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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

2015 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:
Progress has been made although 2 scientific positions have been vacant since the inception of the project and 3 new scientific vacancies occurred during 2014/15 along with several support vacancies. The agreement with University of Puerto Rico continues to be important for advancing genetic materials for research and rejuvenating accessions from the National Plant Germplasm System (NPGS) world rice collection. About 3,300 varieties were planted in the winter nursery and some 1,100 genetic lines were selected for on-going research. The third year of a collaborative grant with the 1890’s University of Arkansas at Pine Bluff has resulted in identification of novel rice germplasm that is resistant to straighthead – a physiological disease associated with soil arsenic. A National Science Foundation (NSF) funded project with University of California, Riverside has identified genomic regions that are associated with agronomic traits that are affected by a transposon mPing. Due to the increasing incidence of diabetes, there is interest in exploring rice genetic variability that impacts starch digestibility. Resistant starch, which escapes digestion in the small intestine, but is partially or entirely fermented in the colon, has promising physiological impact on colon health, and in preventing cardiovascular diseases, and postprandial glycemia and insulinemia and reduces body fat. From the preliminary results of the first field trial, we found high diversity in resistant starch concentration among 42 U.S. and global rice accessions. Rice bran is a rich source of bioactive components that can promote gastrointestinal health. Feruloylated arabinoxylan oligosaccharides, a dietary fiber component, and rice bran polyphenolics are hypothesized to have positive impacts on human gut microbiota. As part of a collaborative grant with scientists at University of Arkansas, Fayetteville, and Arkansas State University, Jonesboro, Arkansas, these compounds were assessed for their ability to increase production of short-chain fatty acids (SCFA), which are known to have positive impact on colon health. Fresh fecal samples collected from healthy adults with no symptoms of bowel disease were treated with these compounds. SCFA were significantly increased as a result of microbiotic fermentation of the feruloylated arabinoxylan oligosaccharides; while synergistic effects of rice bran polyphenolics and arabinoxylan oligosaccharides were observed. Results from this study suggest prebiotic properties of these bioactive components isolated from rice bran. Some of the projects that have been slowed as results of the vacancies include mapping of grain chalk, mapping of grain arsenic accumulation, and developing improved rice germplasm through marker assisted selection. In addition, research on grain arsenic accumulation has been slowed with the finding that the inexpensive assay for total arsenic is not strongly related to inorganic arsenic levels which are determined through more expensive speciation analyses. Thus, resources are being used to assess inorganic arsenic levels among different cultivars in response to irrigation and soil treatments. Other work on the biochemistry of arsenic uptake has indicated that varieties that are arsenic excluders may sequester more arsenic in the leaves and may differ in glutathion metabolism at the seedling stage. Although some milestones have been delayed, it is expected by the end of the project plan significant accomplishments will be made in all objectives. The exception to this is Obj. 2D: Characterize QTLs associated with rice milling yield, which we have now discontinued because the progeny that were to be used to more closely map this trait were found to not be segregating in the targeted region.


4. Accomplishments
1. Bioactive compounds in purple and red rice bran increases glucose uptake in fat cells. Most rice varieties have grain with brown bran but there are others that have purple or red bran. These pigmented rice brans contain bioactive compounds, which are reported to have health-beneficial potential. ARS scientists at Stuttgart, Arkansas, and New Orleans, LA, examined the extracts from purple and red rice brans, as well as typical brown bran, to determine their ability to stimulate glucose uptake in a human cell culture system. Extracts from red and purple brans increased glucose uptake as compared to brown bran and the stimulative effects were attributed to the increase of glucose transporter proteins located in the cultured cell membranes. This study suggests the potential of red and purple bran extracts as an intervention to prevent hyperglycemia by helping to remove glucose from the bloodstream.

2. Growing the right cultivar can reduce accumulation of arsenic in rice. Rice is typically grown under flooded field conditions which results in soil microbial populations developing that can make naturally occurring soil arsenic available for plant uptake. ARS researchers at Stuttgart, Arkansas, and Beltsville, Maryland, and in collaboration with scientists at Texas A&M Agrilife, Beaumont, Texas, determined that rice cultivars differ in the amount of arsenic that is accumulated in the grain. Choosing the right cultivar to grow was much more effective in reducing arsenic in the grain than altering fertilizer applications, using cover crops in the previous season, or growing the rice under conventional or organic systems. Choosing the right variety to grow is a relatively inexpensive method to be assured of low grain arsenic levels in rice.

3. Exploiting the natural genetic diversity in rice to meet the challenges of increased and sustainable production, improved nutrition, and adaptation to climate extremes. Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. Development of new crop varieties that can be grown under sustainable production systems and which are resilient to climate change will be necessary to meet this increased demand. ARS researchers at Stuttgart, Arkansas, in collaboration with researchers at Cornell University and the International Rice Research Institute in the Philippines assembled a large collection of 1,568 rice cultivars from around the world and a set of 700,000 DNA markers, called single nucleotide polymorphisms (SNPs), to characterize the collection at a genetic level. This information provides a new way of evaluating genetic variability among diverse rice cultivars that will help researchers develop better utilization strategies for breeding new cultivars. The SNP markers will help identify genes that control economically important traits which can be efficiently combined in new breeding lines. The power of this methodology was demonstrated by identifying SNP markers linked with grain length, a major factor in determining rice market classes. A better understanding of the relationship of genetic sequence information with important agronomic traits will help breeders deal with the challenges of increasing production especially on marginal land, adapting to extremes in climate, and developing more sustainable agricultural systems.

4. Rice varieties with pigmented bran contain high concentrations of health beneficial compounds. Proanthocyanidins are natural compounds that are associated with red and purple pigments in plants and have been shown to have potential in the prevention and modulation of some chronic diseases. ARS scientists at Stuttgart, Arkansas, have screened some 30 rice varieties from around the world for differences in concentration of proanthocyanidins. A 4.3-fold variation in proanthocyanidins concentration was found, and four rice varieties having red bran were identified with significantly higher concentrations than others. 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.

5. Genetic markers that can aid breeding for improved rice milling quality. Fissuring or cracking of rice kernels can occur prior to harvest or during grain storage and this reduces crop value for producers, millers, and processers because the broken rice kernels command about half the market value of unbroken kernels. ARS researchers in Stuttgart, Arkansas, discovered three new chromosomal regions in rice that appear to possess genes that result in fissure-resistance. It was further shown that when these three regions were combined with three previously discovered chromosomal regions in progeny from a breeding cross, that even greater levels of kernel fissure resistance could be achieved. These results will be useful to breeders for developing new rice cultivars that have high and stable milling quality which will benefit farmers and rice milling companies.

6. Reducing nitrogen fertilizer application does not impact rice processing quality. Rice used in canned, frozen or other convenience products is processed by parboiling and other methods. Industry prefers rice varieties that provide consistent processing quality regardless of field production methods used. ARS researchers at Stuttgart, Arkansas, determined that rice varieties that are suited for parboiling are stable in processing quality across a range of field fertilizer inputs. These results demonstrate that if farmers cut back on fertilizer application, reducing input costs and possible impacts on the environment, that they can still deliver high quality rice to processors.

7. A new genetic resource designed for elucidating gene function and developing superior rice cultivars. Rice is a diploid species having 12 pairs of chromosomes, or 24 total chromosomes. Rice plants with an additional single chromosome, thus three copies of a particular chromosome, have 25 total chromosomes and are called trisomic plants. In many cases, the presence of the additional chromosome changes the growth and development of the rice plant and thus these trisomic plants can be used to identify the chromosomal location of genes which control these traits. A set of trisomic lines was developed using the rice variety IR36 developed at the International Rice Research Institute (IRRI) in the Philippines. ARS researchers at Stuttgart, Arkansas, brought 24 of these IR36 trisomic lines through the U.S. quarantine process, re-selected the lines based on morphology, validated the presence of the additional chromosome by microscopic observation, characterized the lines for plant and grain traits, and made the lines available to the rice research community through the Genetic Stocks-Oryza collection. The trisomic lines will be useful in genetic mapping studies that will expedite rice genomics research and gene discovery.


Review Publications
Chen, M., Mcclung, A.M. 2015. Effects of cultivars, organic cropping management and environment on antioxidants in whole grain rice. Cereal Chemistry. 92(4):364-369. DOI.org/10.1094/CCHEM-11-14-0240-R.
Mohammed, A.R., Cothren, J.T., Chen, M., Tarpley, L. 2015. 1-methylcyclopropene (1-MCP)-induced alteration in leaf photosynthetic rate, chlorophyll fluorescence, respiration and membrane damage in rice (Oryza sativa L.) under high night temperature. Journal of Agronomy and Crop Science. 201:105-116. doi:10.1111/jac.12096.