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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Research Project #425079

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

2017 Annual Report


1a. Objectives (from AD-416):
This project will explore existing genetic rice resources and develop new methods of evaluation to elucidate genetic and environmental factors that influence yield and grain quality. Phenotypic information will be combined with genomic scans to identify chromosomal regions and genes that control these traits. 1: Maintain, regenerate, back-up, characterize, and distribute rice genetic stocks and associated information, and genetically and phenotypically characterize accessions in the NSGC rice collection and elite breeding materials for agronomic and grain quality traits to provide new genetic resources for rice research 1A: Expand and phenotypically and genotypically characterize NSGC collection (Core, Mini-Core, GSOR subsets) for traits essential to rice research community and US rice industry 1B: Develop/characterize a tropical japonica Core collection (TRJ-Core) representing US and international tropical japonica rice germplasm for mining genes for US breeding programs 1C: Evaluate cultivars with divergent processing quality for differences in enzyme activity of starch metabolism genes in response to environmental temperature 1D: Evaluate germplasm with pigmented bran using in vitro cell assays for 1) influence of cooking on bioactivity of phenolics having potential health-beneficial properties against cancer, and 2) bioactivity of bran extracts against diabetes 1E: Assess accessions in rice diversity panels for health-beneficial starch fractions 1F: Assess accessions for bran components that impact storage stability of brown rice 2: Use genome wide association studies and QTL mapping techniques to identify alleles that control yield components and grain quality traits in response to environmental variables 2A: Determine location of QTL and allelic variability associated with yield components in bi-parental mapping populations 2B: Identify QTLs and alleles responsible for transgressive variation in selected yield components found in rice wild species using chromosome segment substitution lines 2C: Identify QTLs for rice grain chalkiness in bi-parental mapping populations, and validate the markers in diverse germplasm 2D: Characterize QTLs associated with rice milling yield 2E: Identify/fine-map/further characterize the mode of action of genomic regions affecting rice grain fissure resistance 2F: Identify/further characterize genes affecting grain mineral nutritional value 2G: Evaluate germplasm/RILs that differ for grain arsenic accumulation and resistance to straighthead disease to understand mechanisms of arsenic uptake from soil and association with staighthead 3: Use marker-assisted selection to introgress novel alleles and to stack genes associated with yield, disease resistance, and grain milling, cooking and nutritional quality into new cultivars and improved breeding stocks 3A: Develop marker analysis platform for marker-assisted transfer of traits from various rice germplasm backgrounds into targeted US cultivars 3B: Utilize genetic resources (RIL, genetic fingerprints, and markers linked to QTLs) to introgress improved alleles for agronomic performance, disease resistance, and stress tolerance into southern US adapted cultivars


1b. Approach (from AD-416):
This project will explore genetic resources using phenotypic and genomic tools to identify novel traits that impact rice yield and grain quality. Chromosomal regions that control these traits will be determined though association mapping techniques using germplasm surveys and QTL mapping of bi-parental and backcross mapping populations. Genetic resources ranging from elite US breeding materials and commercial cultivars, to diverse global germplasm, and wild Oryza species accessions will serve as the basis for extensive phenotyping and genotyping studies. In addition, a new diversity panel based upon tropical japonica germplasm, which is the source of US cultivars, will be developed to mine for novel alleles for traits relevant to the US rice industry. Targeted traits will include yield, disease resistance, and agronomic traits, as well as milling, nutritional, and processing quality. Mapping populations will be developed for diverse tropical japonica parents and from crosses with wild species to identify alleles that are associated with yield components. Compounds in rice bran that have been identified in raw rice that reduce cancer cell growth and glucose uptake in in vitro studies will be isolated and evaluated for their health beneficial properties and their bio-activity following cooking. Global rice genetic resources that have high amylose content will be evaluated for resistant starch to identify germplasm that may be beneficial for reducing spikes in blood sugar associated with diabetes. Enzymes that control starch structure and rice parboiling quality will be evaluated in diverse rice germplasm grown under high temperature. Enzymes that are sensitive to temperature stress and negatively impact processing quality will be identified. These will be targets for genetic improvement to develop improved stability in processing quality. In an effort to increase market use for whole grain brown rice, which is more nutritious than milled rice, components in the rice bran that can reduce rancidity during storage will be identified. Mapping populations that are segregating for grain chalk, milling yield, and grain fissure resistance, factors that impact crop value, will be used to finely map QTL and identify candidate genes associated with these traits. In addition, segregating populations will be analyzed for grain mineral content in an effort to develop nutrient-dense germplasm. Grain arsenic accumulation can occur when rice is grown under flooded, anaerobic conditions. The interaction of diverse germplasm and water management techniques will be studied to identify how these two factors can minimize grain arsenic accumulation while sustaining economically viable yields. The long-term objective of this project is to seek a better understanding of the genetic control of yield and grain quality traits, and this information can be translated into superior rice cultivars that will strengthen domestic and export markets for USA rice.


3. Progress Report:
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.


4. Accomplishments
1. 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.

2. 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.

3. 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.

4. 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.


Review 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.H., Cao, H., Heiman, M.L. 2016. Antidiabetic potential of purple and red rice (Oryza sativa L.) bran extracts. Journal of Agricultural and Food Chemistry. 64(26):5345-5353. https://pubs.acs.org/doi/10.1021/acs.jafc.6b01909.
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.