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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

Location: Dale Bumpers National Rice Research Center

2009 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
Each year rice breeders from the southern US evaluate 200 potential new cultivars as part of the Uniform Rice Regional Nursery (URRN). Data from the six past years of this study have been organized and posted to our website for use by the breeding community. Yield tests were completed that evaluated over 60 breeding lines that were derived from a cross between the cultivar Jefferson and the wild weedy relative O. rufipogon. Results from these tests, along with data from 2007, demonstrated that genes from the weedy species resulted in a 20% increase in grain yield. Two of the best lines from this project have been entered into the 2009 URRN trial. Plans were made and a study implemented in 2009 to evaluate the mini-core for biomass production and yield components that is being conducted in Arkansas and Texas. A collaboration was established with the Southern Regional Research Center (SRRC), New Orleans, LA, to evaluate aromatic cultivars from different sources to determine if a sensory panel can detect different flavors.


4.Accomplishments
1. Development of the USDA rice mini-core collection for mining valuable genes: Because the USDA ARS collection of rice is so large, including more than 18,000 cultivars collected from 116 countries, it is difficult for researchers to know how to effectively use it. ARS scientists in Stuttgart, Arkansas, developed a mini-core subset from the USDA rice collection containing only 217 accessions but which captures the full range in variation of 26 traits found in the whole collection. In addition, evaluation with 70 microsatellite DNA markers revealed over 900 alleles, indicating wide genetic diversity. The rice accessions in the mini-core are publicly available through GRIN and GSOR and can be used by researchers to mine important genes from the USDA world collection of rice.

2. Identification of rice cultivars resistant to straighthead and development of molecular markers for use in breeding: Straighthead is a physiological disorder in rice resulting in poor seed set and yield loss. The only known cultural management methods of control add significant costs to farmers in water and energy use. ARS scientists in Stuttgart, Arkansas, identified rice cultivars resistant to straighthead and developed DNA markers linked with this trait. Forty-two resistant cultivars introduced from 15 countries were identified from 1,002 accessions in the USDA world rice collection. An analysis of the cultivars with 75 microsatellite markers identified markers on chromosomes 5 and 12 associated with straighthead resistance. The resistant cultivars and the associated genetic markers will be valuable to breeders to develop improved cultivars for effective control of this disorder that will reduce rice production costs.

3. Genetic markers are identified that are linked with a trait important for rice hybrid seed production: The length of time that the stigma, the female part of the rice flower, is exposed to pollen is an important factor for cross pollination and hybrid seed production. ARS scientists in Stuttgart, Arkansas, identified DNA markers that are linked with stigma exsertion in rice. Ninety rice accessions selected from the USDA rice core collection were evaluated in the field for nine traits characterizing flowering parts of the rice plant. The genetic material was also evaluated with 109 microsatellite genetic markers. Four markers were associated with single stigma exsertion, six with dual exsertion, and five with total exsertion. These markers will be useful to breeders to select for flowering characteristics that will improve hybrid seed production in rice.

4. Genetic mapping of texture properties in high amylose US rice: High amylose rice varieties fill an important market class in the US rice industry, but their texture (grain firmness and paste viscosity) properties can vary considerably. Scientists at the USDA-ARS Rice Research Unit in Beaumont, Texas, and the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas, have identified and mapped genetic markers indicating the presence of specific genes controlling rice texture characteristics. Results showed that the largest changes of rice texture differences are regulated by a single gene that makes a starch synthesis enzyme in developing rice grains. DNA markers for this gene can be used in marker-assisted breeding to develop improved rice varieties with the textural attributes needed for superior processing quality markets.

5. Effect of cultural management practices on grain quality of two rice cultivars: In order to increase profits, farmers are trying two new ways of growing rice--by crop rotation and increased fertilization. How these two interact to affect the cooking and processing quality of rice is not well understood. Scientists at the Dale Bumpers National Rice Research Center and at the University of Arkansas Rice Research and Extension Center in Stuttgart, Arkansas ,looked at three crop rotation systems (continuous rice, rice/soybeans, rice/corn) and two nitrogen rates (recommended and 1.5 X recommended) and found that increasing nitrogen increased the protein content and changed the processing quality. Crop rotation determined the magnitude of the change, with continuous rice having the least effect and rice/soybeans having the greatest effect. However, the magnitude of the changes were not expected to have a significant impact on processing quality. A manuscript on this work has been published.

6. Rice grain quality as influenced by flooded and aerobic managed production systems: Planting rice in rows can be a great benefit to farmers by reducing their irrigation costs. However, what effect this may have on cooking and processing quality has not been fully evaluated. Scientists at the Dale Bumpers National Rice Research Center in collaboration with scientists at the University of Arkansas Rice Research and Extension Center in Stuttgart, Arkansas, evaluated two rice cultivars to determine the influence of irrigation practices, sources of nitrogen, and crop rotation have on cooking and processing quality. The results showed that although yields were affected, there was little impact on factors associated with processing and cooking quality. A manuscript on this research has been drafted and submitted to a journal.

7. Volatiles that may be linked to flavor differ among aromatic and non-aromatic rice cultivars: Little is known about the flavor compounds of scented rice and whether storage time and temperature has an effect on flavor. Scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas, determined the volatile profiles of nine rice cultivars before and after storage using SPME/GC-MS. Ninety-three volatile compounds were identified, 64 of which had not been previously reported in rice. A number of compounds were identified that were unique to aromatic rice cultivars other than 2-acetyl-1-pyrroline, the compound that gives scented rice its popcorn flavor. However, no pattern of volatile profiles were observed that were unique to basmati- or jasmine-derived aromatic rice cultivars. In addition, storage time and temperature had little effect on the volatile profiles. Further research is needed to relate variation in volatile profiles with differences in quantity of these compounds and how these may impact rice flavor.

8. Development of a single kernel analysis method for detection of 2-acetyl-1-pyrroline in aromatic rice germplasm: Due to increased demand for aromatic rice, rice breeders want to develop improved aromatic cultivars having high yield and milling quality as well as desirable flavor properties. To aid in this process, scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas, have developed an efficient method of detecting varieties that possess the 2-acetyl-1-pyrroline (2-AP) compound which gives aromatic rice a popcorn or nutty natural flavor and distinguishes it from non-aromatic rice. A method was developed that can utilize just a single kernel to detect the 2-AP compound. The method will be useful to researchers in identifying aromatic kernels from non-aromatic kernels; to breeders in developing new aromatic cultivars; and to representatives of the rice industry interested in identifying possible adulteration of aromatic rice products with non-aromatic rice.

9. New method for selecting improved milling quality in rice: Rice milling quality is a complex trait difficult to select for in breeding programs. Scientists at the Rice Research Unit in Beaumont, Texas; Dale Bumpers National Rice Research Center in Stuttgart, Arkansas; and University of Arkansas, at Stuttgart, Arkansas, documented a new method for resistance to rice kernel fissuring using a laboratory technique that requires only a small amount of seed. Seed of genetic lines segregating for milling quality were exposed to controlled levels of humidity. Rice lines that were selected to be resistant or susceptible to fissuring were found to maintain their fissuring rating in subsequent generations. This new laboratory method will help geneticists to map fissure resistance genes and breeders to eliminate fissuring susceptible offspring early in the breeding process so that they can focus on resistant progeny for further trait selection.


6.Technology Transfer

Number of New Germplasm Releases2

Review Publications
Miller, H.B. 2009. Induced postharvest yellowing in Southern U.S. rice cultivars. Cereal Chemistry. 86(1):67-69.

Tabien, R.E., Samonte, O.B., McClung, A.M. 2008. Forty eight years of rice improvement in Texas since the release of cultivar Bluebonnet in 1944. Crop Science. 48:2097-2106.

Agrama, H.A., Yan, W., Lee, F.N., Fjellstrom, R.G., Chen, M., Jia, M.H., McClung, A.M. 2009. Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Science. 49:1336-1346.

Dabul, A., Miller, H.B., Roychowdhury, M., Hubstenberger, J.F., Lorence, A., Phillips, G.C. 2009. Screening of a broad range of rice (Oryza sativa L.) germplasm for in vitro rapid plant regeneration and development of an early prediction system. In Vitro Cellular and Developmental Biology - Plants. 45 (4):414-420.

Yan, W., Agrama, H.A., Slaton, N.A., Gibbons, J.W. 2008. Soil and plant minerals associated with rice straighthead disorder induced by arsenic. Agronomy Journal. 100:1655-1661.

Bryant, R.J., Anders, M.M., McClung, A.M. 2009. Effect of cultural management practices on the grain quality of two rice cultivars. Cereal Chemistry. 86(4):405-409.

Chen, M., Bergman, C.J., Pinson, S.R., Fjellstrom, R.G. 2008. Waxy gene haplotypes: Associations with pasting properties in an international rice germplasm collection. Journal of Cereal Science. 48:781-788.

Last Modified: 7/25/2014
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