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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Research Project #434318

Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

2020 Annual Report

1. Good tasting rice with high dietary fiber. Dietary fiber, which includes resistant starch (RS), is recommended for consumption to prevent chronic diseases. Rice varieties that have higher RS than are commonly found in US varieties have been identified and understanding how RS may impact cooked rice sensory quality and functional properties is important to consumers and food processors. ARS researchers in Stuttgart, Arkansas, and in New Orleans, Louisiana, evaluated cooked rice texture and rice functional properties of ten rice varieties that vary in RS. Trained panelists using descriptive sensory analysis determined that only one of 14 cooked rice texture attributes, roughness, was different between the high RS group of varieties and other US varieties. Moreover, in an evaluation of the functional properties few differences were found between the two groups of varieties. These results demonstrate the potential for increasing RS in US rice varieties that enhances the health benefits of cooked rice while having minimum impact on cooked rice texture or processing quality.

2. Identification of novel quantitative trait loci (QTL) controlling inorganic arsenic levels in rice. Rice grown under typical flooded paddies can accumulate arsenic (As) which is an element that naturally occurs in the soil. Because rice is such an important grain for feeding the world, As accumulation in rice grain is a significant health concern and inorganic arsenic (iAs) is of particular concern because it has increased toxicity as compared to the organic form of As. ARS researchers at Stuttgart, Arkansas, and Beltsville, Maryland, reported seven novel QTLs controlling iAs levels in rice and further documented that the number of days the crop was under alternate wetting and drying irrigation management was related to a decrease in grain iAs concentrations. Furthermore, both the number and combination of QTL significantly impacted grain iAs concentrations. This knowledge will inform plant breeders in an effort to minimize exposure to iAs from rice consumption by coupling irrigation management practices with the development of low iAs accumulating cultivars.

3. Genome sequencing of the heirloom U.S. rice variety Carolina Gold as an improved genomic reference for US tropical japonica rice. Most modern U.S. rice varieties have ancestry tracing back to a relatively narrow genepool of tropical japonica founder cultivars. Carolina Gold is a historically important founder variety that helped establish the US rice industry because of its excellent grain quality. Currently, the reference genome used for most rice genomics studies is a temperate japonica variety which may cause “blind spots” when used in analyses of U.S. tropical japonica varieties. To serve as a better reference genome for the U.S., ARS researchers in Stuttgart, Arkansas, Stoneville, Mississippi, and Ithaca, New York, in collaboration with researchers at the University of Georgia, Mississippi State University, and Cold Spring Harbor, New York, resequenced 166 varieties that represent USA rice breeding efforts over the last century. This dataset allowed characterization of patterns of genetic change across the time course of breeding and selection in the USA. These data resources will help breeders and geneticists discover the sequence changes that have led to important genetic gains and potentially recover useful genetic variation that was inadvertently lost through the bottleneck of selection to enrich future cultivar development efforts.

4. Identification of a novel rice blast disease resistance gene from weedy rice. Rice blast disease is difficult to control due to rapid occurrence of new virulent races. Searching for more effective blast resistance (R) genes from different genetic resources is essential to manage this disease. In a previous evaluation of rice germplasm, it was determined that the rice blast R gene, Ptr, confers resistance to several U.S. blast races except for one of the most virulent blast races, IB33. ARS researchers in Stuttgart, Arkansas, identified a minor amino acid variation encoded by the Ptr allele found in a weedy rice biotype that resulted in an altered Ptr protein conveying resistance to IB33. The R gene, PtrBHA, was mapped with three closely linked genetic markers. The genetic markers linked to this novel resistance gene can be used to deploy resistance to this race of blast that currently does not exist in any U.S. cultivars.

5. Draining rice fields immobilizes naturally occurring arsenic in the soil and reduces its availability for rice uptake. Arsenic (As) which is an element that naturally occurs in soils, can be easily absorbed by rice plants when they are grown in flooded paddies and can result in significant levels of As in rice grain that may present a risk to humans that consume rice as major part of their diet. Draining of rice fields during the vegetative stage of plant growth has previously been reported as an effective cultural practice in reducing the accumulation of As in rice grain as compared to rice produced in saturated, flooded soils. ARS researchers in Stuttgart, Arkansas, along with researchers at Cornell University conducted a study that found that manganese (Mn) and iron (Fe) ratios in paddy soils impact the dissolved concentration of As in soil pore water. A single severe soil dry-down was effective in reducing As in the porewater for about a month due to the formation of iron and manganese oxides that immobilized the As. The biggest decrease in As availability occurred in the top 4 inches (10cm) of soil where field draining had a greater effect on soil drying and where the roots are more concentrated, than at a depth of 10 inches (25 cm) where soil moisture and availability of As, Mn, and Fe in the pore water changed less with field draining. This research demonstrates why soil dry downs during alternate wetting and drying irrigation management are effective in reducing As availability for rice plant uptake and is a cultural means to enhance the nutritional value of the rice crop.

6. Weedy rice relatives harbor novel sheath blight disease resistance genes. Rice sheath blight disease is one of the most devastating diseases of rice and causes significant yield losses worldwide because no source of complete resistance has been found. ARS researchers in Stuttgart, Arkansas, in collaboration with University researchers in Missouri and Massachusetts, with support from the National Science Foundation, evaluated sources of weedy rice, a weed that commonly occurs in rice production fields and negatively impacts yield and quality, for sheath blight resistance. Nine regions of the weedy rice genome were identified that contain markers associated with sheath blight disease resistance. Four of the nine genetic markers are associated with the actual disease resistance response rather than disease avoidance traits like plant height or heading date. Three of these markers have never been identified before and offer unique sources of resistance for breeding new rice varieties that will result in increased economic returns for growers and less reliance on fungicides.

7. Rice plant developmental changes in shoot and root biomass drive changes in the soil microbiome. Interactions between crops and rhizosphere soil microbial communities play an important role in plant productivity, health, and growth. However, there is a lack of understanding of how plant traits, such as root and shoot biomass, and plant developmental stage may impact the structure of the soil microbial community. ARS researchers in Stuttgart, Arkansas, and Beltsville, Maryland, in collaboration with researchers from South Korea, conducted genomic sequencing to evaluate changes in the rhizospheric microbial community structure in response to changes in above- and below- ground biomass as the plants transitioned from vegetative to the reproductive stage. Species identified in this study that were correlated with increases in either root or shoot biomass were involved in nitrogen cycling (Anaeromyxobacter spp.) and methane production (Methanocella avoryzae.) or were other known endophytes (Bradyrhizobium spp.). Furthermore, many of the microbial community genes and their functions observed during heading, when belowground plant biomass is maximized, were representative of cell growth (e.g. carbohydrate and nitrogen metabolism), while functions correlated with physiological maturity, when aboveground biomass is peaked, were indicative of cell decay. This knowledge will inform future plant breeding efforts to optimize beneficial microbial populations that influence methane emissions and soil health.

8. Water conserving management practices in rice production do not negatively affect grain quality. Depletion of irrigation resources represents a threat to U.S. rice production. To conserve water, U.S. rice producers are adopting alternate wetting and drying water management (AWD) which allows the soil to dry to a predetermined level before re-irrigating the field. Thus far, careful management of AWD practices have been shown to be effective in saving water while maintaining grain yield, but information was lacking on how AWD impacts grain quality. ARS researchers in Stuttgart, Arkansas, conducted two AWD studies using seven rice varieties that are diverse in cooking properties based on grain amylose content and gelatinization temperature. Treatments that differed in the degree of soil moisture and the timing of draining the fields were used to compare to a continuously flooded control. Results demonstrated that the AWD treatments did not affect head rice yield, grain chalkiness, grain size, or grain cooking traits. This research demonstrated that AWD cultural management practices that save irrigation water do not negatively impact grain quality traits that are important to determining crop value.

9. Identification of candidate genes affecting the accumulation of manganese in rice grains. Manganese is an essential element for both animals and plants, with the grain mineral content of rice being especially important for human nutrition because rice contributes a high percentage of calories and nutrition in subsistence diets around the world. Unfortunately, manganese deficiency is common when plants are grown in water-logged soils, such as rice grown in flooded paddies. ARS researchers in Stuttgart, Arkansas, in collaboration with scientists in Texas, Delaware and the United Kingdom, identified six chromosome regions containing genes affecting the accumulation and concentration of manganese in rice grains. Fourteen of these candidate genes are reported to have functions predicted to impact root uptake or tissue-to-tissue transport of manganese or chemically similar elements. Identification of genes associated with the complex processes of nutrient uptake and transport in the plant and deposition in the rice grain, is crucial to the breeding of rice varieties having nutritionally dense grains as well as improved plant health.

10. Discovery of a basis for rice blast disease resistance stability in the Southern USA. Rice blast disease caused by the fungus Magnaporthe oryzae is one of the most devastating diseases for rice production in the Southern USA. Resistance (R) genes in rice can effectively prevent blast disease by detecting and responding to avirulence (AVR) genes in the fungus. These AVR genes are highly unstable causing rice cultivars with new blast R genes to become ineffective after several years of large-scale production, and then cultivars carrying different blast R genes must be developed. However, the underlying molecular basis this is unclear. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers at the Noble Foundation and University researchers in Arkansas and Kansas, along with support from a USDA-AFRI Integrated Grant, analyzed molecular changes of eight AVR genes in 849 strains of blast collected from Southern USA rice production fields during 1959 to 2017. Molecular changes of M. oryzae AVR genes were correlated with which R genes were deployed in rice cultivars over time suggesting that rice R genes influenced the potential for blast epidemics. This knowledge will aid the development of more effective strategies to manage rice blast disease through deployment of new resistant varieties.

11. DNA markers enhance the searchability of the USDA rice world collection for genetic and trait diversity. The U.S. rice genebank is a treasure chest for plant breeders because of the phenotypic and genotypic diversity among the historical cultivars that were grown before modern breeding techniques were developed, as well as, cultivars that are grown in widely different ecosystems. Challenges faced in managing this collection of over 19,000 varieties include providing sufficient and accurate trait information to facilitate searching the collection, and controlling redundant accessions, seed mixtures, and mislabeled accessions, as well as identifying gaps in diversity. To help address these issues, ARS researchers in Stuttgart, Arkansas, used a new system that employs genotyping using a small panel of 24 markers that are trait-specific (TSM), used for fingerprinting (FPM), or are unique to subspecies. In addition, TSMs were used to validate phenotypic data for fragrance, pericarp color, grain cooking quality, resistance to rice blast disease, plant pubescence, and plant height of accessions in the collection. Discrepancies identified between genotypic and phenotypic data are useful for quality control during curation or may present opportunities for identifying novel genes among accessions, particularly for TSMs. In addition, over 2,000 accessions were classified by species, subspecies, and subpopulation utilizing a subspecies marker and FPM. The DNA marker panel was also adequate for differentiating among 100 important U.S. cultivars, which are primarily derived from a narrow genetic background. As a result of this study, TSM and FPM descriptors will be added to the GRIN-Global database and will improve the accuracy and breeding value of the U.S. rice germplasm collection and provide new opportunities for gene discovery.

12. Six rice gene mapping populations are developed for incorporating novel genetic variation from a wild ancestral species into U.S. rice varieties. Rice was domesticated from the wild ancestral species, O. rufipogon, which harbors a wealth of ancestral genes that were lost during the domestication process. ARS researchers in Stuttgart, Arkansas, along with researchers at Cornell University and Chungnam National University, South Korea have developed a set of genetic mapping populations that will serve as a means of incorporating these ancestral genes back into cultivated rice that may offer previously unexplored opportunities for developing new varieties that are tolerant to biotic and abiotic stresses. Cultivated rice, O. sativa, has diverged into the two varietal groups, Indica and Japonica. Six different Chromosome Segment Substitution Line (CSSL) populations were developed from crosses between each of three diverse O. rufipogon accessions originating from China, Laos and Indonesia with a Japonica variety, Cybonnet, developed in the USA and an Indica variety, IR64, developed in the Philippines. Each population consists of progeny that possess small chromosome segments from the O. rufipogon donor parents in the background of the either Cybonnet or IR64, both of which are well adapted for production in the USA. These rice lines can be used by breeders to identify novel genetic variation from the wild ancestral species, O. rufipogon, and easily incorporate the desired gene(s) or trait(s) into locally adapted, elite germplasm for the development of new high yielding, resilient rice varieties. In addition, these populations are a powerful genetic resource for systematic dissection of agronomic, physiological and developmental traits in rice.

13. Discovery of chromosomal regions associated with rice sheath blight disease resistance in global rice varieties that are independent of undesirable plant architecture traits. Sheath blight disease is one of the most damaging rice diseases worldwide, reducing grain yields up to 50%. While some cultivars are more susceptible than others, none are known to be immune, and thus, there is a need to identify additional genes to further improve natural sheath blight resistance in modern rice cultivars. Unfortunately, many resistance genes currently reported are associated with undesirable plant architecture traits like excessive plant height, late maturity, and lodging susceptibility. To identify rice germplasm harboring resistance genes (QTLs) not confounded by plant architecture traits, ARS researchers in Stuttgart, Arkansas, in collaboration with researchers at Guangxi Academy of Agricultural Sciences in Nanning, China, evaluated a diverse collection of over 350 global cultivars for sheath blight resistance and agronomic traits under greenhouse and field conditions. Results identified ten potential genes for sheath blight resistance that were not associated with the undesirable plant traits and high levels of resistance were identified in cultivars having at least four of the ten resistance genes. This indicates breeders will be able to increase resistance to sheath blight through stacking several of these genes from global rice into new varieties adapted to the USA.

14. Use of molecular marker forensics to determine the origin and dispersal patterns of weedy red rice in Taiwan and USA rice production fields. Weedy red rice is a troublesome weed in rice production systems that can greatly reduce yields, quality, and market value of rice. Using a molecular research approach, ARS researchers in Stuttgart, Arkansas, in collaboration with researchers at the Taiwan Agricultural Research Institute, helped determine the source of weedy red rice in Taiwan commercial production fields that was causing significant economic losses for farmers. Molecular markers were used to analyze several hundred weedy red rice biotypes found in rice production fields that led to an understanding of their genetic origins and dispersal patterns. The use of contaminated seed sources and contaminated seed production fields were found to be the major source of weedy red rice in commercial production. Many of the weedy red rice biotypes were found to have originated from heirloom varieties of rice with red-bran seeds that had been cultivated on Taiwan farms in the distant past. These findings provided new insights into how to manage this weed in Taiwan rice production fields which is in stark contrast to the basis of weedy red rice infestations in rice fields in the southern USA where there is no history of growing red-seeded rice varieties or using transplant seeding systems.

15. Seeding rates affect rice growth, grain yield, and economic returns in organic systems. The market demand for organically produced rice is greater than what is currently grown in the USA. One of the biggest production constraints in organic rice is yield losses due to weed pressure since synthetic herbicide use is prohibited. ARS researchers in Stuttgart, Arkansas, in collaboration with university researchers in Texas, Arkansas, Connecticut, and Minnesota, conducted a study to determine the optimum seeding rate to use in organic rice production systems as a means of decreasing weed pressure and maximizing economic returns. Yield linearly increased with increased seeding rates and economic models were used to determine the optimum seeding rates for inbred and hybrid cultivars to maximize economic returns. These results contribute to filling the knowledge gap of how to optimize organic rice production practices and provide a reference to develop improved management strategies for growers.

Review Publications
Jia, Y. 2019. Introductory chapter: Protecting rice grains in the post-genomic era- are we there yet? Book Chapter.
Zhang, Z., Jia, Y., Wang, Y., Sun, G. 2020. A rapid survey of avirulence genes in field isolates of Magnaporthe oryzae. Plant Disease.
McClung, A.M., Chen, M., Jodari, F., Famoso, A.N., Addison, C.K., Linscombe, S.D., Ottis, B.V., Moldenhauer, K.A., Walker, T.W., Wilson, L.T., Mckenzie, K.S. 2019. Use of objective imaging systems to assess subjective grain appearance traits important to the USA rice industry. Cereal Chemistry.
Wu, D., Gealy, D.R., Jia, M.H., Edwards, J., Lai, M., McClung, A.M. 2019. Phylogenetic origin and dispersal pattern of Taiwan weedy rice. Pest Management Science.
Maguffin, S.C., Abu-Ali, L., Tappero, R., Woll, A., Pena, J., Rohila, J.S., McClung, A.M., Reid, M.C. 2020. Influence of manganese abundances on iron and arsenic solubility in rice paddy soil. Geochimica et Cosmochimica Acta.
Rohila, J.S., Edwards, J., Tran, G.D., Jackson, A.K., McClung, A.M. 2019. Identification of superior alleles for seedling stage salt tolerance in the USDA rice mini-core collection. Plants.
Chen, M., Bergman, C.J., Grimm, C.C., McClung, A.M. 2019. A rice mutant with a giant embryo has increased levels of lipophilic antioxidants- E vitamers and gamma-oryzanol fraction. Cereal Chemistry.
Barnaby, J.Y., Huggins, T.D., Lee, H., McClung, A.M., Pinson, S.R., Oh, M., Bauchan, G.R., Tarpley, L., Lee, K., Kim, M.S., Edwards, J. 2020. Vis/NIR hyperspectral imaging distinguishes sub-population, production environment, and physicochemical properties in rice. Scientific Reports.
Abbeloos, R., Bauchet, G., Benites-Alfaro, O., Birkett, C.L., Carceller, P., Costa, B.V., Edwards, J., Finkers, R., Guignon, V., Hok, P., Kilian, A., Laporte, M., Lebauer, D., Lyon, D., Marshall, D., Matthews, D.E., Milne, I., Morales, N., Mueller, L., Papoutsoglou, E., Pearce, B., Perez-Masias, I., Ramirez-Gonzalez, R.H., Rauback, S., Rife, T., Robbins, K., Rouard, M., Selby, P., Sempere, G., Shaw, P., Gordon, S., Uszynski, G., Verouden, M., Backlund, J.E., Salido, M.B., Cornut, G., Gao, S.Y., Patrick, K., Lagare, J.E., Lange, M., Larmande, P., Neveu, P., Prommier, C., Tahore, A., Sarma, C., Scholz, U., Mistry, N., Simon, R., Soldevilla, N., Tovar, C. 2019. BrAPI - An application programming interface for plant breeding applications. Bioinformatics.
McClung, A.M., Rohila, J.S., Lorence, A., Henry, C.G. 2019. Response of U.S. rice cultivars grown under non-flooded irrigation management. Agronomy, 10(1).
Jia, Y., Wang, Z., Jia, M.H., Rutger, J.N., Moldenhauer, K. 2019. Development and characterization of a large mutant population of a rice variety Katy for functional genomics studies and breeding. Crop Breeding, Genetics and Genomics.
Goad, D.M., Jia, Y., Gibbons, A., Liu, Y., Gealy, D.R., Calcedo, A.L., Olsen, K.M. 2020. Identification of novel QTLs conferring sheath blight resistance in two weedy rice mapping populations. Rice.
Jia, Y., Jia, M.H., Want, X., Zhao, H. 2019. A toolbox for managing blast and sheath blight diseases of rice in the United States of America. Book Chapter.
McClung, A.M., Edwards, J., Jia, M.H., Huggins, T.D., Bockelman, H.E., Ali, L., Eizenga, G.C. 2020. Enhancing the searchability, breeding utility and efficient management of germplasm accessions in the USDA-ARS rice collection. Crop Science.
Li, X., Dou, F., Watkins, K.B., Wang, S., Chen, K., Zhou, X., McClung, A.M., Storlien, J.O., Hons, F.M. 2020. Seeding rate effects on organic rice growth, yield, and economic returns. Agronomy Journal.