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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

2021 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 500 rice accessions were rejuvenated using summer and winter nurseries. Seed, data, and panicle images were made available to the public through the National Plant Germplasm System. Work is continuing to reduce duplication in the collection by comparing accessions that have the same name in side by side field evaluation and genotyping. Gaps in the collection were identified and 18 accessions from West Africa and 34 O. australiensis accessions from the International Rice Research Institute have been imported. The Genetic Stocks Oryza (GSOR) collection provided 1305 seed packets to domestic and international researchers. A total of 64 non-red pericarp AUS accessions were evaluated under severe drought conditions. Construction of two mapping populations using the two drought tolerant accessions is in progress. A Bayesian Gaussian mixture model was used to identify four phenotypic groups from 222 wild, ancestral O. rufipogon species complex (ORSC) accessions evaluated for 31 morphological traits. A suite of traits that showed the subpopulations, gene flow between O. sativa and ORSC, and mating habits were identified. Germination tests were completed for six Chromosome Segment Substitution Line (CSSL) libraries derived from three diverse ORSC accessions and two commercial cultivars so the lines can be distributed through GSOR. The intermated progeny from an ORSC backcross population with enhanced yield components are due to small introgressions of candidate genes at multiple loci that may be used for yield improvements. For deployment of these yield enhancing genes, rescreening progeny is planned to identify individuals with the desired allele combinations prior to seed amplification and field yield trials. A subset of introgression lines with yield QTL from a cross between the wild species, O. rufipogon, a known source for abiotic and biotic stress tolerance, with a U.S. long-grain variety, Jefferson, were evaluated to determine whether rising CO2 level alters yield. Two introgression lines with yield QTL on chromosome 1, 3, 9, and 10 increased yield by 33-35% indicating that a combination of these quantitative trait loci (QTL) is responsive to rising CO2 levels. The 260 progenies from a cross of the tropical japonica (TRJ) varieties L201 and Cypress lacked any major blast resistance genes identified by genetic markers were exposed to natural disease pressure in Puerto Rico winter nursery and panicles were collected for blast evaluation to map minor blast resistance genes. For the L-202/Trembese (TRJ) recombinant inbred line mapping population, two years of replicated yield component data collection and initial genotyping were completed in preparation for gene mapping analysis. Progress has been made on a National Science Foundation (NSF) project and two recombinant inbred line (RIL) populations derived from weedy rice sources were advanced and will be used to study the genetic basis of plant competitiveness. A resistance gene PtrBHA responsible for preventing infection by the blast strain IB33 was found in a black hull awned weedy rice strain. To identify field avirulent strains that trigger PtrBHA mediated disease resistance, 200 field blast isolates are being examined for virulence under greenhouse conditions. To identify the candidate genes for AVR- PtrBHA, 30 isolates will be selected based on disease reactions for comparative genome sequencing. Blast isolates purified from rice fields from Arkansas, Louisiana and Puerto Rico were analyzed with five avirulence gene specific markers. To select for germplasm screening in FY22 fifty isolates are being tested with different rice varieties with various blast resistance genes. The Minghui63/M202 mapping population was genotyped with 156 genetic markers and phentoyped with ten blast races. This population is being examined for yield related traits to decide if there is a tradeoff between productivity and blast resistance. Studies are being conducted to compare blast resistance under flood and alternate wetting and drying (AWD) using fourteen selected rice genetic stocks. Twenty-three backcross lines of Katy with the Pi-ta blast resistance gene, into M202 (blast susceptible) were selected based on disease reactions seen in Puerto Rico. These selected lines are being examined for seed traits with the goal to break the linkage block of increased disease resistance with reduced yield. Five QTLs positively affecting tiller number, two QTLs affecting root biomass, and three QTLs affecting shoot biomass were identified using 261 RILs derived from the cross of Francis with Rondo. Several candidate genes of these linked traits were identified for breeding. Global supplies of phosphorus (P) are limited and developing crop plants that use less P is desired. Four introgression lines with QTL controlling tiller number and root biomass were evaluated to investigate the response of P uptake to increasing temperatures. Results showed that P uptake was decreased under a warmer temperature, and inbred lines with high tillers and root biomass had two times higher uptake compared to the other lines. Grain chalkiness and grain element analysis are now being performed. Multi-year field evaluations of 192 RILs in the TRJ cross, Cybonnet x Saber, under water limited conditions using AWD was completed. Fifteen RILs were identified with superior agronomic performance compared to the best performing parent (Saber) even under severe drought conditions. Identification of chromosomal regions associated with superior performance is in progress. In a separate study using the TRJ and Indica gene pools in the Lemont x TeQing CSSLs, seven QTLs were identified for increasing grain yield across four chromosomes under AWD. Another subset of these CSSLs is being used to evaluate the effects of tillering and planting density on yield under severe AWD. Two CSSLs from this population that consistently had high yield under AWD were used to develop a population to map AWD-productivity. Phenotypic and genotypic data were used to select F2s and F3 progeny are being evaluated in the field to verify initial findings. As a part of a NSF grant through University of Pennsylvania, RNA modifications during severe water stress under AWD management are being evaluated. Known as epitranscriptomic signatures, they trigger stress tolerance signals and mechanisms under stress conditions. An international collaboration funded through USAID with Egypt supported a meta-analysis of rice production, agronomic performance, and water use of modern rice cultivars as a means of adapting to the effects of climate change in Egypt. Construction of a heat screening chamber has just been completed and germplasm will be evaluated in YR4. Eight regions in Lemont x TeQing CSSLs on four chromosomes were identified for grain yield under heat stress. Due to a critical vacancy, subobj. 3D1, high field temperatures impacting grain processing quality will be dropped. To investigate the effect of rising CO2 on heat-triggered grain chalk formation and yield, ten inbred lines with a combination of three major QTL for grain chalk were grown under ambient and elevated CO2 levels in combination with elevated temperatures during the grain fill stage. Initial results indicate that under the elevated CO2 the inbred line with QTL on chromosome 4 and 2 reduced chalk by 50% and increased yield by 57% while another line w QTL on chromosome 1 and 2 only reduced chalk by 32% and increased yield by 25%. The experiment has been repeated and grain processing is being performed. Some 2000 Katy mutant lines have been screened using VisNIR imaging and 46 lines with distinctive profiles compared to Katy were selected. In Year 4, validation of VisNIR profile, metabolite profiling and genomic analysis are planned to identify genes that alter grain physicochemical properties. Four loci were identified affecting resistant starch (RS), a fiber like grain component, and progeny segregating for the targeted loci are growing in the 2021 field for subsequent validation. Also, progeny from another segregating cross is being analyzed to elucidate the effects of three genes, Waxy, BEIIb, and a putative locus on Chromosome 8, on RS and starch structures. Analyses of anthocyanins and proanthocyanidins in grains from F6 plants from a cross segregating for these traits are in progress to verify a locus regulating anthocyanin concentrations previously identified. A 6.9 fold range in concentration of proanthocyanidins was found in the F5s. Using molecular markers tagging two genes regulating the on/off expression of proanthocyanidins and anthocyanins, progeny lines were selected to represent two groups: one synthesizing both compounds, and one synthesizing proanthocyanidins only. Continuous distribution of proanthocyanidin concentrations in both groups indicated quantitative inheritance, suggesting that multiple genetic factors are regulating the red pigmented proanthocyanidins. To identify soil microbe associated with grain inorganic arsenic (iAs), four introgression lines with QTLs known to affect grain iAs were grown under both continuous flooding, AWD in field and greenhouse conditions, and the profile of soil microbial composition was determined using metagenomic sequencing. Metagenome assembly is being performed on YR1 soil samples. Collaboration with Arkansas State University and ARS-Jonesboro facilitated using drone imaging to evaluate a small panel of diverse rice germplasm and different cultural management methods in field trials to determine the potential of drone imaging for rice phenotyping. New high throughput genotyping abilities established through collaboration with Louisiana State University (LSU) has facilitated the routine genotypic evaluation of the Uniform Regional Rice Nursery by LSU. Physicochemical traits will be evaluated on any new releases as requested by US public breeders on an as-requested basis.

1. The structure of soil microbial communities is linked with high and low methane emitting rice genotypes. Paddy rice supplies 4% of global methane emissions and is considered a major agricultural contributor to global warming. Methane emissions from rice can be mitigated through reduced irrigation practices, but this can increase nitrous oxide emissions, another important greenhouse gas, and decrease grain yield. Key to meeting these challenges is to breed low methane emitting rice cultivars. However, evaluating genetic variation in greenhouse gas emissions is challenging as measuring gas flux is time-consuming, and labor intensive. Rice genetics and the plant-associated soil microbiome are huge untapped resources for addressing this problem. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers in Beltsville, Maryland, have shown that low and high methane emitting genotypes had contrasting soil microbial profiles of methanogens, methane-producing bacteria, and methanotrophs, methane-oxidizing bacteria, and demonstrated that the profile of particular methanogens and methanotrophs varies corresponding to the amounts of methane produced by rice cultivars. This study holds promise to use the soil microbial profile as a potential phenotyping tool to select for rice breeding lines having low methane emissions

2. Genotype and water management impacts on mitigation of inorganic aresnic in rice. Consumption of rice containing levels of arsenic (As) is linked to adverse health impacts including cancer. Limits have been placed on inorganic As (iAs), the highly toxic form, content in milled rice. Recent studies have shown that rice grain total arsenic (As) accumulation can be mitigated by water management practices such as alternate wetting and drying (AWD) during the growing season. However, a severe drying period not only reduced total As levels but also reduced grain yield, and when mild AWD cycles (also known as safe-AWD) was applied to sustain yield, it failed to reduce grain total As. To protect against yield loss, rice farmers implement “Safe”-AWD practices, which minimizes crop stress while maximizing irrigation savings; therefore, it is important to develop rice varieties that accumulate less grain As under “safe AWD” practices. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers in Beltsville, Maryland, have discovered eight quantitative trait loci (QTL) impacting grain iAs accumulation, and further demonstrated that longer drying periods to meet the same soil moisture content resulted in lower grain iAs levels. This study suggests that coupling longer AWD cycles with the use of cultivars developed to possess multiple QTLs that negatively regulate grain iAs concentrations will be helpful in mitigating exposure of iAs from rice consumption.

3. Release of Tiara rice: a purple bran aromatic cultivar having high antioxidant content. Although most rice is consumed milled, the outer bran layer of the grain contains most of the nutrition. Rice with purple or red pigmented bran colors are high in natural antioxidant compounds that have health beneficial properties. Tiara rice was developed by ARS researchers in Stuttgart, Arkansas, and it combines culinary and agronomic desirable traits along with purple bran, rich in antioxidants. Tiara is an aromatic long grain rice that has a popcorn-like flavor. Compared to its parent, IAC600, it has a 25% increase in grain yield, is one week later in maturity, it has 14% longer grain, and the plant is non-pubescent making it easier to harvest and store the seed. Because most purple bran rice is imported, Tiara provides US growers interested in this high value market with an adapted variety available for domestic production

4. Using machine learning to develop a model that links root attributes with above-ground agronomic traits. Because roots allow plants to acquire water and nutrients, it is expected that a vigorous root system is essential for the development of a high yielding crop variety. However, little is known about how the underground root structure architecture contributes to above-ground shoot growth and grain yield. ARS researchers in Stuttgart, Arkansas, used two gene mapping analysis methods to discover marker-associations with root structure attributes. Genes were first identified associated with individual root traits then, using a multi-trait machine learning model (a Bayesian network), analysis was performed with trait-to-trait associations. Genes identified using the network model were able to explain how roots affect above-ground growth, while the genes identified using the individual traits were not only fewer in number, but also less informative of above-ground traits. A multi-trait genomic selection model for root architecture was developed then validated in selected progeny displaying differences in root architecture. This study demonstrated an analysis approach that can be used by breeders to simultaneously select for numerous below-ground and above-ground traits using genomic information.

5. Discovery of chromosomal regions containing genes regulating accumulation of mineral elements in rice grains. To alleviate malnutrition and improve human health, there is widespread interest in increasing accumulation of nutritive elements (e.g., calcium or potassium) in edible grains while limiting the accumulation of toxic elements (e.g., arsenic or cadmium). ARS researchers in Stuttgart, Arkansas, in collaboration with researchers at Nanjing Agricultural University in China, University of Nottingham in the United Kingdom, and Dartmouth College in New Hampshire, identified and molecularly tagged genes affecting the concentrations of 16 elements in grains, roots, and shoot tissues using a set of 240 recombinant inbred lines and a high-density genetic marker map. Grains were produced using flooded and unflooded field plots, and in a semi-flooded greenhouse study, whereas root and shoot tissues were from hydroponic-grown seedlings. Concentrations and ratios of the elements differed more between roots, shoots, and grains than between grains produced under flooded versus unflooded fields. This indicated that tissue-to-tissue transport mechanisms regulate grain element concentrations more strongly than field irrigation practices known to affect element bioavailability and uptake. Individual chromosomal regions were identified that affect uptake of multiple elements. This information provides guidance to breeders as to the most effective genetic means for improving the nutritive value of rice.

6. Resistant starch in cooked rice is linked to controlling health beneficial gut microbiota. Resistant starch (RS) is a dietary fiber that has many health benefits. However, it is not clear how RS in cooked rice is associated with such health benefits. Utilizing three rice varieties containing different levels of RS and two levels of fat contents in diets fed to rodents in a model system, ARS researchers in Stuttgart, Arkansas, Beltsville, Maryland, New Orleans, Louisiana, and Albany, California, in collaboration with scientists from China, found that RS significantly regulated the gut microbiota composition and function. Cooked rice RS increased the abundance of several microbial taxa that produce biologically active short chain fatty acids that have health benefits to the gut and decreased the abundance of several taxa that are associated with obesity and cardiovascular diseases. In addition, the microbial taxa were correlated with gene expression related to carbohydrate and lipid metabolism in the gut. These results suggest that RS consumed in the form of cooked rice can exert positive effects on the gut microbiome and offers the potential to reduce the risk of obesity and chronic diseases.

7. Using beneficial microbes to control rice blast disease. Blast disease of rice is one of the most challenging diseases that significantly affects stable rice production worldwide. Beneficial microbes associated with rice roots can help plant growth and reduce the damage due to the rice blast fungus. ARS researchers in Stuttgart, Arkansas, in collaboration with scientists from China in Jilin Academy of Agricultural Sciences, Shenyang Agricultural University, Jilin Agricultural University, and the Vegetable and Flower Science Research Institute of Jilin Province isolated the bacteria Bacillus subtilis GB519 from the rhizosphere soils of a rice paddy and showed that GB519 promoted plant growth and inhibited nine fungal pathogens of rice in vitro. Among them, the greatest inhibition was seen for the rice blast fungus. Under greenhouse conditions after rice was exposed to GB519, blast disease was reduced 70% which coincided with accumulated hydrolytic enzymes including amylases, proteases, chitinase and lipases, and the defense enzyme activity of the total antioxidant capacity (TAOC), catalase (CAT) and superoxide dismutase (SOD) in rice. These findings show that beneficial bacteria like GB519 can be used as a biological control agent to control a major fungal disease in rice.

8. Extending the shelf life of brown rice based on grain chemistry and genetics. Whole grain rice has health benefits and is enriched with vitamins, minerals, proteins, and phytonutrients; however, it also contains lipids, which during storage is degraded by various mechanisms resulting in rancid flavor unacceptable to consumers. Knowledge about the factors that contribute to the short shelf life of whole grain rice will facilitate breeding efforts to develop cultivars with long shelf life in the marketplace. ARS researchers in Stuttgart, Arkansas and New Orleans, Louisiana, in collaboration with a scientist at University of Nevada, Las Vegas, utilized 19 rice varieties in a one-year storage stability study and found that lipase, total free fatty acid and poly-unsaturated fatty acids were positively correlated with off-flavor volatile compounds during the early and middle stages of storage; while mono-unsaturated fatty acids were negatively associated with the off-flavor volatile compounds by 6 months and beyond. Four rice varieties were found that had low volatile compounds up to 9- or 12-months, while nine varieties had high volatile compounds as early as three months. These results identified multiple chemical factors as well as varieties that can be used as genetic resources to extend whole grain shelf life in rice.

9. The predicted effects of a warming climate on rice production in the U.S. vary by location. The U.S. is the fifth largest rice exporter in the world. Growers are already experiencing negative effects on grain yield and quality due to warming temperatures, and future projections indicate temperatures are likely to increase by several degrees. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers in Beltsville, Maryland, developed a new rice model and validated it for U.S. production conditions using spatial data from the six largest rice producing rice states. Simulations showed declines in yield up to 20% based on 2040 climate predictions, but these varied spatially through the region. These yield variations were correlated with rising temperatures and negative impacts on grain productivity were slightly offset by elevated CO2. Location specific adaptation strategies can be developed by growers, including adjusting planting dates to avoid heat during anthesis and cultivar selection. These simulations can be used for identifying phenotypic traits ideal for location specific cultivar breeding.

10. Release of Santee Gold rice: an heirloom cultivar with improved agronomic and quality traits. Development of specialty rice varieties is a means of increasing crop value for US growers. Santee Gold was derived from an heirloom variety from the 17th century, Carolina Gold, that was renowned as a high-quality export crop and helped establish the US rice industry. However, that original variety has many undesirable agronomic traits in today’s production systems. Santee Gold was developed by ARS researchers in Stuttgart, Arkansas, to possess the characteristic gold grain hull and cooking quality of Carolina Gold but as a result of its other parent, Presidio, it is 25 cm shorter, three days earlier, has improved resistance to blast disease, is 12% higher in yield, is resistant lodging, has greater grain translucency, and has a 11% longer grain. Because of its improved agronomic and quality traits, it is expected to bring greater economic value to growers interested in this specialty market.

11. Genetic markers and resources for improving blast resistance in rice varieties. Rice blast disease is one of the most lethal diseases for sustainable rice production worldwide, and major disease resistance genes are often broken-down shortly after deployment. Minor blast resistance genes are more durable. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers in the University of Arkansas, Stuttgart and Texas A&M AgriLife Research Center, Beaumont, Texas evaluated disease reactions of two rice breeding parents ‘Minghui 63’ and ‘M-202’ with 11 commonly found US blast races. A recombinant inbred line (RIL) population derived from these parents were evaluated with the 11 blast races and genotyped with 156 simple sequence repeat (SSR) genetic markers. Eight disease resistant QTL from Minghui 63 and two from M202 were located and 16 blast resistant genetic stocks were identified. One QTL, qBLAST2, on chromosome 2 was identified providing resistance to 7 blast races. The remaining resistance QTL were mapped on chromosomes 1, 3, 6, 9, 10, 11 and 12. These findings supply useful genetic markers and resources for marker assisted selection in rice breeding programs.

12. Soybean and maize genes are useful for preventing rice blast disease. Rice blast disease is one of the most challenging diseases of rice globally. The product of isoflavones including genistein is a precursor to produce phytoalexins - antimicrobial compounds that induce broad-spectrum disease resistance. Rice does not have isoflavone and it is unknown if products of isoflavone including genistein from soybean and maize can be used to provide effective resistance to rice blast fungus. ARS researchers in Stuttgart, Arkansas, in collaborations with scientists at University of Arkansas-Pine Bluff and Conagen, Inc. expressed three isoflavone biosynthetic genes, soybean chalcone synthase (CHS) and soybean isoflavone synthase (IFS) genes and the maize transcriptional factor C1/R (CRC) in rice and evaluated transgenic lines for rice blast reactions at University of Arkansas at Pine Bluff. The resulting transgenic lines with increased levels of genistein were more resistant to blast. The greatest level of blast resistance was seen in transgenic lines expressing all three transgenes. The enhanced blast resistance correlated with the amount of genistein, suggests that genistein is involved in reducing the damage by blast. These findings demonstrate a novel method of controlling rice blast disease using naturally occurring genes in other crops.

13. Two rice mapping populations are released for exploring valuable traits in weedy crop relatives. Weedy rice, competing with cultivated rice, is a major agricultural pest worldwide. Knowledge on the competitiveness of weedy rice can help the development of improved rice varieties and improve weedy rice control. ARS researchers at Stuttgart, Arkansas, in collaboration with scientists at University of Arkansas, University of Massachusetts, Amherst, Washington University, released two mapping populations from crosses of the Asian indica rice variety ‘Dee Geo Woo Gen,’ with two weedy rice ecotypes, an early-flowering straw hull type from Arkansas and a late-flowering black hull type from Mississippi. These mapping populations were used to find genomic regions associated with weedy traits, as well as resistance to sheath blight and rice blast diseases. These mapping populations and related datasets are a valuable resource for basic rice evolutionary genomic research and applied marker-assisted breeding efforts in disease resistance and plant competitiveness.

14. Release of two tropical japonica rice germplasm lines with increased seeds per panicle and greater grain length. There is a need to increase rice yield since it is a staple food for half the world’s population. The majority of rice grown in the United States is from the Japonica rice subspecies which is difficult to cross with the high yielding Indica subspecies because of genetic incompatibility. Having rice germplasm available in the Japonica genetic background that possesses greater panicle branching and higher seed production will help U.S. rice breeders develop new cultivars with higher yield. ARS researchers in Stuttgart, Arkansas, released SC14_166, a medium grain germplasm line containing alleles for two major genes resulting in a greater number of primary branches, seeds per panicle, and panicle weight, and SC14_072, an extra-long grain germplasm line containing alleles for two major genes resulting in greater grain length, width, thickness, and kernel weight along with the associated DNA markers. These genetic resources will be used in marker assisted selection by breeders to improve yield and grain size in tropical japonica-based rice cultivar development programs.

15. Discovery of 14 chromosomal regions that increase the number of seed heads per plant in rice. Grain yield in a small grain cereal crop like rice is a function of number of seed heads (panicles) per plant, grain number per head, and seed weight. Increasing panicle number (PN) per plant is one strategy for developing varieties with increased yield potential. Panicles form on the apex of a rice tiller (stem), with each tiller able to produce just one panicle. Increased PN and the associated increase in tiller number (TN) per plant can potentially increase susceptibility to rice sheath blight (ShB) disease due to a denser plant canopy. ARS researchers in Stuttgart, Arkansas, in collaboration with scientists in China at Jiangxi Normal University and at Guangxi Academy of Agricultural Sciences, evaluated a diverse collection of over 410 global rice cultivars to map genes for PN, vegetative stage TN, and ShB disease resistance. Results identified 14 chromosomal regions affecting both PN and TN. In contrast, of the 15 TN genes, only five impacted ShB severity and four of these were advantageous in decreasing ShB severity. This is opposite of the hypothesized effect that the denser plant canopy resulting from the increased TN would promote ShB disease development. Rice breeders can use the molecularly tagged PN, TN, and ShB associated genes to develop rice varieties with enhanced ShB resistance along with increased PN for improved yield potential.

16. Identification of stress responsive superoxide dismutases (SODs) splice variants in rice. Under abiotic stress conditions, the reactive oxygen species (ROS) molecules accumulate in various cellular compartments, such as mitochondria, chloroplast, and cause cell death that eventually leads to reduced grain yield. Members of the superoxide dismutase (SOD) gene family are known to alleviate stress effects by degrading excess amounts of ROS molecules in plant cells, but the knowledge and understanding of SOD genetic splice variants was very limited. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers at Oklahoma State University identified patterns in the location and timing of the SOD splice variants associated with the osmotic-, salt-, oxidative-, and cold stress. The generated new knowledge and understanding will help rice researchers to better utilize the SOD gene family for developing stress resilient rice cultivars.

17. Rice plant-soil microbiome interactions driven by differential root and shoot biomass. Soil microbial communities can increase nutrient availability to plants and influence plant growth and overall health. Plant breeding efforts have the potential to make use of beneficial plant–soil microbiome interactions to increase the health and productivity of a crop. However, more needs to be learned regarding how plant developmental stages and their physiological traits influence soil microbial communities before this plant breeding potential can be realized. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers in Beltsville, Maryland, have demonstrated that shoot biomass may be used as a predictor of root biomass for plant trait-based breeding. Using shoot biomass as a breeding trait would be advantageous over root biomass, as root biomass quantification is time–consuming and prone to error, while shoot biomass quantification is more efficient and accurate. This study underscores the potential of exploiting rice phenotypic variation in plant breeding to promote beneficial plant–soil microbiome interactions.

18. Identification of critical factors that maximize grain productivity in irrigated rice. In order to conserve natural resources, reduced irrigation is critically needed for sustainability of rice production. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers at the Rice Research and Training Center, Egypt analyzed impacts of climate variables, improved cultivars, and various cultivar substitution scenarios in a case study. The study revealed that short duration cultivars with higher yield provided greater net savings in irrigation resources. Also, higher relative humidity (RH) during the rice growing season was found to have a positive impact on rice yields emphasizing the importance of inclusion of RH in future water and heat stress studies and for the physiological improvement of rice for profitable production under reduced irrigation systems.

19. Rising atmospheric CO2 impacts plant cold hardiness. Cold stress (freezing or chilling temperatures) is one of the significant environmental stresses that can severely impact crop yields and limit plant species’ geographical distribution. Cold acclimation in plants involves various physiological and molecular changes that enhance freezing tolerance regulated by both CBF (C-repeat-binding factors)-dependent and -independent pathways. ARS researchers in Stuttgart, Arkansas, in collaboration with researchers in Beltsville, Maryland, have demonstrated CO2 signaling in stomata and CBF-mediated cold signaling work in a coordinated way in Arabidopsis to manage abiotic stress. These results demonstrate the complexity of physiological regulation of the plant’s response to environmental stimuli. Studying stomatal responses to CO2 under cold stress will also help us to understand plant cold-responsive mechanisms under climate change conditions. This information can be translated into essential crops to enhance freezing tolerance and productivity.

Review Publications
Fernandez-Baca, C.P., Rivers, A.R., Maul, J.E., Kim, W., McClung, A.M., Roberts, D.P., Reddy, V., Barnaby, J.Y. 2021. Rice plant-soil microbiome interactions driven by root and shoot biomass. Diversity.
Ruang-Areerate, P., Travis, A.J., Pinson, S.R., Tarpley, L., Eizenga, G.C., Guerinot, M., Salt, D.E., Douglas, A., Price, A.H., Norton, G.J. 2020. Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach. Heredity.
Singh, N., Wang, D.R., Eizenga, G.C., Ali, L.M., Kim, H., Akther, K.M., Harrington, S.E., Kang, J., Shakiba, E., Shi, Y., Declerck, G., Meadows, B., Govindaraj, V., Ahn, S., McCouch, S.R. 2020. A coordinated suite of wild-introgression lines in Indica and Japonica elite backgrounds. Frontiers in Plant Science.
Fernandez-Baca, C.P., Rivers, A.R., Kim, W., McClung, A.M., Roberts, D.P., Reddy, V., Barnaby, J.Y. 2021. Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes. Soil Biology and Biochemistry.
Fernandez-Baca, C.P., McClung, A.M., Edwards, J., Codling, E.E., Reddy, V., Barnaby, J.Y. 2021. Grain inorganic arsenic content in rice managed through targeted introgressions and irrigation management. Frontiers in Plant Science.
Saini, A., Rohila, J.S., Govindan, G., Li, Y., Sunkar, R. 2021. Splice variants of superoxide dismutases in rice and their expression profiles under abiotic stresses. International Journal of Molecular Sciences.
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