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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

2022 Annual Report

1. Conserve, regenerate, characterize and expand rice germplasm and blast fungal collections to provide new genetic resources for rice research. 1A. Conserve and characterize the current NSGC rice collection through phenotypic and genotypic analysis to provide true to type and viable genetic resources for distribution to the research community. 1B. Determine the allelic value of Tropical japonica germplasm for improving US rice cultivars. 1C. Identify new sources of germplasm and associated alleles that result in increased grain yield under AWD management system and growing conditions of the southern U.S. 1D. Characterization of agronomic and physiological performance of weedy (red) rice germplasm biotypes in AWD management systems. 1E. Expand the NSGC collection with the development and characterization of an O. glaberrima/barthii and an O. rufipogon rice wild relative diversity panels and evaluate for agronomic and biotic stress tolerance traits. 1F. Characterize the rice blast fungus M. oryzae (Mo) collection for AVR genes and their response to changing climate and production practices. 2. Discover genomic regions and candidate genes/alleles associated with high yield, reduced environmental impacts, resistance to biotic and abiotic stresses, beneficial microbial interactions, and novel/superior grain qualities that are expressed across environments and management systems (GxExM) by developing and utilizing bioinformatics tools, high throughput phenotyping, and omics-driven analyses. 2A. Map QTLs for root architecture at the seedling stage… 2B. Identify QTL associated with quality production under AWD management… 2C. Evaluate three Chromosome Segment Substitution Line (CSSL) libraries… 2D. Fine map yield enhancing loci derived from O. rufipogon introgressions… 2E. Identify genomic regions associated with increased quality production in response to extremes in temperature. 2F. Identify genomic regions associated with increased quality production in response to biotic stress derived from O. sativa and its wild relatives. 2G. Fine-map and conduct candidate gene analyses for kernel fissure resistance (FR)… 2H. Identify genomic regions… 3. Identify optimum gene combinations using modeling of interactions between agronomic traits, reduced environmental impacts, biotic and abiotic stress tolerance, the plant-microbiome, and rice grain quality parameters that are expressed across environments and management systems (GxExM). 3A. Determine impact of reduced input systems on weed suppression. 3B. Identification and validation of effective QTLs for disease resistance… 3C. Determine the impact of AWD irrigation management… 3D. Determine the impact of abiotic stress… 4. Develop and deploy improved rice germplasm for production under existing and new management systems and for new market opportunities. 4A. Develop improved cultivars and germplasm for production in the southern U.S… 4B. Deploy yield enhancing loci derived from O. rufipogon introgressions… 4C. Determine if yield penalty is associated with disease resistance… 4D. Facilitate the development of new rice cultivars… Please see Project Plan for all listed Sub-objectives.

Rice is one of the most important cereal grains and it is important to sustain USA rice production for both domestic and global food security. A major challenge in rice production is diminishing irrigation resources. One approach being adopted uses alternate wetting and drying (AWD) irrigation that reduces water use by 20%. Yet there are many questions as to how to optimize quality production under this management system. In addition, record high temperatures during grainfill have resulted in yield and quality losses. This project will use genetic resources, genomic sequence data, and high throughput phenotyping to understand the genes and physiological processes that impact rice yield and quality under changing cultural practices and climates. The approach includes 1) exploring diverse genetic resources for novel traits and genes for developing improved rice cultivars that are resilient to changing climates and production practices, 2) identifying genes through mapping of quantitative trait loci (QTL), 3) identifying combinations of genes that result in increased yield and grain quality, and 4) developing and deploying unique combinations of genes in germplasm that will benefit the US rice industry. Central to the program is curation of the USDA’s world rice collection of over 19,000 cultivars. Subsets of this collection are used to create diversity panels that explore specific gene pools (e.g. O. glaberrima, O. rufipogon, Aus, etc.) for response to biotic and abiotic stresses. In addition, a collection of US rice blast (Magnaporthea oryzea) pathotypes will be evaluated for their ability to causes disease in response to different rice genotypes, management systems, and climatic environments (G x M x E). Segregating mapping populations developed from bi-parental matings and chromosome segment substitution lines (CSSLs) developed using wild species will be used to map QTL for response AWD and heat stress, yield production, disease resistance, kernel fissure resistance, and grain nutritional quality. Recombinant inbred lines (RILs) and CSSLs that possess QTLs for these traits will be used to determine which combinations of genes/QTLs provide the most robust response to production under systems using reduced inputs and having high disease and weed pressure as well as abiotic stresses such as drought and high temperatures. Although most of our previous research has focused on above ground traits, this project will include evaluation of root architecture traits and plant-soil-soil microbiome interactions that may be driving above ground phenotypes and responses. Outcomes from this research will include identification of unique germplasm, location of important QTLs, new methods for accurate and efficient phenotyping, and genetic markers linked to QTLs that can be used in marker assisted breeding. Our goal is to deploy improved germplasm that can be used directly as cultivars or as parental stocks in breeding programs that possess unique combinations of genes that provide high yield, superior milling and processing quality, are resilient to pest pressures and abiotic stress, and have unique nutritional quality that will result in high crop value.

Progress Report
Over 450 rice accessions were rejuvenated for the National Small Grains Collection using summer nurseries. Seed, data, plant images and panicle images were released to the public through the National Plant Germplasm System. Reduction of duplicate accessions is in progress by comparing those with the same name in the field phenotypically and by genotyping. About 300 accessions received from Fort Collins are being planted in the field for rejuvenation and characterization. The Genetic Stocks Oryza (GSOR) collection provided 5563 accessions to domestic and international researchers. To identify novel alleles for use in U.S. breeding programs, a global diversity panel of over 500 tropical japonica accessions was assembled and characterized for a wide range of agronomic traits in a two-year field study. Skim sequencing will be completed by the end of Fiscal Year (FY) 2022 and used to identify novel alleles for agronomic Quantitative Trait Loci (QTL) using genome wide association studies (GWAS). In addition, a subset of the panel was established as a micro-core that is being phenotyped for various abiotic stress traits and this will be used in genomic prediction studies for the whole tropical japonica core panel. To facilitate annotation of resequenced U.S. rice accessions, a GWAS dataset was compiled with peak Single Nucleotide Polymorphism (SNP) chromosome locations and allele effects for traits including yield components, grain quality, cold and salt tolerance, sheath blight and straighthead resistance, and grain arsenic content. The multiparent advanced generation intercross (MAGIC) population was evaluated for YR2 in the field for yield and yield related traits. YR1 yield component data collection was completed and YR2 panicle and seed data collection are progressing. The population was genotyped with the 7,098 Single Nucleotide Polymorphisms (SNPs) Cornell-IR LD Rice Array (C7AIR) marker panel. Once data collection is completed, QTL and Bayesian network analyses will be conducted to dissect genes underlying yield related traits. Of the 150 accessions included in the Africa Rice Panel, comprising both O. barthii (48) and O. glaberrima (102) accessions, 87 were included in the skim sequencing set and published genotypes will be used for the remaining 63 accessions. Once the genotyping is completed, GWAS will be conducted utilizing the phenotypic data previously collected. The YR2 field evaluations of AUS accessions that were recently received from APHIS import were completed and the GWAS analysis is in progress. A total of 200 blast isolates were purified from rice fields from Arkansas, Louisiana and Puerto Rico and these isolates were analyzed with 5 pathogen avirulence gene specific markers and simple sequence repeat markers and data are being analyzed for identification of new races for germplasm screening. The root structure architecture of ~120 TeQing-into-Lemont backcross introgression lines (TILs) was evaluated in 3 replications. Root images of 2-week-old seedlings were defined using more than 100 data points per sample acquired from analysis of winRhizo images collected in FY 2021. Data are being analyzed for outliers before calculating trait BLUPs for future trait-by-trait and QTL analyses. Global supplies of phosphorus (P) are limited and developing crop plants that use less P is desired. Four TILs with known QTLs controlling tiller number and root biomass were further evaluated to investigate how these traits affect P uptake under increasing temperatures. Results showed that P uptake was decreased under warmer temperature, and further showed root biomass differences had stronger influence over P-uptake than did tiller number differences. Field characterization of a Cybonnet (CYBT) x Saber (SABR) mapping population was completed. All phenotypic measurements were collected, and 12 major QTLs on chromosomes 3, 6 and 9 have been identified for limited soil moisture stress (-30 kPa) tolerance under alternate wetting and drying (AWD) management. A comprehensive genomic analysis on the study is in progress. Three Chromosome Segment Substitution Line (CSSL) libraries with O. rufipogon/O. nivara introgressions from different donors in the IR64 background were phenotyped in the greenhouse and seed amplified for future Dale Bumpers National Rice Researcher Center studies. Seed of 20 IR64 CSSLs with poor (<1%) germination was amplified for distribution through GSOR. Phenotypic data for the three Cybonnet libraries derived from the same 3 donors, was collected in the field and seed amplified for future studies. Three Jefferson introgression lines (ILs) with enhanced yield and O. rufipogon introgressions in chromosome 2, 6 or 8 respectively, were backcrossed to Jefferson. Analysis of the segregating progeny from the three backcross populations revealed the reported yield advantage was not a result of the target O. rufipogon introgressions. Instead, multiple loci were found that each controlled a subset of yield components, thus no single introgression could be targeted for field evaluations. From the Presidio/O. rufipogon (Wild-5) advanced backcross population, 276 progenies with adequate seed for conducting blast evaluations were genotyped with the 1024 SNPs included in the IRRI Rice Custom Amplicon panel (RiCA V4). These progenies will be evaluated for reaction to at least two blast races in YR5. The construction and testing of a greenhouse heat screening chamber is completed and will be used to test AUS and TRJ rice germplasm for heat tolerance. Minghui 63/M202 mapping population was genotyped with 156 genetic markers and phenotyped for resistance to ten blast races, percent chalk and yield components. Identification of the common loci responsible for both disease resistance and yield components is in progress. Increasing dietary intake of resistant starch (RS), a dietary fiber, can stabilize blood sugar levels and decrease cancer risk, making it desirable to increase RS in rice grains. Study of rice grains from F6 progeny lines of IR36m x ‘242’ segregating for RS content verified the effect of two genes, and newly identified 3 genes regulating RS content. Grains from F4 KatyM x IR36m mapping population were also analyzed for RS, and samples provided to collaborator for starch structure analysis to elucidate the effect of 3 gene interactions (Waxy, BEIIb, and the new KatyM mutation on chromosome 8) on RS and starch structures. Also, the IR36m x ‘242’ progeny population is used to study flavonoid biosynthesis genes that regulate the concentrations of anthocyanins and proanthocyanidins. Analyses of anthocyanins and proanthocyanidins in grains from F6 plants were accomplished FY22 and data used to verify a newly detected locus on chromosome 3 as regulating anthocyanin concentrations, and to discover that it similarly contributes to variance in proanthocyanidin content. Three QTL affecting grain arsenic concentration were validated by identification in more than one mapping population. While one of these QTLs contains a single candidate gene, additional genetic recombination within two QTLs will be required to distinguish between the multiple candidate genes in those genomic regions. Thirty TILs selected for having extreme differences in tiller number and root biomass were evaluated for a 2nd year under AWD versus flooded growth conditions. Preliminary analysis in Fiscal Year 2022 of data collected FY 2021 indicated some of these lines better tolerated the severe dry conditions associated with AWD conditions by maintaining a high number of tillers per plant, while other lines retained yield under AWD conditions by maintaining larger panicle size and increased fertility. A 2nd year of plant samples is currently being analyzed. A QTL for maintained tiller number initially mapped to chromosome 4 using F2 data (FY2021) was validated using F2:3 progeny (FY2022). Similarly, using progeny from a second cross, a QTL for high fertility and panicle weight under AWD was mapped (F2, FY21) and validated (F2:3, FY22) to chromosome 5. F3:4 progenies from each cross are being grown in the field to detect and validate additional QTLs for tolerance to AWD-related stress. Due to three critical vacancies most planned activities for the objectives 3 and 4 were dropped. For subobjective 3b, third year evaluation of fourteen blast resistant rice genetic stocks with different combinations of blast resistance genes for yield and yield related traits are being conducted under AWD and Flood conditions. For the subobjective 4c, 50 Pi-ta backcrossed lines based on seed size in 2021 are being grown in the field for final selection for genotyping with markers at Pi-ta blast resistance genes to define the linkage block breakage points for resistance versus seed size. In FY 2021, a collaboration with Arkansas State University and ARS-Jonesboro was established to explore the use of drone imaging to detect agronomic, and growth and development differences among various rice cultivars and differences due to fertilizer rates. The second year of this collaborative field study was conducted in FY 2022.

1. Improving regeneration, characterization, and curation of the rice germplasm. Genebanks are collections of genetically diverse food crops and wild species world-wide. The National Small Grains Collection (NSGC) and Genetic Stocks Oryza (GSOR) genebanks are critical resources for safeguarding the genetic diversity of rice. However, rice genebanks are faced with a multitude of potential issues that must be addressed such as mis-identification of accessions, seed mixtures, redundant accessions, and lack of adequate phenotypic and genotypic characterization. Therefore, to facilitate effective and efficient curation of the NSGC and the GSOR germplasm, ARS researchers in Stuttgart, Arkansas, developed a standard operating procedure (SOP) document. This SOP is the first of its kind developed for rice germplasm curation in the U.S. The implementation of this SOP enhances the value and utilization of the germplasm, especially for economically important traits that U.S. rice breeders select for. The stakeholders can be assured of true-to-type germplasm with good viability and reassure their confidence in the rice germplasm collections for years to come. NSGC and GSOR distribute about 1500 and 9800 rice accessions per year, respectively. The impact of the germplasm collections is evidenced by the numerous peer reviewed publications documenting detailed phenotypic and/or genotypic characterization of NSGC and/or GSOR rice germplasm as part of diverse research projects.

2. Disinfection of rice seeds with bacteria using ultraviolet (UV). Field harvested rice seeds contaminated with bacteria are a concern for rice distribution. A simple method to remove bacteria is currently not available. ARS researchers in Stuttgart, Arkansas and Raleigh, North Carolina, report that most bacteria can be eliminated when rice seeds are treated with ultraviolet photon with a 274 nm wavelength for 5-6 days under a biosafe flow cabinet. Seeds were placed in a sterilized mesh bag and a sterilized coin envelope. Seeds were removed at different times after UV irradiation and placed in a nutrient agar medium in a dark incubator at 29°C for 3 days for counting bacteria and fungi associated with each seed. The rate of germination of UV treated seeds was assessed 5 days after incubation. The results show that rice seeds treated with UV for 5-7 days in a mesh bag, not in a coin envelope with rotation once a day is adequate to eliminate most bacteria from seeds. In contrast, fungi from rice seeds were not significantly impacted by the same amount of UV photons. The germination ability of these treated seeds remains unchanged. This seed disinfection method is useful to eliminate bacteria for global seed distribution and sharing.

3. First report of bacterial leaf blight disease caused by Pantoea ananatis in the USA. Detection of diseases that are uncommon to the USA rice production area is important for sustaining the rice industry and production of this globally important cereal grain. ARS researchers in Stuttgart, Arkansas, with researchers from University of Arkansas Rice Research and Extension Center, and Colorado State University, report the first identification of bacteria leaf blight disease in rice plants in the USA. It was identified in a global collection of rice cultivars grown under field conditions in Arkansas. Subsequent studies determined that this was caused by Pantoea ananatis which is a bacterial organism commonly found in nature, but which has only rarely been associated with disease symptoms in rice. DNA analysis of the bacterium using primers that are specific to the gyrB gene verified that the organism was P. ananatis. To verify pathogenicity, a rice cultivar grown in a greenhouse were inoculated with purified bacteria. After 7 days, bacterial cultures were recovered from the inoculated leaves which were confirmed to be P. ananatis by using DNA specific primers. Based on colony morphology, pathogenicity tests, and DNA analysis, the causal bacterium for the leaf blight-like symptoms was determined to be P. ananatis. Knowledge that P. ananatis causes bacterial leaf blight symptoms in susceptible varieties of rice grown under field conditions of the southern USA is important to develop effective disease management strategies.

4. Release of a blast resistant rice germplasm Eclipse. Rice blast disease is one of the most damaging diseases for sustainable rice production worldwide. Blast disease is managed using fungicides, extra irrigation water and genetic resistance. Water has been a limiting factor for rice growers in the USA. The use of major effect blast resistance genes can reduce water consumption and production cost. ARS researchers in Stuttgart, Arkansas, backcrossed two durable blast resistance genes, Pi-ta and Ptr from the tropical japonica rice variety Katy into the premium medium grain rice variety M202 and evaluated quality and disease resistance using genetic markers. Blast resistance of Eclipse was verified under greenhouse and field conditions in Louisiana and Puerto Rico. Results demonstrated that Eclipse is a blast resistant, rice germplasm with the semidwarf gene sd1 allele from the green revolution donor, Dee-geo-woo-gen. These findings supply a useful rice germplasm along with genetic markers for breeders to use for marker assisted selection to develop blast resistant medium grain rice cultivars.

5. Mechanism of resistance to arsenic-induced straighthead disease. There is global concern that excessive accumulation of arsenic in rice grains can impinge on human health. Arsenic is also toxic to plants and causes a disorder in rice known as straighthead disease. Existence of genetic variation in straighthead resistance suggests that rice has evolved genes and mechanisms that reduce the arsenic toxicity in some way, through reduced arsenic uptake, or detoxification inside the plant. Because these mechanisms would also be expected to reduce the accumulation of arsenic in rice grains, a study by ARS researchers in Stuttgart, Arkansas and St. Paul, Minnesota, studied if genes affecting straighthead would frequently also impact grain-arsenic by mapping QTLs for both traits using a set of diverse rice varieties collected from around the world. Of the33 QTLs for straighthead and 15 QTLs for grain arsenic, only four affected both traits indicating that straighthead resistance and grain-arsenic are more strongly regulated by different genes/mechanisms than by common ones. Further analysis of genes within the QTLs suggested that straighthead resistance is more affected by amelioration of stress induced reactive oxygen species (ROS) than by differences in arsenic uptake.

6. Improving processing quality of nutritious brown rice flour. Brown rice is considered more nutritious than milled rice because it retains the bran layer which is rich in vitamins, oil, and protein. Milled rice flour is growing in popularity as a food ingredient due to its hypoallergenicity and bland taste. However, there is little information about the suitability of brown rice flour for this use. ARS researchers in Stuttgart, Arkansas, collaborated on a study with the University of Arkansas that demonstrated the impact of protein denaturization and/or lipid removal on starch gelatinization temperature of brown rice flour. The treatments altered starch swelling, pasting, and water solubility properties along with the gelatinization temperature of the rice flour. These results showed that such treatments can improve heat and shear stabilities of brown rice flour that may be important for new food products using rice as an ingredient. This will help expand the use of rice by the processing industry and will improve the nutritional quality of food products for consumers.

7. Have a sip of some purple rice. The nutritional beverage market is a rapidly growing industry and some of the products use milled or brown rice as the core ingredient. However, sprouted grains are known to possess a wide variety of compounds that are associated with health beneficial properties, suggesting that sprouted rice may serve as a nutritionally enhanced ingredient for plant-based beverages. In a collaborative study between ARS researchers in Stuttgart, Arkansas and New Orleans, Louisiana, five diverse rice varieties were evaluated for 19 volatile compounds that may affect flavor to identify a rice variety that provides the best combination of sensory traits and nutritional compounds. A purple bran aromatic variety was identified as having the highest levels of favorable volatiles as well as being high in natural anti-oxidant compounds. This research demonstrates expanded opportunities for using rice as a flavorful and nutritional ingredient for new food and beverage products.

8. Rapid scanning of single kernels of rice to predict cooking quality. Rice cooking and processing quality is largely determined by the amount of starch and the temperature of its gelatinization when cooked. Most rice varieties developed in the USA have uniform cooking quality but imported rice or hybrid rice may have variable cooking properties. A single kernal near-infrared (SKNIR) instrument was developed by ARS researchers in Manhattan, Kansas, that can rapidly scan individual raw kernels of milled rice using near-infrared wavelengths. This method has been shown to be able to predict the starch content of a single grain and, in a previous study, predict the gelatinization temperature of the grain when it is cooked. These results demonstrate that such instrumentation may be used to segregate mixed samples of rice to assure uniformity in cooking and processing quality which is important to the processing industry that produces parboiled, instantized, and canned rice.

9. Crop production environments affect the nutritional quality of rice bran – an emerging superfood. Most rice is consumed after removing the outer bran layer through milling. However, rice bran is rich in fatty acids, phytochemicals, B and E vitamins, and soluble and insoluble prebiotic fibers. There is interest in utilizing rice bran as an ingredient in foods and beverages, but the bran can also store toxic elements like arsenic. In a study conducted with Colorado State University and ARS researchers in Stuttgart, Arkansas, rice brans were obtained from 10 global production areas to determine the effect of cultural practices and growing location on arsenic content in rice bran. The survey demonstrated that there is huge variation in total and inorganic arsenic content in rice brans sourced from different countries. However, production under organic or conventional methods did not differ in arsenic, nor did postharvest bran fermentation processes. Given the suite of health benefits and increasing attention to rice bran as a superfood, it is imperative to examine agronomic and postharvest processes that minimize arsenic content in rice bran and will help expand its use as a nutritionally enhanced ingredient.

10. Chromosomal regions for rice tiller number (TN), shoot biomass (SB), and root biomass (RB). Tillering is a key determinant of grain yield and biomass in rice. Another important agronomic trait is the root system which is responsible for water and mineral uptake, competition with weeds, and tolerance to some biological pests. Roots are a critical factor in the two-way interaction between plants and the environment, with RB shown to affect soil microbial populations and rates of methane emission from paddy-grown rice. To better understand productivity in rice as well as the interaction of the rice plant with the environment, this study by ARS researchers in Stuttgart, Arkansas, identified QTLs affecting TN, SB, and RB using a set of some 250 recombinant inbred lines that were genotyped with 7000 DNA markers. Plants were observed at the maximum tillering (vegetative) stage under greenhouse conditions and at maturity in the field which allowed identification of QTLs stable across different environments and growth stages. A total of 11 QTLs were identified, 6 for TN, 2 for RB, and 3 for SB. Candidate genes underlying the 11 QTLs were identified using annotated gene databases and provide an understanding of the genetic and physiological mechanisms underlying these traits which can be used by breeders to develop high yielding rice varieties.

11. New knowledge on regulation of abiotic stress tolerance in plants. Abiotic stress tolerance is an extremely complex trait and often DNA alone is not able to fully explain the tolerance mechanisms. ARS researchers in Stuttgart, Arkansas, with researchers at the University of Pennsylvania and Oklahoma State University, studied the plant epitranscriptome and found that methylation status of mRNAs (transcripts) alters in response to cold stress treatment of Arabidopsis plants. In the study, it was concluded that specifically the abundance of the m6A-containing transcripts was significantly increased, and these differentially methylated mRNA impacted cold stress tolerance capabilities of the plants via modifying expression of several known cold stress tolerance genes and related cold-stress tolerance mechanisms. This novel strategy of mRNA modifications provides new avenues to scientists for fine tuning of abiotic stress tolerance in plants for improving abiotic stress tolerance and climate resiliency in rice and other crop plants.

12. Lost genes identified in Oryza rufipogon species complex (ORSC). Crop wild relatives (ORSC) represent valuable reservoirs of useful characteristics for breeding including tolerance to extremes in climate and plant pests lost during domestication. The ORSC is the ancestral genepool of cultivated rice (O. sativa) and potentially harbors novel alleles for the aforementioned stresses, useful for rice improvement. The ORSC is comprised of perennial, annual and intermediate forms which are designated as O. rufipogon, O. nivara, and Oryza species in genebanks. “Oryza species” refers to an annual form of mixed ancestry possessing combinations of the traits which characterize O. rufipogon, O. nivara and O. sativa. Understanding the relationships between ORSC accessions collected from diverse locations and environments will enable rice geneticists and breeders to make selections for both introgressing novel genes into new cultivated rice varieties and for domestication studies. ARS researchers in Stuttgart, Arkansas, along with researchers at Cornell University and the International Rice Research Institute, characterized a collection of ORSC accessions for standard phenotypic traits used by genebanks. Statistical modeling ascertained three phenotypic groups based on a subset of phenotypic data collected from previously genotyped ORSC accessions. These groups were consistent with the three genebank species designations and similar to the previously delineated genotpyic groups. One phenotypic group was predominantly O. rufipogon accessions, the second group was predominantly O. nivara accessions and the third group had the most accessions identified as Oryza species with levels of cultivated rice (O. sativa) accounting for >50% of the genome. This third group is potentially useful as a “pre-breeding” pool for breeders attempting to incorporate novel variation into elite breeding lines.

13. Novel source of sheath blight resistance in a wild Oryza nivara accession. Sheath blight disease, caused by the Rhizoctonia solani fungus, is one of the most prevalent fungal diseases of cultivated rice and results in significant economic damage to rice production worldwide. No source of complete resistance to sheath blight disease has been identified in cultivated rice (Oryza sativa). The wild Oryza species, which are closely related to cultivated rice, are a potential source of important traits including new resistance genes to fight pests like sheath blight disease. O. nivara is a rice wild ancestral species that can be successfully crossed with cultivated rice. ARS researchers in Stuttgart, Arkansas, in collaboration with a visiting scientist from Guangxi Academy of Agricultural Sciences, China, developed and evaluated the LaGrue/O. nivara (Wild-4) advanced backcross inbred line progeny for reaction to sheath blight disease. The population was derived from LaGrue, a popular southern U.S. long grain variety, which is susceptible to sheath blight disease and a moderately resistant the O. nivara accession. Data analysis revealed one major chromosomal region on the distal region of chromosome 9 associated with the sheath blight resistance attributed to the O. nivara parent. This region was previously identified in cultivated rice but the O. nivara species may possess a novel resistance allele which can be used in the development of elite rice varieties that will decrease crop vulnerability to this important disease.

14. Selection tools for broad-spectrum blast resistance. Broad-spectrum blast resistance is required to protect rice from the recent and mutated blast races. Although major effect blast resistance genes are deployed are highly effective, it is common for resistance genes to lose their effect due to genetic changes in the pathogen. A combination of multiple small to moderate effect genes results in more durable disease resistance. ARS researchers in Stuttgart, Arkansas, evaluated resistance to 11 aggressive blast fungal races in a mapping population derived from the blast resistant variety ‘Katy’ with a blast susceptible rice line PI 312777 and genotyped the population with 7,000 SNP markers. The results verified resistance spectra of major genes Pi-ta/Pi-ta2/Ptr, Pi-ks, and PiGD-3(t) and identified 13 minor resistance QTL. Genomic selection models were developed to predict blast resistance to each fungal race, and a genomic selection rank sum index was developed to select individuals with the highest resistance across all fungal strains. These results demonstrate that genomic selection is effective for achieving broad-spectrum blast resistance and provide a new tool to help plant breeders develop blast resistant varieties.

15. Cultural practices for smart rice in a sustainable agriculture system. Rice is a staple food and primary source of calories and mineral nutrients for much of the world but can also be a dietary source of toxic elements like arsenic and cadmium, and production in traditional flooded paddies requires significant water resources and emits greenhouse gasses. ARS researchers in Stuttgart and Jonesboro, Arkansas, in collaboration with researchers at the University of Arkansas, University of Delaware, and Cornell University, conducted a literature review and identified value in combining two independently developed production modifications. Several studies have shown that growing rice unflooded for all or part of the growing season, known as furrow rice and alternate-wetting-and-drying, respectively, can reduce water usage and reduce the level of arsenic in the harvested rice grains. Use of reduced flooding periods and addition of silicon from rice husks have been shown to independently decrease accumulation of arsenic in rice grains. Because silicon has also been shown to improve rice drought tolerance, combining the two strategies could allow use of even longer dry periods during rice production, which would further decrease grain arsenic, water costs, and greenhouse gas emissions. This literature review showed how combining rice husk application with reduced water production systems could alleviate multiple sustainability challenges in rice production: (1) reduce toxic elements in rice grains; (2) minimize greenhouse gas emissions from rice production; (3) reduce irrigation water use; (4) improve nutrient use efficiency; (5) utilize a waste product of rice processing; and (6) maintain plant-accessible soil silicon levels. This review further provided guidance to scientists by highlighting remaining research issues.

Review Publications
Chen, M., Bett Garber, K.L., Lea, J.M., McClung, A.M., Bergman, C.J. 2021. High resistant starch rice: variation in starch related SNPs, and functional, and sensory properties. Foods.
Jia, Y., Singh, V., Gealy, D.R., Liu, Y., Ma, J., Thurber, C.S., Roma-Burgos, N., Olsen, K.M., Caicedo, A.L. 2021. Registration of two rice mapping populations using weedy rice ecotypes as a novel germplasm resource. Journal of Plant Registrations.
Abdelrahman, M., Wei, Z., Rohila, J.S., Zhao, K. 2021. Multiplex genome editing technologies for revolutionizing plant biology and crop Improvement. Frontiers in Plant Science.
Zhao, H., Liu, Y., Jia, M.H., Jia, Y. 2022. An allelic variant of the broad-spectrum blast resistance gene Ptr in weedy rice is associated with resistance to the most virulent blast race IB-33. Plant Disease.
Jia, Y., Jia, M.H., Yan, Z. 2022. Mapping blast resistance genes in rice varieties ‘Minghui 63’ and ‘M-202’. Plant Disease.
Zargar, S.M., Mir, R.A., Ebinezer, L.B., Masi, A., Hami, A., Manzoor, M., Salgotra, R., Sofi, N.R., Mushtaq, R., Rohila, J.S., Rakwal, R. 2022. Physiological and multi-omics approaches for explaining drought stress tolerance and supporting sustainable production of rice. Frontiers in Plant Science.
Pinson, S.R., Heuschele, D.J., Edwards, J., Jackson, A.K., Sharma, S., Barnaby, J.Y. 2022. Relationships among arsenic-related traits, including grain arsenic concentration and rice straighthead resistance, as revealed by genome-wide association. Frontiers in Genetics.
Morales, N., Ogbonna, A.C., Ellerbrock, B.J., Bauchet, G.J., Tantikanjana, T., Tecle, I.Y., Powell, A.F., Lyon, D., Naama, M., Simoes, C.C., Saha, S., Hosmani, P., Flores, M., Panitz, N., Preble, R.S., Agbona, A., Rabbi, I., Kulakow, P., Peteti, P., Kawuki, R., Esuma, W., Kanaabi, M., Chelagant, D.M., Uba, E., Olojede, A., Onyeka, J., Shah, T., Karanja, M., Egesi, C., Tufan, H., Paterne, A., Asfaw, A., Jannink, J., Wolfe, M., Birkett, C.L., Hershberger, J.M., Gore, M.A., Robbins, K.R., Rife, T., Chaney, C., Poland, J., Arnaud, E., Laporte, M., Waring, D.J., Brown, A., Bayo, S., Uwimana, B., Akech, V., Yencho, C., De Boeck, B., Campos, H., Swennen, R., Edwards, J., Mueller, L.A., Kulembeka, H., Salum, K., Mrema, E. 2022. Breedbase: a digital ecosystem for modern plant breeding. G3, Genes/Genomes/Genetics.
Li, X., Jiang, J., Guo, J., McClung, A.M., Chen, K., Velarca, M., Torbert Iii, H.A., Dou, F. 2022. Effect of nitrogen application rate under organic and conventional systems on rice (Oryza sativa L.) growth, grain yield, soil properties, and greenhouse gas emissions. Journal of Plant Nutrition.
Siaw, M.O., Yang, Y., McClung, A.M., Mauromoustakos, A.S. 2021. Effect of protein denaturation and lipid removal on rice physicochemical properties. LWT - Food Science and Technology.
Weber, A.M., Baxter, B.A., McClung, A.M., Lamb, M.M., Becker-Dreps, S., Vilchez, S., Koita, O., Wieringa, F., Ryan, E.P. 2021. Arsenic speciation in rice bran: agronomic practices, postharvest fermentation, and human health risk assessment across the lifespan. Environmental Pollution.
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