Research Project: Broadening and Strengthening the Genetic Base of Rice for Adaptation to a Changing Climate, Crop Production Systems, and Markets

Location: Dale Bumpers National Rice Research Center

2025 Annual Report

Objectives
1. Develop new climate-resilient rice with stable and high-quality yield, reduced irrigation needs, and lower methane emissions for sustainable U.S. agricultural production, and safer food supplies using new technologies. 2. Characterize and strengthen the rice germplasm collection and the blast fungal collection for genetic diversity to foster adaptation to climate change and to reduce vulnerability to biotic stress. 3. Identify the genes and gene networks that underlie beneficial rice traits to produce rice with increased economic productivity, resistance to biotic and abiotic stress, and enhanced value for human nutrition and processing. Identify the genes and gene networks that underlie beneficial rice traits to produce rice with increased economic productivity, resistance to biotic and abiotic stress, and enhanced value for human nutrition and processing. 4. Identify for critical environments the optimum gene combinations for climate-resilient, stable agronomic performance, and biotic/abiotic stress tolerance using artificial intelligence/machine learning approaches to analyze genomic information and high-throughput phenotyping data. Please see copy of upload Project Plan for all subobjectives; due to character limit they will not fit in this field.

Approach
The approach includes 1) developing germplasm and tools for breeding climate-resilient rice for sustainable U.S. agricultural production, 2) exploring diverse genetic resources for novel traits and genes to foster adaptation to climate change and to reduce vulnerability to biotic stress, 3) identifying the genes and gene networks that underlie beneficial traits to produce rice with increased economic productivity, resistance to biotic and abiotic stress, and enhanced value for human nutrition and processing, and 4) identifying optimum gene combinations for climate-resilient rice with stable agronomic performance and biotic/abiotic stress tolerance using artificial intelligence (AI) /machine learning to analyze genomic information and high-throughput phenotyping data. Marker assisted selection and rapid generation advance will be used to develop conventional and specialty breeding materials for release to US breeding programs. Efficient new methods will be developed for phenotyping traits associated with climate resilience and grain quality. Interactions between soil microbes, greenhouse gas emissions, grain quality and quantity under different irrigation systems will be evaluated. Mapping populations will be developed and evaluated to discover novel alleles from rice wild relatives that provide adaptation to abiotic and biotic stress. The USDA’s world rice collection of over 19,000 cultivars will be mined to discover useful novel alleles through the characterization of sub collections including a Tropical japonica Core (TRJC) collection, an aus subpopulation collection, weedy rice, and rice wild relative collections of O. glaberrima, O. barthii and O. australiensis. In addition, the US rice blast (Magnaporthea oryzea) field isolates will be characterized to guide the deployment of blast resistance genes. Several mapping populations will be used to identify genes and gene networks including a Japonica Multi-parent Advanced Generation Inter-Cross (MAGIC) population for yield components, an aus nested association mapping (NAM) population for water deficit and high temperature stress tolerance, and biparental populations for grain mineral accumulation. Genes and gene interactions involving biotic stress will be investigated using yeast two hybrid (Y2H) screening, and tradeoffs between biotic and abiotic stress responses will be investigated by gene expression analysis of varieties with differential blast resistance genes. Machine learning and artificial intelligence methods will be developed and deployed for high-throughput phenotyping using UAV or ground-based imaging systems. A database will be developed for genomic selection and a rapid cycle recurrent selection (RCRS) breeding pipeline will be established for fast rice breeding. The RCRS pipeline will be used to breed germplasm with increased quantitative resistance to sheath blight and cold tolerance. Outcomes from this research will include new public germplasm, new methods for accurate and efficient rice breeding, and genetic markers linked to traits that can be used in marker assisted breeding.

Progress Report
Under Objective 1: To develop improved climate resilient rice germplasm with high yield and quality, progeny of complementary crosses of elite US germplasm are undergoing self-pollination at BC2 and BC3 generations. The Tropical Japonica (TRJ) micro core (133) accessions plus twelve check varieties were assessed for salt tolerance at an electroconductivity (EC) level of 6.00 under greenhouse conditions. The Presidio x O. rufipogon (Wild-5) advanced backcross inbred line (BIL) population, consisting of 240 BILs, was evaluated for reaction to rice leaf blast disease using six different blast races (IA1, IB33, IB49, IB45, IB54 and IE1K). Three BILs exhibited resistance to all six races and based on 249 DNA markers, the chromosome 6 O. rufipogon introgression from 25.3 to 30.8 megabases (Mb) common across the three BILs, suggesting the blast resistance gene resides in this region. The three chromosome segment substitution line (CSSL) libraries in the Cybonnet (CYBT) background with introgressions from three different ancestral donors (O. rufipogon or O. nivara), identified as CYBT/OrA, CYBT/OrB and CYBT/OrC, are currently being evaluated in the greenhouse for drought tolerance contributed by the ancestral donor at the tillering and reproductive stage using six different measurements of drought stress. At harvest (maturity), four additional indices of drought stress will be determined. Under Objective 2: The Genetic Stocks Oryza (GSOR) shipped 7,471 seed packets from 58 seed requests. GSOR provided 6,863 packets to domestic researchers and 608 to international researchers. The National Small Grains Collection (NSGC) received seed and phenotypic data of 182 rejuvenated accessions and GSOR added seed and phenotypic data of 75 rejuvenated accessions from the 2024 growing season. In FY25, approximately 831 NSGC and 58 GSOR accessions are being rejuvenated using experimental fields and greenhouses. Approximately, 128 accessions requested from Fort Collins are being evaluated in the 2025 field season. Grouped sets of 351 NSGC accessions that are redundant by name (RBN) are being evaluated phenotypically and genotypically in the 2025 growing season to address redundancy. In collaboration with researchers at Purdue University, West Lafayette, Indiana and the International Rice Research Institute (IRRI) in the Philippines, the set of 32 tropical japonica accessions selected for early growth stage drought tolerance were evaluated under alternate wetting and drying (AWD) and irrigated conditions in field study at Stuttgart, Arkansas for the second season, using measurements of photosynthesis, biomass production and yield related traits. In collaboration with a researcher at Marquette University, Milwaukee, Wisconsin, QTL (quantitative trait loci) mapping for seedling stage cold tolerance was completed for two of the four subpopulation specific recombinant inbred line (RIL) populations. Mapping in the aus (Phudugey x NC 1/536) population revealed five different regions associated with cold tolerance and mapping in the TRJ (Taichu Mochi 59 x British Honduras Creole) population revealed four different regions. No overlapping regions were found between the aus and TRJ QTL regions, suggesting these genes are subpopulation specific. To identify superior alleles for drought tolerance from the aus rice genetic subpopulation, a panel of 100 accessions including 84 aus with non-red pericarps and 16 checks were evaluated under AWD stress conditions. Currently, this panel of 100 accessions is being phenotyped in the field. About 100 blast isolates were collected from the experimental station at Stuttgart along with 50 from fields with neck blast infections from California, and their race identity and existence of avirulence genes are being analyzed under laboratory and highly contained greenhouse conditions. Selected isolates from these blast populations will be added to an existing blast test panel designed to identify resistance genes present in all rice grown in the USA. About 250 rice varieties are being grown in triplicate under field conditions for evaluation after inoculation with mycelia grown on rice and corn chips, and results of sheath blight reactions will be used to identify sheath blight resistant varieties. Bacteria Pantoea ananatis were used for repeated inoculation and analysis with polymerase chain reaction (PCR) and seed and pollen transmission of pathogen have been predicted. Two crosses involved in susceptible rice variety JBA were made and about 240 F2 seeds of one cross were harvested and seeds for an additional cross are being harvested for mapping the resistance genes from US rice varieties. These efforts will save time and money for the US rice breeders to develop rice cultivars that are sustainable and marketable. In regards to Objective 3: To accomplish the objective of dissecting the genetic basis of rice improvement for reduced irrigation, a set of 200 accessions that were part of the Aus-NAM (nested association mapping) population were selected randomly, and the generation advance, and phenotypic data collection were completed. The genotyping step is now in progress and a training/testing/validation population for genomic prediction will be created for a field test in the summer of 2026. To investigate the impact of reduced irrigation on essential grain elements such as iron, zinc and potassium, and toxic elements such as arsenic, the ionomic analysis was completed but the data analysis was delayed due to two critical vacancies on this subobjective. After repeated screening of a yeast two hybrid library, no meaningful interacting proteins were identified. However, the interactions of Pi-ta with AVR-Pita were identified by AlphaFold2. Using AlphaFold2, a leucine rich region of Pi42(t), another blast resistance gene nearby and Pi-ta were also identified. Further pairwise interaction tests using AlphaFold2 are planned to determine interaction specificity Ptr to gain insight signaling recognitions of Pi-ta and Ptr mediated defense response. Differential rice varieties with different combinations of blast resistance genes Pi-ta, Ptr, Pi-b were examined under extreme temperature and water conditions under chamber and greenhouse conditions. Responses to abiotic stress and biotic stress have not been easily controlled due to environmental conditions. Further experiments will require equipment with better temperature, humidity and light control. Once resources are available to determine if plants will gain enhanced resistance to biotic stressors after exposure to abiotic stressors. A project supported by the Arkansas Rice Research and Promotion Board to identify fissure resistance genes, chalkiness and head rice related genes in collaboration with scientists of the University of Arkansas was initiated with 180 selected ARS germplasm in a replicated field plot experiment. The data on traits related to the head rice yield are being collected for gene identification. User friendly genetic markers will be developed to improve the head rice yield that will benefit rice producers and millers. Under Objective 4: A previously developed convolutional neural network (CNN) image–based biomass prediction method was expanded with additional training data, and the method was benchmarked comparing its greenhouse-derived estimates against field-measured biomass and trait data, validating its performance in real-world conditions. To develop an information resource that searches for accessions with optimal gene/allele combinations, a haplotype-based bioinformatics pipeline was implemented to identify haplotypes with sequence variants that are predicted to have phenotypic effects and summarize their frequencies in each rice subpopulation. In addition to standard variant effect prediction (e.g., stop codons and non-synonymous changes), AI-based variant prediction is being implemented in collaboration with researchers at the University of Texas at Arlington. The variant prediction AI models being evaluated include a CNN model to predict sequence variants affecting gene expression, and cross-species DNA language models. Progress on development of a relational database of genome-wide association study (GWAS) data has been limited by the need for manual curation; however, use of AI-based variant prediction is being evaluated as an effective alternative. In collaboration with researchers at the University of Arkansas Rice Research & Extension Center in Stuttgart Arkansas, a panel of 554 rice breeding lines genotyped with a 550-marker panel was used to compare the performance of 13 genomic selection (GS) models for seven key agronomic and grain quality traits. The results are useful for choosing the optimum GS model for each trait being targeted for genetic improvement. Further useful information for optimizing genomic selection was obtained through a collaboration with researchers at the University of California-Davis, where multi-trait genomic prediction models that incorporate simulations of weather, soil, and management factors were tested and found to be more accurate than traditional single-trait approaches. Together, these efforts will reduce the cost of developing marketable rice varieties for the US rice industry.

Accomplishments
1. Low phytic acid disease resistant rice germplasm released. ARS researchers in Stuttgart, Arkansas suggests phytic acid acts as an antinutrient, binding to essential minerals like iron, zinc, calcium, and magnesium and hinder their absorption in the human digestive system. Low phytic acid rice varieties reduce this chelation, making these vital minerals more bioavailable and improve the overall nutritional value of the rice as well as other foods that are concurrently consumed. This is especially beneficial for populations where rice is a staple food and micronutrient deficiencies are prevalent, contributing to problems like anemia (iron deficiency) and zinc deficiency. Low phytic acid rice holds promise as a tool to combat malnutrition, lessen environmental pollution caused by agricultural practices, and contribute to a more sustainable food system. Blast disease is a major concern for staple rice production in the USA and its control often requires fungicides and water management practices, which are costly. The development of varieties with blast resistance and low phytic acid presents challenges, including potential impacts on yield while maintaining desirable agronomic performance. ARS scientists at Stuttgart, Arkansas successfully developed two blast resistant rice germplasm, USDA-GKZ4 and USDA- GKZ61, with desirable yield potentials. Among them, GKZ4 yields 8,157 kg/hectare in Arkansas field plots, a yield comparable to commercial rice varieties, and it contains an extremely low level of phytic acid which can benefit rice consumers and help alleviate malnutrition globally.

2. Release of an aromatic rice cultivar. Thai Jasmine is one of the major aromatic imported rice varieties. ARS scientists at Stuttgart, Arkansas developed a rice cultivar, USDA-ARS-Sallah from a progeny of Jasmine 85 crossed to rice variety Lemont. Sallah is a premium aromatic long grain rice that has been specially selected for growth conditions in the Southern USA. Rice blast and sheath blight diseases are two costly constraints for rice production in the USA. Sallah contains adequate disease resistance that is comparable to other long grain US rice varieties. Sallah and Trinity were both resistant to the common US blast races IB17, IB49, and IE1k while Presidio was susceptible to IB17 and Ozark was susceptible to both IB1 and IB17. Under naturally infected field conditions in Louisiana, Arkansas and Puerto Rico, Sallah was resistant to blast infection and had moderate resistance to sheath blight disease. From two-year field trials in Arkansas, Louisiana, and Texas Sallah had a total milled rice yield of 67.5%, a head rice yield of 56.37%, a rough rice yield of 9,309 kg/hectare, an excellent ratoon yield of 4,712 kg/hectare, and a very low chalkiness of 5.21%. Sallah had a significantly higher head rice yield (56.37%) than Ozark (48.25%) and Presidio (44.83%) and performed better than Trinity (53.73%), indicating that USDA-ARS-Sallah has good milling qualities. Ozark had the highest rough rice yield at 11,816, followed by Sallah with 9,309 kg/hectare, Presidio at 8,273 kg/hectare, and Trinity with 7,224.5 kg/hectare. Sallah is unique from other varieties due to being a US adapted long grain aromatic rice containing disease resistant genes, low chalk, and excellent ratoon yield potential. Sallah offers US rice farmers and consumers a high quality, aromatic rice that is American grown and will provide an alternative to foreign imported aromatic rice that currently dominates the US marketplace.

3. Overexpression of the QTL OsABC9 enhances resistance to rice sheath blight. ARS researchers in Stuttgart, Arkansas believe rice sheath blight, caused by Rhizoctonia solani, is a serious threat to U.S. rice production. It leads to significant yield losses and reduced grain quality. Most rice varieties lack strong resistance, and growers rely heavily on fungicides, increasing costs and environmental concerns. The disease thrives in warm, humid conditions. With limited sustainable options available, developing resistant cultivars and alternative controls is critical to maintaining yield, profitability, and long-term sustainability in U.S. rice farming. However, the molecular basis of sheath blight resistance in rice remains elusive. Adenosine triphosphate (ATP)-binding cassette (ABC) transporters play critical roles in substance transport, plant growth, development, and responses to abiotic stress. OsABC9 is a major quantitative trait locus (QTL) identified in the sheath blight-resistant indica rice cultivar Jasmine 85. ARS scientists at Stuttgart, Arkansas in collaborations with scientists at Ohio State University validated the function of OsABC9 in rice resistance to sheath blight. OsABC9 was highly expressed in the stems of Jasmine 85 but shows minimal expression in the stems of the japonica cultivar Nipponbare. Localization studies indicated that the OsABC9-GFP fusion protein is situated in the nucleus. Overexpression of OsABC9 in rice enhanced resistance to sheath blight by inducing pathogenesis-related genes and facilitating the scavenging of hydrogen peroxide (H2O2) through the activation of H2O2-degrading enzymes. These results suggest that OsABC9 plays a pivotal role in activating rice immunity against R. solani, potentially revealing novel ways to develop sheath blight resistant rice cultivars.

4. Koi-rice co-culture developed. With limited land and water resources available it has become critical to maximize output for agricultural products while maintaining sustainable farming practices. Rice-fish co-culture can be used to maximize limited land and water resources for production of rice and fish concurrently and reduce the need of chemical inputs. While rice-fish co-culture has been practiced in Asia for centuries, very few studies have examined the feasibility and economic impact of rice fish co-culture in the USA. USDA ARS scientists at Stuttgart, Arkansas conducted two studies from 2023-2024 to determine if co-cultivation of Koi carp and rice in the Southern USA could enhance rice production and quality while providing additional economic return from Koi carp. Our studies showed that Koi carp with two different initial weights can be grown concurrently in a flooded rice-fish production system and result in enhanced rice yield, milling yield, and protein content, while providing positive estimated net returns for Koi carp production. This system appears to offer USA rice farmers a potential diversification strategy for smaller fields where specialty rice varieties are grown.

5. Non-destructive rice biomass estimation using machine learning. Optimized plant biomass contributes to greater rice yield and quality, and helps plants better withstand abiotic and biotic stresses. Ideally, plant breeders could monitor biomass easily throughout the growing season without damaging the plant. Accurate biomass measurement is critical for selecting high-performing, stress-tolerant rice varieties, but current methods require destructive cutting and weighing of the entire plant. This destructive process limits researchers’ ability to track growth over time and slows breeding progress. ARS scientists in Stuttgart, Arkansas, in collaboration with the University of Arkansas at Pine Bluff, developed and validated a machine learning tool that estimates above-ground biomass from simple plant images, without the need for harvesting or expensive equipment. The tool accurately estimated biomass under real-world conditions without requiring controlled lighting or precise setup. This new approach enables rapid, low-cost, and non-destructive biomass estimation. By making it easier to monitor plant growth over time, this method supports the development of rice varieties with better yield and stress tolerance. It reduces labor and resource costs for breeders and researchers and can be used widely in rice improvement programs to enhance productivity and efficiency.

6. New sources of sheath blight resistance identified. Sheath blight caused by the soil borne fungus Rhizoctonia solani is one of the most destructive rice pathogens worldwide. ARS scientists at Stuttgart, Arkansas selected 400 rice varieties from National Small Grains Collection based on growth speed and architecture under US growing environments. Using a greenhouse microchamber inoculation method, 93 varieties exhibiting moderate to high resistance were evaluated in the summer 2024 under field conditions and 32 varieties were verified to have statistically significant resistance to sheath blight disease compared to the susceptible check variety Lemont. Of these, approximately 20 varieties also displayed optimal plant architecture and height, making them ideal as breeding parents to introduce sheath blight resistance. These discoveries are expected to accelerate marker-assisted selection (MAS) strategies and support breeders in developing high-performing, disease-resistant rice varieties.

7. Release of six ancestral rice, Oryza rufipogon species complex (ORSC) chromosome segment substitution line (CSSL) libraries in elite Indica and Japonica rice backgrounds. Cultivated rice is a primary cereal in the human diet, highlighting the importance of exploring new avenues for improving rice yields and tolerance to diseases, insect pests, drought and heat stress. Two rice varietal groups, Indica and Japonica were identified in ancient times. The ancestral rice wild species, Oryza rufipogon and Oryza nivara, collectively identified as the ORSC, are a largely untapped reservoir of genetic variation available to plant breeders as they confront the challenges of disease, insect pests and abiotic stresses. ARS scientists at Stuttgart, Arkansas made crosses between three genetically and phenotypically diverse ORSC accessions and either the Japonica variety, Cybonnet or the Indica variety IR64, resulting in six populations (CSSL libraries) which had small segments of ORSC DNA in the background of either IR64 or Cybonnet. The 218 progeny lines comprising the three IR64 libraries and the IR64 parent were characterized for 14 traits related to the plant phenotype in the greenhouse in Arkansas and the 216 progeny lines comprising the three Cybonnet libraries and the Cybonnet parent were previously characterized for 22 yield-related traits over two field seasons in Arkansas. The three Cybonnet libraries revealed a total of 31 different genes attributed to the ORSC parents controlling the traits evaluated and 13 of these genes were validated in the three IR64 libraries. Currently, these six libraries are available for rice breeders and researchers to identify and incorporate novel traits identified in the ORSC donors that would enhance the resilience of the rice varieties currently grown. Having only short ORSC segments introgressed into the cultivated background will enable the desirable trait to be easily incorporated into an adapted rice without the undesirable wild, weedy traits.

8. The Seedborne Nature of the Bacterial Pathogen Pantoea ananatis in rice. Pantoea ananatis is a bacterium that can cause bacterial leaf blight disease in rice, as well as other diseases like grain discoloration and stem necrosis. The disease, first reported in the southern USA, can lead to leaf streak, panicle sterility, and reduced yields in susceptible rice varieties. ARS scientists at Stuttgart, Arkansas in collaboration with scientists from University of Arkansas, Texas A&M, Oklahoma State University, Colorado State University, and Louisiana State University highlighted P. ananatis’ seedborne nature and capacity to initiate early infection, compromise seedling vigor, and reduce seed production. Through laboratory and greenhouse experiments using three rice varieties, JiBoYa, Pratao, and Branco de Brejo, JiBoYa was found to have the highest seed contamination and disease severity, resulting in significant yield loss. The research used colony PCR and Pantoea Genus Species Agar for rapid pathogen identification and emphasized the need for new diagnostic tools and seed health protocols. These findings are positioned to generate coordinated, science-based strategies to manage P. ananatis, support grower decision-making, and enhance the resilience of rice production systems in the face of weather and biological threats.

9. Mechanisms of disease susceptibility uncovered. Rice blast disease caused by the fungus Magaporthe oryzae is one of the most damaging diseases and avirulence genes in M. oryzae are predicted to be involved in pathogen pathogenicity and fitness. However, rice plants have evolved robust resistance genes such as Pi-kD whose encoded proteins are predicted to directly detect the protein products of these cognate avirulence (AVR)-genes in triggering innate immunity. ARS scientists at Stuttgart, Arkansas, with scientists of University of Arkansas analyzed 709 M. oryzae genomes, from isolates collected between 1954 and 2022, across five continents, 45 countries, and representing 38 host species or families. AVR-PikD is a single-copy gene in 61.8 % of isolates and 16 novel alleles were identified. Four of these differ from the AVR-PikD protein by up to five amino acids causing an altered protein with 113 polypeptides. The remaining 12 haplotypes contain single nucleotide polymorphism, insertions or deletions that introduce premature stop codons or frameshifts, generating truncated (26–56 aa) or extended (115–125 aa) proteins. Using machine learning, 23 genes from rice varieties without the cognate resistance gene Pi-k were identified to bind AVR-PikD, and eight of which bind through Leucine Rich Repeat (LRR) domains, five through protein-kinase domains, and ten through combined LRR and protein-kinase interfaces. These findings reveal that the natural variation of the AVR-PikD gene is driven not only by point mutation but also by gene restructuring, producing effector variants that may evade PikD-mediated immunity. These high-confidence AVR-Pik-binding genes provide a valuable resource for functional validation and for breeding strategies aimed at durable rice resistance to blast disease.

10. Regional blast population characterized. Rice blast, caused by fungus Magnaporthe oryzae, is one of the most destructive diseases of rice. Major resistance (R) gene mediated resistance to M. oryzae is often overcome by the fungus due to the occurrence of new races with altered corresponding avirulence (AVR) genes. ARS scientists at Stuttgart, Arkansas collaborated with scientists from the University of Arkansas in selecting regional blast disease samples from experimental stations and commercial rice fields in Arkansas, Louisiana and Puerto Rico from 2017-2019 to determine the efficacy of major R genes, Pi-ta, Pik, Pizt, Pib, Pi9, and Pi33 in these regions. A total of 185 blast isolates were purified to examine the existence of corresponding AVR genes AVR-Pita1, AVR-Pib, AVR-Pik, AVR-Pizt, AVR-Pi9 and ACE1. AVR-Pizt and AVR-Pita1 were found in all isolates and AVR-Pi9, ACE1 and AVR-Pib were found in most isolates suggesting that major R genes Pizt, Pi-ta, Pizt, Pi33 and Pib are effective at preventing infections by these isolates. Among them, 117 of 185 contain all 6 AVR genes and three other groups contain 3-5 AVR genes suggesting that different degrees of race shift are exhibited in these isolates. To compare the genetic diversity of blast isolates, their genotypes were examined with 10 simple sequence repeat (SSR) markers. SSR data revealed that genetic backgrounds of isolates from Arkansas were endemic but some isolates from Louisiana share the same fingerprints as isolates from Puerto Rico. Genetic structure analysis of SSR data suggests that there are three major clusters with 46 combinations of SSR markers. The isolates from Arkansas showed high genetic diversity dominated by one genotype. The isolates from Louisiana were more genetically diversified without any obvious predominant group. The isolates from Puerto Rico have the lowest heterozygosity. These data reveal contemporary genetic changes of rice blast fungus and are useful for guiding the deployment of major R genes in these regions.

11. New mechanism of the durability of blast resistance in weedy rice uncovered. Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most problematic diseases for rice production, threatening global food security. Genetic resistance to some M. oryzae races can be achieved using major resistance (R) genes that recognize their corresponding fungal avirulence (AVR) genes. The R gene cluster, Pi-ta/Pi39(t)/Ptr has been effectively deployed in cultivated rice for blast management to prevent infections by the race IG1 and IC17 except IB33 and IE1k. Weedy rice, a close relative of cultivated rice that competes with the crop, has evolved unique genetic mechanisms to resist the infections of M. oryzae; thus, weedy rice can serve as an excellent resource for blast control. ARS scientists at Stuttgart, Arkansas in collaboration with scientists at Washington University at St Louis, Missouri assessed disease scores of 183 recombinant inbred lines (RILs) derived from a cross of weedy rice with a cultivated rice. A Black Hull Awned weedy rice and the aus-196 rice variety were used to generate a biparental mapping population which was tested with four distinct common USA blast races, IB33, IG1, IE1K and ICI7 under greenhouse conditions. The parental lines were resistant to all blast races; however, RILs showed a wide degree of variation in resistance indicating the presence of minor resistance genes. Genotyping-by-sequencing of the RIL population and parents generated 1498 genetic markers which were used to construct a linkage map for mapping. A minor resistance gene from weedy rice was mapped to the known major gene cluster, Pi-ta/Pi39(t)/Ptr locus on chromosome 12. Identification of alleles from Pi-ta/Pi39(t)/Ptr in weedy rice provides resistance to virulent races IB33 and IE1k which sheds new insights into the evolution and adaptation of weedy rice and can aid in development of durable blast resistant rice varieties through marker-assisted selection.

12. Rice germplasm and component traits of rice yield and grain quality under higher temperatures during cropping season. Higher ambient temperatures during rice cropping season poses significant challenges to rice production in Southern US rice belt. So far, the complex dynamics between rice yield, grain quality, and high daytime temperature (HDT), high nighttime temperature (HNT) remain largely unknown. ARS scientists at Stuttgart, Arkansas, in collaboration with scientists from Clemson University, SC identified that the HNT has more impacts on rice yield and quality compared with HDT. The study focused on US adapted rice varieties in rice breeding programs for improving heat stress tolerance. The comparison of various maturity groups of rice varieties, such as early, medium and late maturing varieties, and analyzing the component traits of yield and grain quality against HDT and HNT, it was found that the early maturing variety groups showed greater tolerance to HNT stress. These findings serve as a resource tool for the US rice breeders and provide directions and guidance towards developing heat stress tolerant rice varieties for improving profitability of the southern US rice growers and the US rice industry.

13. Effect of soil amendments on grain yield, yield components, and milling qualities in organic rice production. Nitrogen (N) management is a big challenge to keep a profitable crop yield under an organic rice system. ARS scientists at Stuttgart, Arkansas in collaboration with scientists at Texas A&M University System, Beaumont, Texas performed field trials in 2010, 2015, and 2017 in Beaumont, Texas to see how different types and rates of organic fertilizers affected grain yield and milling qualities. A 2010 study looked at six organic N fertilizers and found that five of them increased grain yield with higher N supply. Additional field studies in 2015 and 2017 using a selected organic fertilizer, Nature Safe, showed that the grain yield and plant height increased with different nitrogen rates. Also, grain milling quality was significantly improved by using Nature Safe, including whole grain percentage and whole grain yield. Yield plateaus were not observed, even at higher N rates, in any of the three studies, indicating agronomically high N applications are recommended to achieve the yield potential of the rice cultivar.

14. Stable grain yield, milling quality and better nutritional profile are achievable in rice production utilizing water conserving management practices. Reduced irrigation management practices such as alternate wetting-drying (AWD) have been shown to save water resources because such irrigation management systems allow soils to dry intermittently to a certain extent, but the US rice growers hesitate to dry beyond safe-AWD (i.e., no visible dry surface) because conventional season-long flood irrigation in rice has been practiced for centuries. ARS researchers in Stuttgart, Fayetteville, Arkansas, and New Orleans, Louisiana along with researchers in Japan demonstrated that the soil drying beyond safe-AWD around maximum tillering stage of rice could maintain two important agronomic traits of a long and a short grain rice varieties: grain yield, and milling quality, along with no effect on lowering essential grain elements such as iron, zinc, potassium, magnesium. Additionally, it was found that the water conservation, beyond safe-AWD, irrigation was able to reduce the toxic element, arsenic, in both its organic as well as inorganic forms. However, none of the varieties under any irrigation management accumulated arsenic at levels that met the criteria for human health concern. The results indicated that the water conserving irrigation managements are useful for the US rice growers and provide an excellent opportunity to capture rainwater in rice paddies and increasing profitability. This study also underlines the possibility of using water conserving management practices in other rice varieties and saving underground water, saving labor costs, and increasing profitability of rice production in the US.

15. Ten genes that are potentially associated with reduced grain arsenic in rice are identified. Studies have shown rice can be particularly efficient in assimilating arsenic (As) from paddy soils into rice grains. This is problematic when rice grows in areas which have concerning levels of inorganic As, because human intake of inorganic As has been associated with several health problems. (For this study only total grain As content was measured, whereas other studies report the concentration of both inorganic As, the more toxic form, and organic As, the less toxic form.) To breed rice cultivars with low grain As content, quantitative trait loci (QTLs) or genes that restrict inorganic grain As accumulation (uptake) need to be identified. Subsequently, molecular markers can be developed for the genes that decrease As uptake and these markers used to introgress the desired genes into new varieties which produce grains with lower As levels. For this study, the grain As data collected from a diverse collection of 235 rice accessions grown in five field environments at four geographic sites, was reanalyzed using 3.5 million DNA markers and several improved statistical procedures for analyzing marker-trait associations. This vastly improved the ability to identify QTL, such that genetic differences within the genes could be detected! From these analyses, 10 QTL (genes) associated with As accumulation were discovered. One gene, an ABC transporter (OsABCC1), revealed that a greater than 10% reduction in grain As could be achieved. The OsABCC1 gene is particularly interesting for US rice breeding because the desired allele (variant) is not widespread among US rice varieties but is already in two historically grown US varieties, making it easier for breeders to introduce this gene into US varieties currently under development. (Note that further study will be required to determine if the novel allele reduces total grain As content by reducing the more toxic inorganic As.).

16. Improved rice breeding with multi-trait genomic prediction. Rice breeders can efficiently develop high-yielding, stress-tolerant varieties by accurately predicting plant performance using genetic information and knowledge of growing conditions. Breeding progress is slowed when trait predictions are based on limited data or only one trait at a time. These methods often fall short under the range of seasonal weather and field conditions across the rice-growing regions. A large, diverse set of rice varieties was grown across three southern U.S. states and evaluated for key traits such as plant height, maturity, yield, and seed-bearing shoots. ARS scientists at Stuttgart, Arkansas, in collaboration with scientists at the University of California, Davis, tested multi-trait genomic prediction models, incorporating simulations of weather, soil, and management factors. Multi-trait models produced more accurate predictions than traditional single-trait approaches. The study also revealed genetic differences and similarities among southern rice breeding programs, providing a valuable resource to guide future variety development. This research helps rice breeders make more reliable selections, especially under varying field conditions. Improved prediction tools can speed up the development of higher-yielding, stress-tolerant varieties, supporting stable production and greater profitability for U.S. rice growers.

Review Publications
Gouda, A., Sangare, J., Wambugu, P., Huggins, T.D., Ndjiondjop, M. 2024. Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq. Crop Science. https://doi.org/10.1002/csc2.21395.
Farag, F., Huggins, T.D., Edwards, J., McClung, A., Hashem, A., Causey, J., Bellis, E.S. 2024. Manifold and spatiotemporal learning on multispectral unoccupied aerial system imagery for phenotype prediction. The Plant Phenome Journal. https://doi.org/10.1002/ppj2.70006.
Jia, Y., Gibbons, J., Jackson, A.K., Dunlap, H.N., Zhao, H., Wang, X., Jia, M.H., Fomoso, A., Groth, D. 2025. Registration of three long grain rice germplasm lines with improved blast resistance with the Ptr gene, low chalk, excellent milling quality, and good yield. Journal of Plant Registrations. 19:1. https://doi.org/10.1002/plr2.20407.
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