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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

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
Significant progress was made in all aspects of the project. Due to budget restrictions and technician vacancies a few of the milestones were not met by year end. A number of the NPGS rice accessions were not successfully increased in our winter nursery due to poor seed viability. These materials will be recovered using greenhouse facilities or embryo rescue methods. The GSOR collection was expanded by 528 entries this year, for a total of 34,512 accessions. Included is a rice diversity panel developed as part of a NSF-funded project with Cornell University. For the first time, rice genetic marker data was uploaded to GRIN using data from this panel of 409 accessions and 36 markers. GSOR has shipped 3541 rice samples to US researchers and 5372 samples to international researchers in eight countries this year. The Mini-Core collection representing 1% of the entire NPGS rice has been used in association mapping studies to identify chromosomal regions linked with yield, disease resistance, and grain nutrient content. In addition, this year we completed an association analysis of the Mini-Core for hull silica content, which can be used in the production of high-valued industrial compounds. The second year of a field study to evaluate variation in rice cultivars for parameters that impact processing and canning quality was conducted, and analytical tests were completed for the first year of the trial. Due to budget limitations, all enzyme analyses associated with the starch biosynthesis pathway will not be completed until 2013 for this study. Research originally proposed to evaluate the impact of various cultural management aspects on grain cooking and processing quality has demonstrated little positive impact. Thus, resources were redirected to study new methods of analysis and genetic variability for compounds that influence rice flavor and aroma. Two new methods were developed to measure the compound that causes the popcorn-like flavor in aromatic rice. In addition, nearly 100 volatile compounds were identified that may influence flavor, and some of these were unique to aromatic cultivars. A study was conducted with the Southern Regional Research Center to develop a sensory lexicon for describing flavor of whole grain brown rice. This is the first step in studying the sensory and nutritional components of brown rice having different bran colors that may lead to new food products. Initial plans to evaluate the 1800 entries of the NSGC Core collection for paste viscosity variation were modified to use a smaller set (190) of accessions that are also being used to study grain nutritional compounds. This will save resources by using genotypic information already collected on the smaller set in an association analysis. We are making progress in identifying genetic markers associated with grain chalk. This year, two mapping populations that are segregating for chalk are being produced in the field, and an improved method for quantifying grain chalk using an image analysis system has been developed. Phenotypic analysis will be conducted after this year's harvest, and initial QTL mapping will be completed by the end of 2012.


4.Accomplishments
1. Improvement of grain yield in rice using genetic markers. Yield is the most important and complex trait in crops, and it is difficult to improve through breeding. Yield improvement in rice will directly impact food production in the USA and world. ARS scientists at Stuttgart, Arkansas, and researchers at the University of Arkansas and Zhejiang University evaluated the USDA rice Mini-Core collection for 14 yield-related traits and with 155 molecular markers. This work led to the identification of four markers directly associated with yield, along with 17 other markers that indirectly impacted yield potential. These markers and the characterized genetic accessions can be used by breeders to efficiently improve yield potential in new cultivars.

2. Identification of rice genetic accessions resistant to sheath blight disease for use in cultivar improvement. Sheath blight is one of the most devastating diseases in rice production worldwide, but no sources of absolute genetic resistance have been identified. ARS scientists at Stuttgart, Arkansas, and researchers at the University of Arkansas and Zhejiang University screened the USDA Rice Core Collection and identified 52 accessions having greater resistance to sheath blight than had been previously identified. These resistant accessions are globally available for cultivar development and will help reduce yield losses due to this disease.

3. The USDA Rice Mini-Core Collection is a resource for gene mapping. Having an understanding of the genetic structure and diversity within a germplasm collection is the first step for utilizing the collection for breeding and for mapping important genes. ARS scientists at Stuttgart, Arkansas, and researchers at the University of Arkansas and Zhejiang University comprehensively characterized the Mini-Core collection for 14 traits and 128 molecular markers. The results demonstrated that the Mini-Core is an ideal collection for gene identification and mapping because it is a relatively small collection that is representative of global rice germplasm diversity.

4. Only a few markers are needed to classify diverse rice accessions. Cultivated rice is grown in many different growing environments but can be classified into five basic sub-populations. Depending on the objectives of breeders and geneticists, germplasm may be chosen from one or more of these sub-populations for crossing or other genetic studies. Having the means to quickly classify the genetic background of genetic resources is essential for the design of various genetic studies and cultivar improvement projects. ARS and University of Arkansas scientists at Stuttgart, Arkansas, developed a molecular marker panel using the diverse USDA Rice Core Collection that will clearly differentiate the five rice sub-populations. Each panel consists of only 3 – 4 microsatellite markers and has more than 90% accuracy for population assignment. These markers provide a quick and inexpensive method to classify rice germplasm for initiating breeding and genetic studies.

5. Improvement of rice nutritional quality with water management. In some parts of the world, rice is grown where natural levels of arsenic in the soil and water are high. Under these conditions, arsenic can be absorbed by the rice plant and accumulate in the grain. Because arsenic is potentially toxic to humans, it is important to reduce rice grain arsenic concentrations, particularly in populations that rely upon rice as their primary source of food. ARS scientists at Stuttgart, Arkansas, and researchers at Texas A&M University found that growing rice using intermittent irrigation rather than continuous flooding decreased arsenic concentration in the rice root zone by 41-81% and by 31-48% in the rice grain. The arsenic reductions were due to changes in the microbial communities, including bacteria and fungi, that were affected by water management in the rice field. These results demonstrate that farmers can improve the nutritional quality of rice through modified irrigation management.

6. 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.

7. Sustainable rice production practices have no negative impact on rice cooking quality. Farmers are continually adopting new production practices that will conserve resources and yet maintain high field yields. ARS and University of Arkansas researchers conducted a study to determine the impact of crop rotation systems and new water-saving irrigation and nutrient management practices on rice cooking and processing quality. It was found that the addition of slow release fertilizers and crop rotation with soybeans did alter grain protein concentrations in rice, but had little impact on other measures of grain cooking quality. Thus, farmers have flexibility in using cultural management systems that reduce production costs and save resources without negatively impacting cooking quality.

8. Identifying the volatile compounds in cooked rice. When rice is cooked, natural compounds in the grain are released that give it a unique grain flavor. Aromatic rice cultivars are some of the most valued in the marketplace because they are known to possess specific compounds that give a buttery or popcorn flavor. ARS researchers at Stuttgart, Arkansas, identified 93 different volatile compounds in a set of aromatic and non-aromatic rice cultivars. Sixteen compounds were found only in aromatic cultivars, and some of these were unique to specific cultivars. This study showed that there is a great diversity of volatile compounds in both aromatic and non-aromatic rice, which may lead to a better understanding of the combination of compounds that gives a cultivar a unique flavor.


Review Publications
Bryant, R.J., McClung, A.M. 2011. Volatile profile of aromatic and non-aromatic rice cultivars using SPME/GC-MS. Food Chemistry. 124(2):501-513.

Li, X., Yan, W., Agrama, H., Hu, B., Jia, L., Jia, M.H., Jackson, A.K., Moldenhauer, K., McClung, A.M., Wu, D. 2010. Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection. Genetica. 138(11):1221-1230.

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.

Nelson, J.C., McClung, A.M., Fjellstrom, R.G., Moldenhauer, K.K., Boza, E., Jodari, F., Oard, J.H., Linscombe, S., Scheffler, B.E., Yeater, K.M. 2011. Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm. Theoretical and Applied Genetics. 122(2):291-309.

Somenahally, A., Hollister, E.B., Loeppert, R.H., Yan, W., Gentry, T.J. 2011. Microbial communities in rice rhizosphere altered by intermittent and continuous flooding in fields with long-term arsenic application. Soil Biology and Biochemistry. 43(2011):1220-1228.

Li, X., Yan, W., Agrama, H., Jia, L., Shen, X., Jackson, A., Moldenhauer, K., Yeater, K., McClung, A., Wu, D. 2011. Mapping QTLs for improving grain yield using the USDA rice mini-core collection. Planta. 234(2):347-361.

Jia, L., Yan, W., Agrama, H.A., Yeater, K.M., Li, X., Hu, B., Moldenhauer, K., McClung, A.M., Wu, D. 2011. Searching for germplasm resistant to sheath blight from the USDA Rice Core Collection. Crop Science. 51(4):1507-1517.

Bryant, R.J., Anders, M.M., Mcclung, A.M. 2011. Impact of Production Practices on Physicochemical Properties of Rice Grain Quality. Journal of the Science of Food and Agriculture. DOI 10.1002/jsfa.4608.

Grimm, C.C., Champagne, E.T., Lloyd, S.W., Easson, M.W., Condon, B.D., Mcclung, A.M. 2011. Analysis of 2-Acetyl-1-Pyrroline in rice by SBSE/GC/MS. Cereal Chemistry. 88(3):271-277.

Miller, H.B., Grace, S.C. 2010. Variations in bran carotenoids levels within and between rice subgroups. Plant Foods for Human Nutrition. 65:358-363.

Hua, B., Yan, W., Wang, J., Deng, B., Yang, J. 2011. Arsenic accumulation in rice grains: Effects of cultivars and water management practices. Environmental Engineering Science. 28(8):591-596.

Somenahally, A.C., Hollister, E.B., Yan, W., Gentry, T.J., Loeppert, R. 2011. Water management impacts on arsenic speciation and iron-reducing bacteria in contrasting rice-rhizosphere compartments. Journal of Environmental Science and Technology. 45:8328-8335.

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.

Last Modified: 9/10/2014
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