplasm and genes useful for breeding biofortified rice varieties, 1763 rice accessions collected from 114 countries around the world were grown side-by-side in a replicated field study, resulting in the identification of rice cultivars having exceptionally high or low concentrations of one or more of 16 mineral elements. The selected rice cultivars were used as parents for creating cross-progeny to further characterize the inheritance of biofortification genes. Cross-progeny segregation patterns indicated that, for 6 of the 16 elements observed, the extreme grain phenotypes observed among the accessions were controlled by a single major gene. This will enhance breeding efforts for biofortification, because traits controlled by single major genes are more readily bred into improved varieties than traits known as quantitative or multi-gene traits.

7. Irrigation practices that reduce water use do not change rice cooking quality. Because most rice is grown under flooded field conditions, having sufficient water resources to sustain rice production in the USA is a major concern for the future. Research has been conducted to determine if rice can be economically grown using a furrow system with intermittent watering instead of a season-long flooded field. In addition to determining the impact upon yield and pest pressures in a furrow system, little is known about the impact this would have on rice cooking quality. ARS researchers in Stuttgart, Arkansas, in collaboration with the University of Arkansas, determined that adding or removing the flood mid-season using a furrow system would have little or no effect on grain cooking and processing quality. Thus, rice can be produced in a furrow system that reduces water use because the field is flooded for only part of the growing season with no negative impact on rice end-use quality.


Review Publications
Min, B., McClung, A.M., Chen, M. 2014. Effects of hydrothermal processes on antioxidants in brown, purple and red bran whole grain rice (Oryza sativa L.). Food Chemistry. 159:106-115.
Zhang, M., Pinson, S.R., Tarpley, L., Huang, X., Lahner, B., Yakubova, E., Baxter, I.R., Guerinot, M., Salt, D.E. 2014. Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain. Theoretical and Applied Genetics. 127(1):137-165.
Hu, B., Wan, Y., Yan, W., Xie, J. 2013. Phenotypic characterization and genetic analysis of rice (Oryza sativa L.) with pubescent leaves and glabrous hulls (plgh). Crop Science. 53:1878-1886.
Eizenga, G.C., Ali, L.M., Bryant, R.J., Yeater, K.M., McClung, A.M., McCouch, S. 2013. Registration of the Rice Diversity Panel I for genomewide association mapping studies. Journal of Plant Registrations. 8(1):109-116.
Pinson, S.R., Jia, Y., Gibbons, J. 2013. Three QTLs conferring resistance to kernel fissuring in rice (Oryza sativa L.) identified by selective genotyping in two tropical japonica populations. Crop Science. 53:2434-2443.
Norton, G.J., Douglas, A., Lahner, B., Yakubova, E., Guerinot, M., Pinson, S.R., Tarpley, L., Eizenga, G.C., Mcgrath, S.P., Zhao, F., Islam, M., Islam, S., Duan, G., Zhu, Y., Salt, D.E., Meharg, A.A., Price, A.H. 2014. Genome wide association mapping of grain arsenic, copper, molybdenum, and zinc in rice (Oryza sativa L.) grown at four international field sites. PLoS One. 9(2):e89685.
Pinson, S.R., Tarpley, L., Yan, W., Yeater, K.M., Lahner, B., Yakubova, E., Huang, X., Zhang, M., Geurinot, M., Salt, D.E. 2015. World-wide genetic diversity for mineral element concentrations in rice grain. Crop Science. 55:1-18. doi:10.2135/cropsci2013.10.0656.
Shakiba, E., Eizenga, G.C. 2014. Unraveling the secrets of rice wild species. In: Yan, W., Bao, J., editors. Rice - Germplasm, Genetics and Improvement. InTech. DOI. 10.5772/58393.
Bett Garber, K.L., Lea, J.M., McClung, A.M., Chen, M. 2013. The correlationship of sensory, cooking, physical and chemical properties of whole grain rice with diverse bran color. Cereal Chemistry. 90-6:521-528.