Progress 07/10/13 to 03/25/18
Outputs
Progress Report 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 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. This is the final report for project 6028-21000-010-00D, which has been replaced by new project 6028-21000-011-00D. For additional information, see the new project report. Although there were four scientist vacancies for three years of this project, over 38 peer reviewed journal publications were produced. Viable seed stocks of approximately 20% of the USDA world rice collection were rejuvenated and made available to the public. A new diversity panel was created using Tropical japonica germplasm (TRJ Core) as a means of mining new genes for use in USA rice breeding efforts. Another internationally important diversity panel, Rice Diversity Panel 1 (RDP1) having some 400 accessions, was expanded to 1,848 accessions by importation from the Philippines and bringing the materials through the one year Animal and Plant Health Inspection Service (APHIS) quarantine process. A set of IR36 trisomics lines was made available to further expedite rice genomics research and gene discovery. These expanded resources allow researchers to better utilize the genetic variability among diverse rice accessions for breeding new cultivars. To further exploit the variability of agronomically important traits in Japonica germplasm, diverse parents from nine TRJ and two TEJ accessions were used to develop four biparental populations and a Multi-parent Advanced Generation InterCross (MAGIC) population. Significant progress was made on improving the nutritional value of rice. We demonstrated that rice bran promoted resistance to Salmonnella colonization and increased animal immunity to infection, as well as suppressed colon cancer cell growth in cell assays. Rice with pigmented bran (red or purple) is more phytonutrient rich than brown bran rice. A rice variety with purple bran was reported to activate intestinal immunity. In a separate study, red and purple rice brans were shown to increase glucose uptake as compared with brown bran. This suggests the potential of red and purple bran extracts as an intervention to prevent hyperglycemia by helping to remove glucose from the bloodstream. Due to the promising health beneficial potential of red and purple rice, we determined differences in concentrations of major flavonoid compounds in red and purple brans, and found 4.3-fold and 25-fold variation in proanthocyanidins and anthocyanins, respectively. These findings show that genetic resources are available to enhance flavonoids in pigmented rice using breeding techniques. Since rice is consumed cooked, understanding the impact of hydrothermal processing on whole grain antioxidant levels is also critical in promoting whole grain rice consumption. We found that parboiling and wet cooking enhanced some lipophilic antioxidant contents and decreased some flavonoids suggesting that when establishing dietary guidelines for these health beneficial compounds consideration must be given to cooking effects. We explored the potential of optimizing the harvest of the health beneficial compounds in rice for use in functional foods, a new market opportunity, and found that immature grain has the highest amount of tocopherols, while the levels of the other antioxidants can be optimized by harvesting grain at maturity. We found that organic crop management does not change the health beneficial compounds in rice and this finding supports new market opportunities for pigmented bran rice cultivars grown under organic systems. Our research indicates that natural compounds in bran of some varieties of rice have potential for use in nutritional therapy. Key to successful commercialization of a new rice variety is consumer acceptance of the eating quality. We 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. In addition, because brown rice has more health beneficial compounds than white rice, a one-year brown rice shelf life project was designed to understand the relative impact of multi-factors on storage stability of brown rice. Nineteen genotypes selected for the study, based on publicly available data and un-published results, possess superior quality of at least one of the many factors hypothesized to improve storage stability of brown rice, i.e. high total antioxidant capacity, high contents of phytochemicals that have inhibitory activity against lipase enzyme, low lipase activity, and high ratio of saturated/ unsaturated fatty acid. Initial results of the first three sampling time- points (0-, 3- and 6- months) showed a wide range in concentrations of the lipid break down products as well as lipase activity indicating that these traits could be selected for in a breeding program to improve storage quality. The flavor of U.S. aromatic rice cultivars was compared with that of imports and found that U.S. aromatic rice developed for the basmati and jasmine rice markets were similar in flavor to imported jasmine rice and could be differentiated from the preferred imported aromatic rice. This knowledge will be used to develop aromatic rice and whole grain rice varieties with improved palatability and consumer acceptance. Resistant starch (RS) is considered a form of dietary fiber and has potential in prevention of colon cancer and inflammatory bowel disease. We evaluated resistant starch in cooked rice of 40 varieties, all with high amylose, and found a few varieties have more than 2-fold increase in RS than typical U.S. cultivars. The findings of this research indicate that rice cultivars can be improved for resistant starch/dietary fiber that may promote colon health. Rice varieties that provide consistent processing quality is important to the industry. Research determined that rice varieties suited for parboiling are stable in processing quality across a range of field fertilizer inputs, tillage practices, and water management systems. High night temperature (HNT) is recognized as a cause of losses in rice yield and quality. HNT triggers increased production of ethylene, a plant hormone, leading to oxidative stress and resulting in yield loss. By treating plants with ethylene blocker, we reduced the stress response of plant to HNT and increased yield. Transgressive segregation for improved grain yield attributed to a wild rice parent, was first noted in a Jefferson (O. sativa)/O. rufipogon population. A greenhouse study showed this was due to a longer growing cycle, more above-ground biomass, longer flag leaves and longer panicles. Recent evaluation of a Nipponbare/O. nivara population revealed 46 Quantitative Trait Locus (QTL) associated with 19 traits important to domestication and yield improvement. The presence of grain chalk, opaque white areas in the rice grain, can reduce milling and cooking quality, thus reducing crop value. We discovered that a gene associated with reduced phytic acid in rice grain was also associated with a significant increase in chalk. Nine other genomic regions associated with chalk across multiple growing environments were also identified. These results will assist breeders use of marker-assisted selection for development of new varieties that have translucent grain and high economic value. Kernels are more likely to break during milling if they developed stress fissures before or after harvest. A laboratory method for evaluating grain fissuring (FR) was used in a segregating cross for fine-mapping of the qFIS1-2 grain fissuring gene and was found to be independent of the semidwarf plant height (sd-1) gene on chromosome 1. Candidate genes were identified and markers found linked to the FR QTLs that can be used to incorporate FR genes into improved varieties. In collaboration with researchers in Texas, New Hampshire, and Scotland we discovered new genes affecting nutritional elements such as calcium, magnesium, and arsenic. QTLs for multiple elements were often co-located, indicating element x element interactions affect uptake and accumulation. One QTLs affecting copper in rice grain was fine-mapped, analyzed for candidate genes, and discovered to be a transporter that sequesters copper into root vacuoles. This is the first copper transporter documented to impact sequestration of copper into cell storage areas and was the first copper transporter gene discovered from natural variation (vs mutations), making it readily useful to breeders. In addition, QTLs for arsenic, copper, molybdenum, and zinc were identified and accessions having extremely high grain- element concentrations of some 16 elements were identified and crossed with a U.S. cultivar as a common parent. Mendelian segregation indicated that grain concentration of six elements was simply inherited. Genetic markers were used to map grain-arsenic loci to chromosomes 8, 10, and 11, and a grain-calcium locus to chromosome 11. These genomic regions had not been previously associated with grain calcium and arsenic, making these new gene discoveries. During the course of this project, new bioinformatic tools were developed to help the rice research community in gene discovery and rice improvement. Ricebase was developed as a database that integrates genetic variation, pedigrees, and whole-genome-based data to enable discovery and design of molecular markers. Rice researchers now have the opportunity to make new genetic discoveries by exploring their results in the context of surrounding genes and genomic diversity, and design molecular markers to make rice breeding more efficient. Using genetic marker technology on the most advanced breeding materials in the southern U.S. was done to facilitate U.S. varietal development programs. Accomplishments 01 Public release of �Scarlett�- the first red bran rice variety high in anti-oxidants. The outer bran layer of the rice grain is the site of most of the nutritional value of the grain as compared to the interior endosperm which is composed primarily of starch. Although most rice that is consumed has brown bran, varieties with purple or red brans exist and generally have greater contents of health beneficial compounds. In an effort to develop new high value markets, ARS researchers at Stuttgart, Arkansas, and at Cornell University have developed Scarlett rice which contains high levels of lipophilic antioxidants and polyphenols in its red bran. The source of the red bran comes from one of the parents which is a weedy wild relative of cultivated rice. Scarlett rice will benefit rice growers because of the high yield potential when grown in the southern U.S. along with its nutritionally dense red bran. 02 Genotypes with low lipase activity for improving shelf life of whole grain rice. Whole grain rice, which has the bran layer intact, contains more nutrients and health beneficial compounds than milled rice (bran moved) and its consumption was associated with reduction of several chronic diseases. However, the bran layer is also where most lipids are deposited along with lipid degrading enzymes, lipase and lipoxygenase, which shorten the shelf life of whole grain rice. ARS researchers at Stuttgart, Arkansas, determined lipase induced hydrolytic rancidity (HR) levels in the bran of a set of diverse cultivars and found more than 15-fold variation in HR. Among them, genotypes of red and brown brans had lower HR than other bran color classes, purple, light brown and white. Total phenolic compounds in the purple brans was negatively associated with HR. Within the light brown bran color class, the typical bran color of U.S. cultivars, genotypes of lower lipase activity than U.S. cultivars were found and could be used as breeding materials to improve storage stability of U.S. cultivars. 03 New yield enhancing genes found for rice. To meet the growing demand for food, it is essential to understand the plant processes that control grain yield. ARS researchers in Stuttgart, Arkansas, in collaboration with scientists at Cornell University and support from the National Science Foundation previously evaluated a collection of over 400 diverse rice cultivars, identified as the Rice Diversity Panel 1 (RDP1), for 25 traits related to yield improvement. Quantitative trait loci (QTL) were identified that are linked to rice grain yield. To genetically dissect yield related traits a mapping population of the tropical japonica cultivars, Estrela and NSFTV199, was evaluated and 41 known genes for yield-related traits were identified and two regions had no known gene. Based on these results, DNA markers associated with panicle architecture and seed size are under development and selected lines are being evaluated in field trials for release as germplasm lines to breeders. Having both the germplasm lines and DNA markers will allow breeders to accelerate their breeding efforts to increase U. S. rice yields by incorporating and selecting for panicle and seed traits. 04 Purple bran rice is high in tricin, a flavonoid compound with numerous health benefits. Tricin, a flavonoid compound, has been reported to have numerous health benefits including anti-cancer properties and has been proposed as a candidate for cancer prevention clinical trials. Tricin has been identified in many plant species including rice. ARS researchers at Stuttgart, Arkansas, in collaboration with Rutgers University, studied the flavonoid compounds in rice of four bran color classes, light brown, brown, red and purple. Purple bran had higher tricin content as well as a broader range of other flavonoid compounds, including the anthocyanins that give the bran purple color. These results provide direction to breeders interested in improving the nutritional content of whole grain rice. 05 Allele mining for grain quality traits in diverse U.S. rice germplasm collections. A broad range of traits determine rice grain quality including grain shape, translucency, milling yield, cooking characteristics, sensory traits, and nutritional aspects. U.S. rice germplasm collections contain a diversity of rice with a tremendous range in grain quality traits. ARS researchers at Stuttgart, Arkansas, evaluated a genetically diverse panel of rice cultivars using high density genotyping data and genome-wide association (GWA) analysis of grain quality. Molecular markers were discovered that are associated with starch, cooking quality, grain dimensions, translucency, and protein content. Molecular markers will be deployed for use in marker assisted selection (MAS) to accelerate breeding for grain quality. 06 Detection of genes controlling grain chalk using NIR spectroscopy. One of the bottlenecks in germplasm evaluation is the labor intensive and time-consuming nature of phenotyping. Having a means to rapidly and accurately evaluate thousands of genotypes is needed to fully utilize the wealth of genomic data currently available. ARS researchers at Stuttgart, Arkansas, in collaboration with ARS researchers at Beltsville, Maryland, have evaluated 200 diverse rice accessions of the USDA Rice Minicore with a genomic data set of 3.3 million SNP markers along with hyperspectral imaging as a high-throughput phenotyping tool to understand the genetic control of grain physicochemical traits. A specific wavelength range detected rice grain chalk and was linked with novel chalk related genes. These results will assist breeders in developing environmentally resilient rice varieties with ideal grain quality. 07 Breeding rice varieties with increased concentration of molybdenum (Mo) in grains and tolerant of Mo-deficient soils. Molybdenum (Mo) is an essential micronutrient for most living organisms, and cereal grains are the major dietary source of Mo for humans and animals. Although cases of Mo deficiency in humans is rare, Mo deficiency in plants is fairly common, especially in the tropics, where rice is predominantly grown. ARS researchers at Stuttgart, Arkansas, in collaboration with University researchers in China, the United Kingdom, and Delaware, U.S. determined that the gene underlying a QTL for grain-Mo concentration in a biparental population was the OsMOT1;1 molybdate transporter gene, which was mainly expressed in roots, and affected uptake of Mo from the soil as well as translocation to shoots. This newly discovered natural allelic variation in OsMOT1;1 can be used by breeders to develop rice varieties more tolerant of Mo-deficient soil, as well as, producing rice varieties with increased grain-Mo concentrations. 08 Whole grain rice bran is a rich source of bioactive components that have potential to promote gastrointestinal health. Among these components, feruloylated arabinoxylan oligosaccharides, a soluble portion of non-digestible fiber after enzymatic hydrolysis (FAXO), and red pigmented rice bran polyphenols (RBPP) were investigated for their prebiotic potential and the impact on human gut microbiota in vitro by ARS researchers at Stuttgart, Arkansas, in collaboration with researchers at University of Arkansas, Fayetteville and at Arkansas State University, Jonesboro. Fresh fecal samples collected from ten healthy adults with no signs or symptoms of bowel diseases or conditions received 5 treatments including FAXO and RBPP, separately and combined. Results showed that treatment with FAXO significantly increased the production of short chain fatty acids, the fermentation products of the colonic bacteria that are beneficial to the gut health. FAXO and RBPP had synergistic effects on increasing the abundance of bacteria that generate butyrate short chain fatty acid, a fatty acid with protective effects of colon cells against cancer. Results from this study suggested that FAXO and RBPP from rice bran can potentially promote colon health through a prebiotic function. 09 Rice cultivars with low glycemic index and preferred sensory properties. Rice has high glycemic index (GI) and diets high in GI are associated with chronic diseases. Decreasing the rate of starch digestion lowers GI, improving nutritional properties of rice. However, the effects of starch digestive fractions, rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS), on cooked rice texture which impact end-use properties need to be understood. ARS researchers at Stuttgart, Arkansas, and at New Orleans, Louisiana, evaluated seven U.S. rice cultivars for contents of starch digestive fractions and for texture attributes by a descriptive sensory panel. In addition, apparent amylose (AAC), lipid contents, and paste viscosities were determined. Multiple linear regression models showed that RS and AAC were the major predictors and lipids and SDS played minor roles in texture attributes. Among high amylose cultivars, preferred digestive properties and palatable texture can be selected to meet diverse consumer markets. 10 Improvement of whole grain nutritional quality can be accomplished by increasing the proportion of bran in whole grain rice. Rice bran, the outer most layer of the whole grain, is the primary site of deposition of most nutrients, minerals and bioactive compounds, however, rice bran accounts for a very small portion of the whole grain by weight. Increasing the weight proportion of the bran to whole grain will enhance whole grain rice nutritional value. ARS researchers at Stuttgart, Arkansas, determined the total bran weight and bran weight per surface area (BWS) of the whole grain for 134 diverse rice genotypes and found more than 2.3- and 2.5-fold variation, respectively. Mean comparison of BWS among bran color classes showed that purple bran genotypes had the highest BWS, followed by red, white, light brown and brown. This report showed high bran weight genotypes can be selected for in a breeding program to improve whole grain nutritional quality.
Impacts
(N/A)
Publications
- Poulev, A., Chen, M., Cherravuru, S., Raskin, I., Belanger, F.C. 2017. Variation in levels of the flavone tricin in bran from rice genotypes varying in pericarp color. Journal of Cereal Science. 79:226-232.
- Pham, T., Savary, B., Chen, M., Lee, S., Mcclung, A.M. 2017. In vitro fermentation patterns of rice bran components by human gut microbiota. Nutrients. 9(11):1237.
- Zhao, D., Hamilton, J.P., Vailancourt, B., Zhang, W., Eizenga, G.C., Cui, Y., Jiang, J., Buell, C., Jiang, N. 2018. Evolutionary trajectory of Pack- MULEs is determined by their epigenetic status. Nucleic Acids Research.
- Heuschele, D.J., Pinson, S.R., Smith, A.P. 2017. Metabolic responses to arsenic in rice seedlings that differed in grain arsenite concentration. Crop Science.
- Chen, M., Mcclung, A.M., Bergman, C.J. 2017. Phenolic content, anthocyanins and antiradical capacity of diverse purple bran rice genotypes as compared to other bran colors. Journal of Cereal Science. 77:110-119.
- Pinson, S.R., Jia, Y., Jia, M.H., Gibbons, J.W. 2018. Novel QTLs affecting rice kernel fissure resistance discovered in the cultivar �Saber� augment those from �Cybonnet�. Crop Science.
- Eizenga, G.C., Sanchez, P., Jackson, A.K., Edwards, J., Hurwitz, B.L., Wing, R.A., Kudrna, D. 2017. Genetic variation for domestication related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population. Molecular Breeding.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report 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 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. A key component of this project plan is the rejuvenation, characterization and curation of the National Small Grains Collection (NSGC) world collection of rice. Although the CAT 4 position overseeing this project has been vacant for 3 years annual milestones have been achieved. In this year, 1,051 NSGC accessions were successfully rejuvenated, characterized and data provided for uploading to Germplasm Resource Information Network (GRIN)-Global. In addition, Dale Bumpers National Rice Research Center (DBNRRC) has initiated genotypic evaluation of the NSGC accessions with a small set of fingerprint markers and some 1, 500 accessions will be genotyped this year. The purpose of this genotyping will provide information to GRIN users on major genes controlling grain cooking quality, blast disease resistance, and sub- population structure. The Genetic Stocks Oryza (GSOR) collection that is curated at DBNRRC, grew by 3,742 for a total of 37,693 accessions. This includes the RDP2 diversity panel imported from the International Rice Research Institute, and 1,257 accessions have been successfully rejuvenated so far. About 73 will be grown in a quarantine greenhouse because rejuvenation has been unsuccessful. Some 7,500 GSOR accessions were distributed during the year to USA researchers as well as those in Austria, Belgium, Canada, China, Egypt, Israel, Italy, Japan, Pakistan, Spain, Taiwan, United Kingdom, and Vietnam demonstrating the global importance of this resource. Progress has been made in developing a tropical japonica diversity panel (TRJ Core) with successful completion of single plant selections and seed increase of 690 accessions and characterization for nine traits. During the next year the panel will be genotyped with in-house microsatellite markers instead of genotyping-by- sequencing (GBS), at least initially, as a cost-saving measure. DBNRRC initiated a collaborative effort with ARS labs in Stoneville, Mississippi, (sequencing) and Cold Spring Harbor, New York (assembly and gene annotation) and with the Arizona Genomics Institute (high molecular weight DNA extraction) for de novo sequencing of the founder U.S. tropical japonica rice variety �Carolina Gold� to serve as a reference genome for tropical japonica germplasm and enhance our understanding of tropical japonica genomic diversity. The sequencing has been completed using single molecule real time sequencing technology and the assembly and gene annotation are in progress. Information from this project will be used to guide future genotyping efforts on the TRJ Core. Data analysis is commencing on the study evaluating the impact of heat stress on cultivar paste viscosity profiles and starch structure with the expected completion and submission to a journal in FY 18. Due to an extended absence of support staff the project looking at brown rice shelf life has been delayed but progress has been made on developing hydroperoxide assay for quantifying lipid hydrolytic rancidity. A mapping population was created by crossing the high resistant starch mutant line and a line with high anti-radical activity, high flavonoid content with the goal to identify Quantitative Trait Loci (QTLs) linked with concentrations of resistant starch and pigmented flavonoids. F3 plants selected for homozygosity at the Waxy locus (coding for high or zero amylose content) are growing in the 2017 field in replicated trials. Grain will be analyzed for resistant starch and genomic analysis for starch mutant gene will be performed. A rice sensory study including primarily high amylose U.S. cultivars, in comparison with typical U.S. long grain rice cultivars, is being conducted in collaboration with Southern Regional Research Center (SRRC), New Orleans, Louisiana, to determine factors affecting eating quality of cooked rice. Traits included human sensory data, resistant starch, rapidly and slowly digestible starch fractions, along with various functional traits. A second sensory study is being conducted focusing on a panel of 10 of the highest resistant starch varieties (2 fold higher than U.S. high amylose cultivars) identified from a previous study. These 10 varieties have different processing and physicochemical properties. The goal is to determine if varieties with high resistant starch have eating and processing quality comparable to commercialized U. S. high amylose cultivars. Bi-parental TRJ mapping populations have been developed that are segregating for yield components. The genotyping is nearly complete and QTL mapping will follow. The final selections for the CSSL libraries developed with three wild species crossed with Cybonnet, U. S. variety, and with IR64, indica, were genotyped using GBS. The two Cybonnet libraries are currently being evaluated for yield components under field conditions. A new high throughput phenotyping method for chalk has been developed using hyperspectral imaging. It was found that the wavelength range of 660 to 700 nm is highly correlated with the chalky grain phenotype. This was used to assess the mini-core and progeny from a bi-parental population that differed for grain chalk. It was shown that the genetic loci associated with a peak within the 660-700nm wavelength region are the same as the ones associated with the chalk phenotype. This imaging technique could lead to more accurate phenotyping method for measuring grain chalk and, with further research, may reveal structural, chemical, and genetic mechanisms that cause chalky grains. In a separate study, data collected in collaboration with Louisiana State University is being analyzed to validate QTLs associated with rice grain chalk. The project to evaluate progeny that are segregating for grain element accumulation has been delayed in part due to new resources being obtained through a Headquarters funded post-doc that studied arsenic uptake in hydroponic seedlings of parental lines which was published this year. Plans to evaluate the Mini-core for multiple grain elements has been delayed in order to use resequencing data that has been recently made available. This analysis will be completed in FY 18 along with a separate Minicore analysis looking at the relationship of grain-arsenic, hull-silica concentrations and straighthead. Using a bi-parental population, progeny were selected for extreme differences in straighthead response in the F2 generation and were validated in F3:4 progeny. Progeny verified as resistant to straighthead had, on average, lower grain- arsenic concentrations than progeny verified as susceptible. When FY 16 results indicated that grain-arsenic concentrations were associated with increased leaf sequestration and detoxification of arsenic, a process that requires sulfur, it was hypothesized that increased concentration of leaf sulfur might reduce grain-arsenic concentrations. However, a replicated field study indicated that foliar application of a potassium and sulfur fertilizer mixture did not alter either straighthead severity nor grain-arsenic concentrations among six cultivars known to vary for both. The 200 elite breeding lines in the 2016 Uniform Regional Rice Nursery (URRN) were evaluated for grain quality traits and genetic markers linked to quality, blast resistance genes, pubescence, and Clearfield herbicide resistance. Data were transferred to the U.S. breeders at the annual breeders meeting in January 2017 and archived along with some 35 years of URRN data in CyVerse, accessible to the breeders. For the 2017 URRN study, DNA has been extracted and marker analysis will be completed during FY 17. A new database called Ricebase has been developed as a tool for breeders. For the first time, this provides an integrative genomic database that combines various marker datasets for global rice germplasm, includes recently published QTLs, and uses gene annotations from the Rice Annotation Project (RAP). Since its release in FY 17, it has had 7,980 page views and has been visited by 789 new users from 57 countries. ARS submitted five elite breeding lines to the URRN multi-location study in 2017 including one conventional long grain, two aromatics, and two specialty cultivars. In addition, two varieties developed by ARS, Presidio and Rondo, are included in the trial as checks for grain quality and yield potential, respectively. A new specialty red rice variety that is high in anti-oxidant activity will be released this year. This was developed from a prior collaborative project with Cornell University that was funded by the National Science Foundation that explored the use of wild crop relatives for cultivar improvement. The parent material is based on the ARS cultivar, Jefferson, with the red bran pigment and high anti-oxidants coming from Oryza rufipogon introgressions. Accomplishments 01 Recovering yield enhancing genes lost in rice domestication from the wild ancestral species, Oryza nivara. Increasing genetic diversity by introducing genes lost during the domestication process is one method of improving crop plants. New genes have been discovered from a wild crop relative of rice that may enhance breeding new cultivars with higher yield potential. ARS scientists in Stuttgart, Arkansas, in collaboration with scientists at the University of Arizona and with support from the National Science Foundation, evaluated offspring from crossing Nipponbare, a cultivated rice, with the ancestral rice, O. nivara, to identify genes controlling 19 important yield and domestication traits. Of the 46 chromosomal regions identified in the cross, alleles from the O. nivara parent resulted in trait increases at 28 regions, including increased flag length, panicle length, seed length, and seed width, among other traits. Having genetic markers linked to these genes derived from O. nivara, will help breeders incorporate desirable traits from this wild species into new rice varieties having enhanced yield and adaptation. 02 Genetic markers for breeding rice with reduced grain chalk and high economic value. To achieve the highest market value, milled rice grain must be translucent. However, grain chalkiness, opaque white areas in the grain is a major concern limiting U.S. rice exports to some markets. ARS scientists in Stuttgart, Arkansas, discovered new genetic markers linked to grain chalkiness. The markers discovered in a biparental rice mapping population were validated in a large set of global rice varieties indicating the markers will be broadly useful in breeding programs. These results will benefit breeders that use genetic markers to assist in selection and development of new varieties that have translucent grain and high economic value. 03 Assembly of metabolic building blocks to increase health beneficial compounds found in red rice bran. Proanthocyanidins are flavonoids, compounds that are associated with the pigment found in red bran rice varieties and are proposed to reduce the impact of some chronic human diseases. ARS scientists in Stuttgart, Arkansas, studied the mechanism of accumulation of proanthocyanidins during seed development in four red bran rice varieties. Two mechanisms of accumulation were observed � one accumulated the compound to a high level during early seed development but dropped to a very low level in mature seeds, and one accumulated to moderate level early, but maintained its level in mature seeds. These results suggest that through breeding, these two accumulation mechanisms can be combined into new varieties that will have high proanthocyanidins biosynthesis and accumulation rates throughout the development of the grain and will result in red bran cultivars with very high levels of these health beneficial compounds. 04 Two new genetic factors that improved rice milling quality and economic value were discovered. Industry and consumers desire rice that remains intact when they are milled. Kernels are more likely to break during milling if they developed stress fissures before or after harvest. ARS scientists in Stuttgart, Arkansas, discovered two new genetic loci that improve rice kernel fissure resistance. The two new fissure resistance genes were identified through association with molecular markers in a biparental rice mapping population where they were observed enhancing the fissure resistance conferred by the three previously known rice fissure resistance genes. Breeders will be able to use the molecular markers found linked to these new fissure resistance genes to develop new varieties that better resist fissuring and break less upon milling.
Impacts
(N/A)
Publications
- Edwards, J., Jackson, A.K., Bryant, R.J., McClung, A.M. 2017. Genetic architecture of grain chalk in rice and interactions with a low phytic acid locus. Field Crops Research. doi:10.1016/jc.fcr.2017.01.015.
- Ghazi, I.A., Zarei, I., Mapesa, J.O., Wilburn, J.R., Leach, J.E., Rao, S., Broeckling, C., McClung, A.M., Ryan, E.P. 2016. Rice bran extracts inhibit invasion and intracellular replication of Salmonella typhimurium in mouse and porcine intestinal epithelial cells. Journal of Applied Research on Medicinal and Aromatic Plants. doi:10.4172/2167-0412.1000271.
- Sater, H.M., Pinson, S.R.M., Moldenhauer, K., Siebenmorgen, T.J., Mason, R. E., Boyett, V.A., Edwards, J. 2017. Fine mapping and introgressing qFIS1-2, a major QTL for kernel fissure resistance in rice (Oryza sativa L.). Crop Science. doi:10.2135/cropsci2016.09.08213.
- Chen, M., Bergman, C.J., McClung, A.M., Everette, J.D., Tabien, R. 2017. Resistant starch: variation among high amylose rice varieties and its relationship with apparent amylose content, pasting properties and cooking methods. Food Chemistry. doi:10.1016/j.foodchem.2017.04.170.
- Boue, S.M., Daigle, K.W., Chen, M., Cao, H., McClung, A.M., Heiman, M. 2016. Antidiabetic potential of purple and red rice (Oryza sativa L.) bran extracts. Journal of Agricultural and Food Chemistry. 64(26):5345-5353.
- Bett Garber, K.L., Bryant, R.J., Grimm, C.C., Chen, M., Lea, J.M., McClung, A.M. 2017. Physicochemical and sensory analysis of USA rice varieties developed for the basmati and jasmine markets. Cereal Chemistry. 234:180- 189.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report 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 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. As part of the NSGC system, ARS rejuvenated 1,089 rice accessions and provided 5,630 datapoints on trait characterization for uploading to GRIN. New to these activities, ARS determined marker allele calls on some 800 rice accessions. These molecular markers are being used as a cost savings measure to replace some phenotypic traits like amylose content, alkali spreading value, aroma and glaborousness and add greater value to the collection by revealing the presence of known disease resistance genes and subpopulation identification. These data will be added to the GRIN database. The Genetics Stocks Oryza collection (GSOR) was expanded by another 647 accessions for a total of 33,951. Shipments totaling 39,713 accessions were sent from GSOR in 238 orders, with about half going to USA researchers and half going to researchers in 10 other countries. Some 1,100 rice accessions that are part of the RDP2 diversity panel developed at the International Rice Research Institute (IRRI) completed the one year quarantine growout and 449 of these will complete seed amplification this year for public distribution through GSOR. A new diversity panel focused on a tropical japonica (TRJ) collection is being developed. Some 743 global rice accessions are undergoing some combination of seed purification, seed amplification, and genotyping to result in a panel of about 500 TRJs. A TRJ bi-parental mapping population has been completely phenotyped for yield component traits and will be genotyped next year for QTL mapping. In a collaborative effort with ARS Stoneville, MS, two major genotyping projects are being conducted. De novo sequencing is being performed for the variety Carolina Gold that will serve as a genomic reference for the TRJ rice subpopulation that is the primary genepool for USA rice. In addition, a chromosome segment substitution line (CSSL) population is undergoing genotyping by sequencing (GBS) and the data will be used to identify QTL linked with reduced water use and heat stress tolerance. Final selections for the CSSL libraries developed with three wild species crossed to each of Cybonnet, a USA variety, and IR64, an indica variety, were made and seed amplification is being performed for use in future studies. A new mapping population was created for identifying QTL linked with several health beneficial traits. A mutant variety with a high concentration of reisitant starch was crossed with a variety that is a source of high antiradical activity in the bran. In addition to QTL mapping for these traits, the population will be used to understand the interaction of amylose and amylopectin on resistant starch concentration and development of new germplasm that combines the two health beneficial traits. Grain chalk is a major concern limiting U.S. rice exports to some markets. A two year study was completed to identify genetic markers that could be used by breeders to select for lower grain chalk. A major QTL that explained 23.8% of the variation in chalk was located on chromosome 2 and was associated with the phytic acid pathway in this population. A mapping population was used to determine the role of arsenic in inducing straighthead, a physiological disease. Offspring that were resistant to straighthead accumulated 0.2 ppm less total arsenic (inorganic and organic) in the grain than susceptible plants. The location of a gene for grain-arsenic concentration was previously mapped to a region of chromosome 11 and those results are being verified among other segregating progeny. While grain-arsenic and straighthead susceptibility were found positively associated, allele distributions among the progeny were not as expected suggesting there may be complex gene x gene interactions underlying grain-arsenic accumulation. We have validated a lipase enzyme assay, one of the two major enzymes responsible for short shelf life of whole grain (brown) rice. Significant progress has been made on lipoxygenase enzyme assay, a second enzyme responsible for rancidity in whole grain rice. Seed is being produced of eighteen rice genotypes having various traits that have potential to prolong shelf life of whole grain rice and will be used for a subsequent storage stability study. Genotyping of 200 elite rice varieties from the southern US breeders' Uniform Regional Rice Nursery (URRN) with 5 microsatellite, 7 single nucleotide polymorphisms (SNPs), and 2 indels was completed and data presented at the annual breeders meeting. A new barcoding system using globally unique identifiers as tracking numbers was implemented for more efficient and accurate tracking of tissue samples for genotyping. In addition, a novel software program was created to parse and error check current and historic USA breeding pedigrees to reveal genetic inter- relationships. Thirty years of historical URRN agronomic data were compiled and will be made available to URRN cooperators through CyVerse (formerly iPlant). In addition to identifying germplasm with valuable traits and their associated markers, a goal of the project is to use this information to develop improved germplasm and cultivars. This goal has been delayed due to several critical vacancies, however, genetic resources developed by the project will be used in crossing during the next year. Accomplishments 01 Whole grain rice naturally fortified with higher bioactive compounds. Phenolic compounds have potential in reducing incidence of chronic diseases or their risk factors. Anthocyanins, a major subgroup of phenolic compounds in purple bran rice, have been demonstrated in animal studies and human clinical trials to possess these health beneficial effects. Scientists at Dale Bumpers National Rice Research Center in Stuttgart, Arkansas studied the anthocyanin concentration and antiradical capacity among 25 genetically diverse purple-bran rice cultivars. More than 8.0- and 25-fold variation in antiradical capacity and total anthocyanin concentration, respectively, were found in the bran. 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. 02 Sequestration in plant leaves may reduce grain arsenic accumulation in rice. There is public concern over arsenic levels in rice and other food products. The flooded conditions under which most rice is produced makes soil arsenic more bioavailable for uptake, and rice plants transport a portion of the arsenic into the grain. Scientists at Dale Bumpers National Rice Research Center in Stuttgart, Arkansas studied six rice varieties known to produce either high or low in grain arsenic (As) concentrations and asked if they exhibited differences for rates of As uptake, transport, sequestration, and/or detoxification of secondary stress compounds in seedling roots and leaves. The most striking difference was that exposure to high levels of As induced all three varieties low in grain-As, but none of those high in grain-As, to double leaf production of glutathione, a compound necessary for sequestration of As into cell vacuoles. This suggests that one metabolic method of limiting As accumulation in the grain is by trapping it in leaf cell storage areas (i.e. vacuoles). Finding genes that control this sequestration process will help breeders to develop new rice varieties with that exclude As from the grain. 03 Database for rice breeding. Rice breeding can be accelerated by using genomic and genetic diversity data. A database specifically designed for use by rice breeders (Ricebase) was developed by ARS scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas along with researchers at the Boyce Thompson Institute in Ithaca, New York. For the first time the Ricebase program integrates genetic variation, pedigrees, and whole-genome-based data to enable discovery and design of molecular markers. Application of these molecular markers in marker-assisted selection makes rice breeding faster and more efficient. 04 Wild ancestral species improve grain yield in the USA rice cultivar, Jefferson. Increasing diversity by introducing new genes lost during the domestication process is one method of improving yields in crop plants. ARS scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas evaluated eight accessions developed from crossing of the USA cultivar, Jefferson, with O. rufipogon with each having different chromosomal segments of the wild ancestral species. Earlier field studies identified these accessions as having increased yield when compared to the Jefferson parent. Greenhouse studies determined the increased yield was due to a longer growing cycle, more above-ground biomass, longer flag leaves and longer panicles. This demonstrates that DNA from an inferior wild species can contribute variation that increases yield in a commercial rice cultivar. These lines are currently available to the rice breeding community for use in expanding the genetic diversity in their cultivar development program. 05 Improving copper content and the human nutritional value of rice. Rice not only provides more than one fifth of the daily calories for half of the world�s population but is also a major source of mineral nutrients like copper that is important for preventing osteoporosis and anemia. We identified the gene for a protein that transports copper into root vacuoles, and further showed that natural variation in this transporter gene affects how much copper gets transferred to and accumulated in the grains of field cultivated rice. While other copper transporters were previously shown to impact other aspects of copper tissue-to-tissue transfer (such as from roots to the plant vascular system), this is the first copper transporter documented to impact sequestration of copper into cell storage areas (i.e. vacuoles). While most plant metal transporters have been identified using deleterious knock-out mutants, we identified alternative forms of this transporter gene within two high-yielding rice varieties. The identification of natural genetic variation may offer rice breeders the opportunity to fine-tune the copper concentrations in rice grain to improve the diet of the people that rice sustains. 06 Rice with higher resistant starch, a dietary fiber. Resistant starch, a fraction of the starch that resists digestion in the small intestines of healthy humans and is considered part of dietary fiber content, has potential in prevention of colon cancer and inflammatory bowel disease. Resistant starch concentration correlates with grain amylose content in studies using rice varieties with amylose ranging from 0 to 26%. Scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas evaluated resistant starch in cooked rice of 40 cultivars, all with high amylose. More than a 2-fold difference in resistant starch concentration was found and more than three-fourths of the cultivars had higher resistant starch concentration than Dixiebelle, a high amylose US cultivar. The findings of this research indicate that rice cultivars can improved for resistant starch/dietary fiber that will promote colon health. 07 Genetic linkage between kernel fissure resistance and the sd-1 semidwarf gene in rice. Fissures, or cracks, in the rice grain result in reduced milling quality and crop value. An experiment was conducted by researchers at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas to finely map a region on chromosome 1 that was associated with kernel fissure resistance but also included the sd-1 semidwarf locus. Most of the offspring from the fissure resistant x fissure susceptible cross that had high resistance to kernel fissuring were fixed (non-segregating) for the sd-1 allele making them short statured. However, several of the offspring were determined molecularly and phenotypically to contain the Sd-1 allele for taller plant height. This demonstrated that the gene for fissure resistance is linked to but different from the sd-1 gene, and can be used by breeders to improve the fissure resistance of tall as well as semidwarf rice cultivars.
Impacts
(N/A)
Publications
- Eizenga, G.C., Neves, P.C., Bryant, R.J., Agrama, H.A., Mackill, D.J. 2015. Evaluation of a M-202x Oryza nivara advanced backcross population for seedling vigor, agronomic traits, yield components, yield and grain quality. Euphytica. 208:157�171. doi: 10.1007/s10681-015-1613-y.
- Chen, M., Bergman, C.J. 2016. Vitamin E homologs and y-oryzanol levels in rice (Oryza sativa L.) during seed development. Cereal Chemistry. 93:182- 188.
- Bryant, R.J., Yeater, K.M., Mcclung, A.M. 2015. Effect of nitrogen rate and the environment on physicochemical properties of selected high amylose rice cultivars. Cereal Chemistry. 92(6):604-610. doi.org/10.1094/CCHEM-02- 15-0035-R.
- McCouch, S.R., Wright, M.H., Tung, C., Maron, L.G., McNally, K., Fitzgerald, M., Singh, N., DeClerck, G.A., Agosoto Perez, F., Korniliev, P. , Greenberg, A., Naredo, M.B., Mercado, S.M., Harrington, S.E., Shi, Y., Branchini, D.A., Kuser-Falcao, P.R., Leung, H., Ebana, K., Yano, M., Eizenga, G.C., McClung, A.M., Mezey, J. 2016. Open access resources for genome wide association studies (GWAS) in rice (Oryza sativa) illustrate the power of population-specific mapping. Nature Communications 7:10532. doi: 10.1038/ncomms10532.
- Huang, X., Deng, F., Pinson, S.R., Guerinot, M., Salt, D.E., Ma, J. 2016. A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain. Nature Communications. 7:121138. doi10.138/ncomms12138.
- Goodyear, A., Ehrhart, E.J., Swanson, K.S., Grusak, M.A., Leach, J.E., Dow, S.W., McClung, A.M., Ryan, E. 2015. Dietary rice bran supplementation prevents salmonella colonization differentially across varieties and by priming intestinal immunity. Journal of Functional Foods. 18:653-664.
- Chen, M., McClung, A.M., Bergman, C.J. 2016. Concentrations of oligomers and polymers of proanthocyanidins in red and purple rice bran and their relationships to total phenolics, flavonoids, antioxidant capacity and whole grain color. Food Chemistry 208:279-287.
- Eizenga, G.C., Edwards, J., Yeater, K.M., McCouch, S.R., McClung, A.M. 2016. Transgressive variation for yield components measured throughout the growth cycle of Jefferson rice (Oryza sativa) x O. rufipogon introgression lines. Crop Science 56:1-12. DOI: 10.2135/cropsci2015.10.0603.
- Chen, M., McClung, A.M., Bergman, C.J. 2016. Bran data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity, and profiles of proanthocyanidins and whole grain physical traits of 32 red and purple rice varieties. Data in Brief 8:6-13.
- Edwards, J., Baldo, A.M., Mueller, L.A. 2016. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data. Database: The Journal of Biological Databases and Curation. 2016:baw107.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report 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 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. 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. Accomplishments 01 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. 02 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. 03 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. 04 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. 05 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. 06 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. 07 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.
Impacts
(N/A)
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.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report 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 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. 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. Accomplishments 01 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. 02 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. 03 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. 04 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. 05 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. 06 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. 07 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.
Impacts
(N/A)
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. 2014. World-wide genetic diversity for mineral element concentrations in rice grain. Crop Science. 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.
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