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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
2011 Annual Report


1a.Objectives (from AD-416)
Objective 1: Phenotypically and genotypically characterize the rice National Small Grains Germplasm Collection (NSGC) and conserve genetic stocks, mutants, and mapping populations in the Genetic Stocks Oryza (GSOR) to promote greater use by the research community. Sub-objective 1.A. Characterize accessions in the NSGC rice collection for 27 descriptors and rejuvenate seed of low inventory genetic seedstocks. Sub-objective 1.B. Perform structure analysis following genotypic and phenotypic evaluation of the NSGC Core collection. Sub-objective 1.C. Expand the GSOR collection to 15,000 accessions and establish a web-based ordering and distribution system. Objective 2: Evaluate rice germplasm to identify genetic resources having enhanced nutritional properties and added-value for the food industry. Sub-objective 2.A. Identify genetic variability for antioxidant capacity and the content of main classes of polyphenols and carotenoids in rice germplasm. Sub-objective 2.B. Structurally identify and quantify major flavonoid and proanthocyanidin compounds in rice genotypes with different bran color. Sub-objective 2.C. Determine the effect of processing on rice bran phytochemicals. Sub-objective 2.D. Identify quantitative trait loci (QTL) associated with rice grain elemental content. Sub-objective 2.E. Measure genotype and environment interactions on starch structure and grain quality. Sub-objective 2.F. Determine the impact of non-conventional cultural management practices on rice grain quality. Objective 3: Map new resistance genes for blast disease and straighthead disease identified in germplasm accessions. Sub-objective 3.A. Mine novel blast resistance genes from indica rice germplasm for use in U.S. breeding programs. Sub-objective 3.B. Decipher genetic mechanism for resistance to straighthead, a physiological disease. Objective 4: Map genes associated with grain quality traits, including rice paste viscosity and grain chalk. Sub-objective 4.A. Genetically map starch paste viscosity variation as a predictor of rice processing quality. Sub-objective 4.B. Genetically map grain chalk formation which influences milling quality.


1b.Approach (from AD-416)
Additional germplasm and data will be added to the NSGC rice collection for distribution to the public via GRIN. The Core collection will be characterized for sheath blight disease resistance, grain mineral accumulation, straighthead tolerance, protein content, and cold tolerance, and genetic markers will be identified that are associated with these traits. The Genetics Stocks Oryza (GSOR) collection will be expanded to 15,000 accessions that are curated and distributed to the research community through a searchable on-line database. Selected accessions from the NSGC collection will be evaluated for health- beneficial compounds like polyphenols, flavonoids, and carotenoids, and the influence of the environment and processing methods on levels of these compounds will be evaluated. Germplasm will be evaluated under flooded and aerobic conditions to understand the genetic mechanisms controlling nutrient uptake. Mapping populations will be developed,and rice gene microarray chips will be used to identify chromosomal regions associated with nutrient uptake. The genotype x environment interaction on key enzymes in the starch pathway will be studied to determine how they impact starch structure and processing quality. In an effort to understand how rice quality will be impacted by crop rotation systems, 5 to 10 rice cultivars will be grown using conventional tillage/no-till, permanent flood/intermittent-flushing, different fertilization rates, and different crop rotations, and agronomic and cooking quality traits will be evaluated to provide insight as to how changing cropping systems will impact rice milling and cooking quality. Novel genes for blast and straighthead disease resistance will be identified using mapping populations. Markers and germplasm will be released to breeders for developing improved cultivars. Sequence variation around a SNP in exon 10 of the rice Waxy gene will be evaluated to determine what impact it has on RVA paste viscosity characteristics. Genetic markers will be developed that can be used in breeding for elevated pasting profiles, which is desired for rice used in canning, instantizing, and other food preparation processes. We will fine map several QTL previously identified to be associated with grain chalk. Progeny from the selected recombinant lines will be grown in two environments and chalk amounts quantified with a Winseedle Image analysis system. Segregation of tightly linked SSR and SNP markers will be analyzed to pinpoint recombination points and candidate genes in the finely mapped region. Genetic markers developed from this research will be used by breeders to develop new cultivars that have greater translucency, higher milling yield, and consistent cooking quality.


3.Progress Report
Progress was made in the rice breeding program, with nine advanced lines being entered into the five-state Uniform Rice Regional Nursery. One of these entries was developed from a cross with a wild species of rice, Oryza rufipogon, as part of an NSF-funded project with Cornell University. A summary of three years of advanced yield trials demonstrated that this line has improved yield potential as a result of incorporation of portions of the wild species genome, and it will be released as an improved genetic stock for use by breeders. In addition, genetic marker analysis was conducted on the 200 rice entries in the Uniform Rice Regional Nursery, and results were presented to researchers at the annual breeders meeting. This information is used to verify presence of disease resistance genes and cooking quality traits in cultivars before they are released for commercialization. As a next step in our on-going research on organic rice production, segregating breeding lines were evaluated under both conventional and organic fertility inputs. The objective is to determine if there is a difference in which are selected as the best performing lines depending on the fertility inputs used. Six rice cultivars were produced under both conventional and organic management, and were evaluated for concentration of several antioxidant compounds in the grain, which are associated with human health benefits. Results indicated that cultural management methods generally did not significantly change concentrations of antioxidants, but year of production and choice of cultivar had larger effects. This indicates that cultivars can be selected that possess high concentrations of specific antioxidant compounds that may have human health benefit.


4.Accomplishments
1. Wild species of rice possess high levels of health beneficial compounds. The demand for rice bran and its oil is increasing as consumers learn about its potential to reduce the incidence of chronic diseases. Antioxidants, including vitamin E and gamma-oryzanols found in rice bran and oil, are associated with some of these health benefits. Although wild species of rice are known to contain valuable traits, such as resistance to diseases, pests, and abiotic stress, they have not been evaluated for health-promoting compounds in the grain. Researchers in Beaumont, Texas, and at the University of Nevada, Las Vegas, identified higher levels of antioxidants in wild species compared to cultivated rice, suggesting that these Oryza species could be used as breeding materials for rice improvement. Development of a cultivar with enhanced levels of these fractions would be desirable for use in the production of high gamma-oryzanol margarine, shortening, and frying oils.

2. Registration of 'Jazzman', an aromatic long-grain rice. The demand for aromatic rice has dramatically increased over the past two decades in the United States, and currently there are three major classes of aromatic rice in the U.S. market, which include Jasmine, Basmati, and Della types. Most of the soft-cooking Jasmine and elongating Basmati rice in the U.S. market is imported, and the volume of such imports is increasing every year. Currently, there are few cultivars that can be domestically produced that are suitable for these markets. Scientists in Beaumont, Texas, and at Louisiana Agricultural Experiment Station in Crowley developed an aromatic rice cultivar Jazzman, which is well-adapted to the Gulf- and mid-south rice growing regions. This cultivar should enable the U.S. rice industry to better compete with imports targeted at this high-valued niche market.

3. Registration of a genetic population for fine mapping genes in rice. TeQing is a rice cultivar from China that is known to have high yield and pest resistance traits. Identifying the genes that control these traits and incorporating them into U.S. adapted genetic stock will provide a rich resource for breeders to develop new cultivars. ARS scientists at Beaumont, Texas developed a new rice mapping population from Lemont, a U.S. cultivar, and TeQing using the backcrossing method. The population contains 123 chromosome segment substitution lines that are predominantly Lemont but possess small portions of the TeQing genome that are tagged with genetic markers. This population has already proven useful for verifying and precisely mapping chromosomal regions associated with sheath blight disease resistance, tiller production, and flowering time. The population can be used to transfer these traits into new modern U.S. rice cultivars, as well as to identify new gene-trait associations.

4. Exploring rice genetic resources for improved nutritional quality. In some areas of the world where rice is grown under flooded conditions, high levels of naturally occurring arsenic can be found in soils and irrigation water, and then can accumulate as inorganic arsenic in the edible rice grains, posing a threat to human health. It would be desirable to develop rice varieties that accumulate less arsenic in their grains, either through reduced uptake from the soil or by sequestering the arsenic in non-edible portions of the plant, such as roots or leaves. ARS scientists at Beaumont, Texas, in collaboration with an international research team, evaluated arsenic content of over 300 international rice varieties grown under six global field environments in the USA, Bangladesh, and China. They determined that inorganic arsenic levels can be accurately predicted using a method that measures total grain arsenic. They also found that choice of variety was a large determining factor in grain arsenic content, indicating cultivars low in grain arsenic could be developed through breeding. Three varieties that were especially low in grain arsenic content across the various environments were identified and will be used in future studies to determine the physiological and genetic factors that limit the accumulation of arsenic in rice grains.

5. Unraveling the complex genetic factors that control rice milling yield. Rice crop value is largely determined by field yield and milling quality, the proportion of whole grains produced after milling. However it is difficult to breed for improved milling quality because it is a trait controlled by many genes. ARS researchers participated in a multi-state USDA-funded project called RiceCAP that endeavored to identify chromosomal regions and genetic markers that could be used to select for improved rice milling quality. Four chromosomal regions were identified that were consistently associated with higher milling across the two years that the study was conducted in California. Other traits were found to influence milling quality, but were not good predictors for making breeding selections. Results demonstrated that further research is needed to study how grain structural development is influenced by the growing environment before marker-assisted selection can be used for milling quality in rice.


Review Publications
Min, B., McClung, A.M., Chen, M.H. 2011. Phytochemicals and antioxidant capacity in rice brans of different color. Journal of Food Science. 76:C117-126.

Heuberger, A.L., Lewis, M.R., Chen, M., Brick, M.A., Leach, J.E., Ryan, E.P. 2010. Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice. PLoS One 5:e12915.

Sha, X., Linscombe, S., Jodari, F., Chu, O., Groth, D., Blanche, S., Harrell, D., White, L., Oard, J., Chen, M., Theunissen, S., Blake, H. 2011. Registration of 'Jazzman' aromatic long-grain rice. Journal of Plant Registrations. 5:304-308.

Chen, M., Fjellstrom, R.G., Christensen, E.F., Bergman, C.J. 2010. Development of three allele-specific codominant rice Waxy gene PCR markers suitable for marker assisted selection of amylose content and paste viscosity. Molecular Breeding. 26:513-523.

Traore, K., McClung, A.M., Chen, M., Fjellstrom, R.G. 2011. Inheritance of starch paste viscosity is directly associated with a rice Waxy gene exon 10 SNP marker. Journal of Cereal Science. 53:37-44.

Bergman, C.J., Goffman, F.D., Chen, M.-H. 2011. Evaluation of antioxidant, lipid, and protein fractions of accessions of Oryza Species. Cereal Chemistry. 88:283-290.

Last Modified: 8/29/2014
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