Climate Resilient Cultivars

Abiotic stresses negatively impact rice yield and quality. Changes in weather patterns also provide conducive conditions for pest and disease outbreaks and may reduce the effectiveness of host resistance genes. Since current rice cultivars and the production practices are not designed to mitigate the adverse impacts of climate change, our strategy is to use genetic, genomic, physiological, high throughput phenotyping, and AI-based tools to design novel rice genotypes that will maintain high performance under future climate change scenarios.

Abiotic Stresses

Tolerance to multiple early season stresses: We will study 200 types of rice plants to see how they handle different stresses like cold temperatures and drought during the early growing season. We will measure things like emergence, leaf behavior, and photosynthesis to see which plants are best at handling multiple stresses. By studying their genes and using special tests, we can find out which genetic traits make some plants better at tolerating stress, and then use that information to improve rice crops in the future.

• Drought Stress Tolerance Screening of Elite American Breeding Rice Genotypes Using Low-Cost Pre-Fabricated Mini-Hoop Modules
• Elevated atmospheric CO2 and the future of crop plants
• High temperature stress during flowering and grain filling offsets beneficial impact of elevated CO2 on assimilate partitioning and sink-strength in rice

Tolerance to drought and heat stress: In this study, we will evaluate different types of rice plants and specific populations to see how well they perform under drought and high-temperature conditions. We will measure various traits such as grain yield, quality, and physiological characteristics to identify the plants that are more tolerant to these stresses. Using this data, we will develop a model that can help breeders select the best traits and combinations to achieve maximum yield and quality in rice crops under drought and high-temperature conditions.

• Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches
• Response of U.S. Rice Cultivars Grown under Non-Flooded Irrigation Management

Pyramiding of thermotolerance traits/genes: In this project, we will cross a thermotolerant rice line with a heat-tolerant japonica line to combine their genes for better thermotolerance in the offspring. We will use marker-assisted selection to identify and select the lines with desired traits. Additionally, we will evaluate a set of germplasm to find new rice varieties that flower early in the morning, which can help improve seed production under heat stress. We will develop a mapping population to identify the genes responsible for this trait and introduce them into elite rice lines using marker-assisted backcrossing.

• Species, ecotype and cultivar differences in spikelet fertility and harvest index of rice in response to high temperature stress

• Is early morning flowering an effective trait to minimize heat stress damage during flowering in rice?

• The Difference in Sterility due to High Temperatures during the Flowering Period among Japonica-Rice Varieties

Nutrient and water use efficiencies: The japonica diversity panel will be evaluated for water use efficiency (WUE) and nutrient use efficiency (NUE) in both hydroponic/greenhouse and field experiments to identify superior donors for use in the breeding program. The Δ13C-labeled and Δ15N-labeled (NH4)2SO4 stable isotopes will be used to evaluate water and nitrogen use efficiencies, respectively. The data collected on traits associated with WUE and NUE will be used in conjunction with the genotyping data to conduct the GWAS analysis to identify the genomic regions responsible for improved WUE and NUE which can be used to develop molecular markers for MAS.

• Carbon Isotope Discrimination Accurately Reflects Variability in WUE Measured at a Whole Plant Level in Rice

• The Impact of Global Warming on Agriculture: A Ricardian Analysis

• Assimilation of N-15 Labeled Fertilizer Injected at Various Depths by Delayed-flood Rice

Application of omic tools and artificial intelligence: Three ILs (Introgression Lines) showing tolerance to abiotic stresses (drought, heat, and salt) will be selected for further analysis. These ILs, along with their donor and recurrent parents, will undergo whole-genome sequencing and RNA-sequencing. Differentially expressed genes (DEGs) will be identified by exposing the plants to stress conditions and sampling spikelets and leaves at specific time points. The DEGs and their expression patterns will be validated using real-time quantitative RT-PCR, and the whole-genome sequences will be compared to identify introgressed donor segments and variants. Metabolomic and imaging technologies such as NMR, LC-MS, and Raman microscopy will be used to analyze the metabolic profiles and assess stress levels in the plants. Additionally, artificial intelligence (AI) techniques will be employed to synthesize novel cultivars with desired traits by integrating mutation components and utilizing neural networks for trait prediction. The candidate cultivars will be filtered based on desirable agronomic and metabolic traits using the RiceVarMap database, and the breeding network will predict the properties of the resulting cultivars using various data inputs. The selected candidate lines will then be validated in field conditions.

• Field evaluation of advanced breeding lines: Several advanced breeding lines with salt tolerance at the seedling and reproductive stages have been identified. Additional seedling stage salt tolerant lines will be evaluated for reproductive-stage tolerance to identify lines with tolerance at both stages. The selected breeding lines with salt tolerance at both stages will undergo field trials at two different locations to assess their performance under saltwater irrigation. In parallel, drought, cold, and temperature-stress tolerant lines will be crossed with the promising salt tolerant lines using marker-assisted selection to develop breeding lines with combined tolerance to multiple stresses. These breeding lines will be evaluated for stress tolerance, yield, and agronomic traits in field trials at research stations, aiming to create adaptable and sustainable rice varieties.

Biotic Stresses

Integrative Approach to Characterize Genomic Variants for Bacterial Panicle Blight Resistance in Rice: The study aims to analyze the genome sequence variants associated with resistance to bacterial panicle blight (BPB) in LM-1, a cultivar derived from the susceptible variety Lemont182. Through bulked segregant analysis, fifteen lines with consistent resistant or susceptible responses will be selected from a cross between Lemont and LM-1 to identify genomic regions related to resistance. Additionally, a recombinant inbred line (RIL) population consisting of 283 lines from a Bengal and Jupiter cross will be utilized to identify quantitative trait loci (QTLs) for BPB resistance, employing QTL-seq analysis with 15 resistant and 15 highly susceptible RILs, complementing the QTL mapping. Finally, the RBG2 trait will be introgressed into the indica cultivars Kele75, Jupiter, Bengal, and Cocodrie using marker-assisted selection.

Screening and Genetic Analysis of Kernel Smut Fungus Resistance in Rice for Effective Control Strategies: A comprehensive study will be conducted to screen over 250 inbreds, hybrid cultivars, and breeding lines from various locations in the United States for resistance to kernel smut fungus. The screening will involve secondary sporidia inoculation at different growth stages in the greenhouse, followed by field evaluations in Texas and other participating states. Additionally, more than 300 Tilletia barclayana isolates will be collected nationwide to assess their virulence, genetic diversity, and population structure through sequencing techniques. Field trials will be conducted to evaluate the effectiveness of seed treatments and foliar-applied fungicides, including propiconazole and mancozeb, with different timing strategies to identify the most optimal combinations for controlling the fungus. The integrated use of fungicide seed treatments and foliar applications will also be assessed.

Comprehensive Evaluation and Genetic Analysis of Insect Resistance in Rice for Improved Cultivar Development and Seed Treatment Strategies: A comprehensive evaluation will be conducted on a diverse panel of genotypes to assess their resistance to water weevil (Lissorhoptrus oryzophilus) and stem borer (primarily Eoreuma loftini) through field and greenhouse trials. The genetic basis of insect resistance will be investigated using genomics and physiological tools, with the aim of identifying highly resistant genotypes for integration into rice breeding programs. Field trials will be conducted across multiple research stations in rice-growing states to evaluate the economic benefits of insecticidal seed treatments, considering both individual insecticides and their combinations, and developing region-specific optimal seed treatment strategies. The results of these studies will contribute to the development of seed treatment selection guides to assist growers in making informed decisions.

Expected outcomes:

Overall, this research component will result in the identification of new stress-tolerant donors and advanced breeding lines, introgression lines (ILs), QTL information, candidate genes, and markers associated with stress-tolerance traits. Modeling will help in predicting yield and phenotyping of breeding populations. We will identify the knowledge gaps on the disease development associated with weather and genotype. Development of fungicide and insecticide resistance will be monitored in the rice-growing regions, insecticidal seed treatment will be optimized to reduce production costs and undesirable environmental impacts.