Resilient Cultivars

Abiotic Stresses

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 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 scenarios.

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.

Genetics of Abiotic Stress Tolerance

Team members:

• Prasanta Subudhi (PD) – Louisiana State University Agricultural Center
• Ravi Kiran Reddy Kondi (Graduate Student) – LSU AgCenter
• Prabhat Rana (Graduate Student) – LSU AgCenter
• Chanderkant Chaudhury (Postdoctoral Fellow) – LSU AgCenter
• Benedict Labaco (Graduate Student) – LSU AgCenter

Year 1 Activities

• We secured a specialized group of rice plants (the LSU japonica panel) from our collaborator, Dr. B. Angira at the LSU AgCenter Rice Research. This material was shared with our partners at the University of Arkansas and Mississippi State University for further research.
• We received genetic data for this rice panel, which was analyzed by Mississippi State University collaborators to map out how the rice plants respond to different environmental stresses, like drought and increased CO2.
• Various rice populations were planted and harvested to grow more seeds. These plants will be used in future studies to identify the genes responsible for tolerance to stress.
• We also obtained a different group of rice plants known as the "aus panel" from the USDA to study traits like early morning flowering and tolerance to drought and heat.
• Crossbreeding was done to create new rice varieties that can tolerate high levels of salt in both the early and flowering stages.
• Further crossbreeding was conducted to develop advanced rice lines that combine traits for heat and drought tolerance.
• We analyzed the full genetic makeup of a salt-tolerant rice line (JN100) and compared it to other related rice varieties to identify key genetic regions that help these plants tolerate salt.
• We conducted RNA-sequencing to identify genes that respond to salt stress in three types of rice plants: a salt-tolerant rice line (JN100), its salt-tolerant parent (NB), and a salt-sensitive variety (JU). This revealed specific genes and proteins that are active in the salt-tolerant varieties but not in the sensitive ones, offering insights into how rice plants adapt to saline environments.

Key Findings:

• The research showed that certain genes in the salt-tolerant rice line are more active when exposed to salt stress. These genes help the plant manage the stress by controlling the movement of molecules and enhancing protein production, making the plant more resilient.
• The genetic information from this study will help us better understand how rice adapts to tough conditions like high salt levels, and it will guide future breeding efforts.

Year 2 Plan:

• Continue evaluating rice diversity panels to find plants that perform well under drought, high temperatures, and early morning flowering (a trait that helps with heat tolerance).
• Publish a manuscript based on further analysis of the genetic and RNA data from salt-tolerant rice plants.
• Keep working on breeding rice varieties that can tolerate multiple environmental stresses.
• Continue trials of salt-tolerant rice lines at test sites in Charleston and LSU AgCenter Macon Ridge Research Station.

Salt tolerance response of salt tolerant IL JN100, recurrent US variety Jupiter, salt tolerant donor TCCP, and highly salt susceptible check variety IR29 at the seedling stage in a sand culture experiment.

Field Evaluation for Salt Tolerance

Team Members
R. Karthikeyan (Co-PD) - Clemson University

Year 1 Activities

• Initiated gathering of DSSAT-CERES-rice data.
• Managed and supervised the rice salinity trial in Charleston, SC.

Key Findings on Rice Seedlings Under Salinity Stress

1. Growth Comparison:
   • JN100 maintained taller heights than Jupiter across all salinity levels, indicating superior growth resilience under stress.
2. Reproductive Potential:
   • Both genotypes experienced a decrease in tiller and panicle numbers with increasing salinity, but JN100 had a moderate reduction, suggesting it better sustains reproductive potential.
3. Grain Quality:
   • JN100 exhibited lower levels of grain sterility and a more stable grain size ratio compared to Jupiter, indicating better adaptability to reproductive challenges caused by salinity.
4. Yield Maintenance:
   • JN100 showed a smaller reduction in yield per plant under salinity stress compared to Jupiter, highlighting its capacity to maintain productivity in high-saline conditions.

Conclusion
These findings suggest that JN100 is more resilient to salinity stress compared to the Jupiter genotype, making it a promising candidate for cultivation in saline-prone areas.

Year 2 Plan:

• · Continue the same trial with the addition of a few more salt-tolerant breeding lines.
• · Continue gathering of DSSAT-CERES data for crop modeling.

Experimental procedure in sequence.

Physiological Basis of Chilling Tolerance and CO2 Responsiveness

Team Members

• K.R. Reddy (Co-PD) - Mississippi State University
• R.B. Rangappa (Co-PD) - Mississippi State University
• Brijesh Angira (Collaborator) - Louisiana State University Agricultural Center
• Manoj Kumar Reddy Allam (Graduate Student) - Mississippi State University
• Raveendra Chandavarapu (Graduate Student) - Mississippi State University

Year 1 Activities

Screen rice panel for early-stage chilling tolerance and CO2 responsiveness:

Evaluated a japonica rice panel (n=236) and four checks (N-22, IR24, Teep, and IRGC 32567) for early-stage low-temperature stress. Plants were exposed to two temperatures resembling southern U.S. early (22/14 °C) and regular planting (30/22 °C) conditions for 14 days after the two-leaf stage. Key findings included:

• Genetic variability was noted in aboveground traits (seedling height, leaf number, shoot weight, and plant vigor) and belowground traits (root length and weight).
• Significant reductions were recorded under chilling stress: leaves (54%), shoot length (57%), root length (7%), shoot biomass (133%), root biomass (109%), and vigor index (33%).
• Chilling stress increased the root-shoot ratio by 15%.
• The vigor index correlated strongly with root length (r=0.90, p<0.001) and seedling length (r=0.73, p<0.001).
• This data will help identify genetic loci for chilling tolerance.

• Screen rice diversity panel for eCO2 responsiveness:
  Phenotyped a diversity panel (n=103 accessions) along with four checks to identify rice accessions responsive to elevated CO2 (eCO2) using the Soil-Plant-Atmosphere-Research (SPAR) facility. Key observations included:
  • Significant variability in traits, except leaf temperature, with eCO2 inducing notable differences in shoot height, number of leaves, and root-to-shoot ratio.
  • Stomatal conductivity decreased by 57%, electron transport rate by 53%, chlorophyll content by 80%, and nitrogen balance index by 50%.
  • Accession RU1601105 performed best under ambient CO2, while INIA09 showed the highest vigor at eCO2.
  • The data will aid in discovering genetic loci linked to eCO2 responsiveness.
• Identifying genetic loci for multiple stress tolerance:
  Received high-density SNPs for the japonica panel from collaborators, filtering a total of 1.7 million high-quality SNPs. GWAS will be performed on each trait to identify common and treatment-specific loci, utilizing the Genomic Association and Prediction Integrated Tool (GAPIT).

Year 2 Plan

• Analyze data collected on the japonica diversity panel for chilling tolerance and conduct GWAS analysis.
• Analyze data collected on the japonica diversity panel for CO2 responsiveness using GAPIT.
• Continue evaluation of the LSU panel for early-season drought and other stresses.

Metabolomics of Abiotic Stress Tolerance

Team Members

Manas Gartia (Co-PD) - Louisiana State University
Kirti Agrawal (Graduate Student) - Louisiana State University

Year 1 Activities

Combining Multi-Omics Data with Raman Spectroscopy: We hypothesize that abiotic stressors will change the metabolites and lipids, and these metabolite changes can be detected by Raman spectroscopy.

• Developed the protocol for extracting lipids and metabolites from plant samples (leaves) and performed nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS) experiments to identify the metabolites and lipids after salt stress.
• Conducted an extensive literature search to identify the Raman molecular signature for plant leaves.
• NMR-Based Method to Identify Changes in Metabolites Post Salt Stress: Used a salt-sensitive rice variety (Jupiter) and subjected it to 18 EC salt stress for 24 hours. Collected both control and salt-stressed leaves and prepared samples for NMR analysis. Identified 13 different metabolites using NMR experiments: sucrose, allantoin, mannitol, glycine, glycine betaine, asparagine, glutamine, succinate, glutamate, leucine, alanine, lactate, and valine. Except for leucine and glycine, the rest of the metabolites increased due to salt stress, with alanine and glycine betaine showing the highest increases. The relative intensity of glycine for stressed to control conditions was approximately 0.4. NMR peak annotation was performed based on available literature; however, NMR has low molecular resolution to identify metabolites due to overlapping peaks. Hence, we employed LC-MS to identify metabolites for our next set of samples.
• LC-MS-Based Method to Identify Changes in Metabolites Post Salt Stress: Collected control and salt-stressed leaf samples from a salt-tolerant rice line, ‘Nona Bokra,’ subjected to 18 EC salt stress for 24 hours. Samples were prepared for LC-MS, using the reference genome of Nipponbare, and identified a total of 357 unique metabolites (the top 50 metabolites are shown in the heat map).

Year 2 Plan

• Collect samples from plants exposed to abiotic stresses for metabolomics, lipidomics, and Raman spectroscopy work.
• Complete analysis and publish the findings on metabolomics using a salt-tolerant introgression line (IL), donor, and the recurrent parent.

Field Evaluation of Mapping Populations for Drought and Heat Tolerance

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

Team members
Dr. Jai S. Rohila (Co-PD) - USDA Dale Bumpers National Rice Research Center, Stuttgart, AR
John Mitchell (Research Associate) - USDA National Rice Research Center, Stuttgart, AR

Year 1 Activities

• Our goal is to evaluate two mapping populations and identify QTLs for tolerance to drought and heat stress.
• Received seed of two mapping populations (Mermentau x N22, BC3F6, 251 lines; Cheniere x Dular, BC3F5, 238 lines) from PD Subudhi after execution of the material transfer agreement between LSU AgCenter and the USDA-ARS Office of Technology Transfer.
• Planted and seed increased for both populations at Stuttgart, AR, to conduct alternate wetting and drying (AWD) field tests in Years 2 and 3.
• Sent out seeds of AUS diversity panel (197 accessions from around the world) to PD Subudhi, LSU AgCenter, after executing the MTA between LSU AgCenter and the USDA-ARS Office of Technology Transfer. This panel will be used for genetic mapping for drought and heat-stress-associated traits such as early morning flowering, heat tolerance, and reduced chalkiness.

Year 2 Plan

• Evaluate two introgression lines mapping populations for performance under alternate wetting and drying regimes under -30 kPa of soil tension at 15 cm below the soil surface in the summer of 2024 and 2025.
• Collect data on grain yield per meter row basis, grain quality traits such as grain dimensions (e.g., length, width, thickness, % chalk in brown rice), phenology and agronomic traits (e.g., plant height, days to heading and maturity), and physiological traits (e.g., leaf temperature).

Field Evaluation of a Diversity Panel for Drought and Heat Tolerance

Team members
Christian Deguzman (Co-PD) - University of Arkansas
Brittany McCollum (Lab Technician) - University of Arkansas

Year 1 Activities

• Our first-year objective is to determine the heading dates of the LSU Rice Research Station japonica panel to synchronize flowering for drought stress and heat treatment.
• Planted 271 lines of the panel in the greenhouse on two planting dates (September 25, 2023, and November 29, 2023). There was a wide range of variation in heading dates in both planting dates.
• Grouped the lines based on the heading dates of the first planting: 66 Early maturity (68 to 89 days), 191 Mid-maturity (90 to 96 days), and 10 Late maturity (129 to 154 days). Most mid-maturity varieties are US rice varieties and breeding lines.
• Grouped lines of the panel based on heading dates in the second planting: 38 Early maturity, 46 Mid-maturity, and 156 Late maturity.

Year 2 Plan

• Obtain and multiply the tropical japonica diversity panel for drought and heat tolerance studies due to unsuitability of the previous panel from LSU Rice Research Station.

Improving Bacterial Panicle Blight Resistance

Team Members

• Jong Hyun Ham (Co-PD) - Louisiana State University Agricultural Center
• John Ontoy (Graduate Student) - Louisiana State University Agricultural Center
• Jobelle Bruno (Graduate Student) - Louisiana State University Agricultural Center
• Jose Cortes (Postdoctoral Fellow) - Louisiana State University Agricultural Center
• Inderjit Barphaga (Research Associate) - Louisiana State University Agricultural Center

Year 1 Activities

• Characterizing Genome Sequence Variants for BPB Resistance
  Conducted bulked segregant analysis (BSA) to identify genome sequence variants associated with BPB resistance in LM-1, a disease-resistant mutant line derived from the susceptible cultivar Lemont.
  • Generated whole-genome sequences for Lemont and LM-1 using both short and long reads (Illumina and PacBio) to identify, filter, and annotate SNPs and InDels associated with resistance.
  • Verified seed sources and confirmed BPB-resistance phenotypes in LM-1 and Lemont using markers and greenhouse disease evaluation.
  • Created an F2:3 mapping population of 750 plants from the Lemont x LM-1 cross, using polymorphic SSR markers, to further genetic mapping efforts for BPB resistance.
• QTL Identification for BPB Resistance in Bengal/Jupiter RIL Population
  Utilized a recombinant inbred line (RIL) population from a cross between Bengal (susceptible) and Jupiter (moderately resistant) to locate QTLs for BPB resistance.
  • Discovered a significant BPB resistance QTL on chromosome 3 using a genotyping-by-sequencing (GBS)-based map across 164 RILs. This QTL aligns closely with a previously identified QTL in a Jupiter/Trenasse population.
  • Completed a transcriptome analysis on early BPB infection responses in Jupiter and Bengal, with a manuscript prepared for publication.
  • Evaluated seedling blight phenotypes in the RIL population (another BPB symptom caused by Burkholderia glumae) and identified QTLs linked to BPB resistance at the vegetative growth stage.
• Introgressing RBG2 into US Rice Varieties
  Worked to integrate the BPB-resistance gene RBG2 from the indica variety Kele into US cultivars using marker-assisted selection.
  • Developed a multi-parental population to combine RBG2 (Chromosome 1) from Kele with the qBPB3.1 resistance QTL (Chromosome 3) from Jupiter, to strengthen BPB resistance in US rice varieties.
  • Generated 237 F2 lines from a double-cross hybrid (Jupiter/Kele // Jasmine85/Trenasse) and genotyped them, categorizing into four groups based on presence/absence of QTLs from Kele and Jupiter.
  • Evaluated these groups to determine the effectiveness of single or combined QTLs on BPB resistance, identifying promising lines with both QTLs for potential future breeding in US rice varieties.

Year 2 Plan

• Continue mapping BPB resistance QTLs and genes using QTL-Seq and bulked segregant analysis.
• Progress the introgression of RBG2 into US varieties
• Resistance phenotype evaluation of rice cultivars LM-1 and Lemont against bacterial panicle blight (BPB) using stem, leaf, and panicle assessments.

Resistance phenotype evaluation of rice cultivars LM-1 and Lemont against bacterial panicle blight (BPB) using stem, leaf, and panicle assessments.

Improving Kernel Smut Resistance

Team Members
Shane Zhou (Co-PD) - Texas A&M University
Sabita Tripathi (Graduate Student) - Texas A&M University
Sabin Khanal (Postdoctoral Fellow) - Texas A&M University

Year 1 Activities

• Evaluation of Rice Genotypes for Resistance to Kernel Smut
  Evaluated 32 rice varieties for resistance to kernel smut in the field disease nursery at Beaumont, Texas, in 2023. Each variety was individually injected with kernel smut secondary sporidia during the late-boot stage, assessing disease severity based on the percentage of symptomatic kernels at maturity. Results showed infection rates from 0 to 11.3%, with over half of the varieties, including Jupiter, Cheniere, Presidio, and PVL03, exhibiting susceptibility. Addijo, DGL274, and Roy J were among the most resistant, with hybrid varieties generally showing more resistance than inbred varieties.
• Investigation of Fungal Population Virulence and Genetic Diversity
  Conducted a preliminary kernel smut survey in Texas, collecting five isolates of the kernel smut fungus. Ten additional isolates were collected from Louisiana, totaling 78 isolates. These isolates will support genetic diversity analysis across U.S. pathogen populations.
• Fungicide Application Timing Trial
  Field trials were conducted to evaluate three fungicides (Amistar Top, Tilt, and Dithane M-45) with three application timings (PD + 7 days, mid-boot, and a combined application at PD + 7 days and mid-boot). Smutted seeds of variety Trinity were drill-seeded, and plots were treated with secondary spores at late boot and heading stages. Despite low disease pressure due to drought, all fungicide treatments significantly reduced kernel smut compared to untreated control, with reductions from 67% to 100%. Mid-boot application timing was identified as optimal, with Amistar Top, Tilt, and Dithane M-45 achieving up to 100% efficacy under the conditions.

Year 2 Plan

• Continued Screening
  Expand kernel smut resistance screening in the field disease nursery to include additional rice varieties and lines.
• Isolate Collection for Genetic Diversity Analysis
  Increase the collection of kernel smut isolates from different U.S. locations to enhance the understanding of virulence and genetic diversity within the pathogen population.
• Seed Treatment and Fungicide Efficacy Studies
  Continue to assess the efficacy of fungicide treatments and application timings to optimize control strategies for kernel smut.