Performing Department
(N/A)
Non Technical Summary
Excessive heat (summer temperature above optimum) during flowering and grain fill significantly threatens rice yield and quality. Many rice-growing regions, including the USA, have experienced heat stress during the reproductive and grain development stages, causing grain yield and quality losses. Despite the significant impact of heat stress on rice production, the genetic basis of rice grain yield, quality, and nutrition under diverse conditions is mostly unexplored. Genetic enhancement of heat stress resilience offers the global rice industry multiple benefits. Our team at Mississippi State University (MSU, Mississippi), Dale Bumpers National Rice Research Center (DBNRRC, Arkansas), and the International Rice Research Institute (IRRI, Philippines), will focus on improving productivity, quality, and nutritional traits of rice under heat stress. This partnership combines scientific expertise, genomic tools, and unique facilities to quantify the impacts of heat stress and map genetic loci associated with yield potential and grain quality under heat stress. Therefore, this plant breeding partnership aims to (1) phenotype a novel Heat-MAGIC population for heat stress-induced changes to yield, grain quality, and nutrition traits using different natural environments (fields) and controlled environmental facilities across three centers, (2) map loci associated with heat tolerance, and 3) characterize haplotypes carrying favorable loci for improved tolerance to heat stress using field-based tents. The proposed research is built on existing physiological, breeding, and genomic resources and drives innovation to tackle the impacts of heat stress on rice grain yield, quality, and nutrition. Outcomes from this partnership will help to develop climate-resilient rice with healthy grains for current and future rice-growing climates.
Animal Health Component
0%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Goals / Objectives
This partnership aims to identify heat stress-resilient rice genotypes with improved grain yield, quality, and nutrition to address the challenges of climate change and malnutrition. This will ensure sustainable rice production and contribute to food and nutritional security. The partnership aims to phenotype the Heat-MAGIC population under different growing environments and map genetic loci associated with grain yield, quality, and nutrition under heat stress. Further, the effectiveness of the identified heat-tolerant haplotypes will be characterized to strengthen the rationale for developing novel heat-tolerant rice varieties. The specific objectives are as follows: (1) Phenotype a Heat-MAGIC population for heat stress-induced changes to yield, quality, and nutrition using field hot spots and controlled-environment facilities; (2) Map genetic loci associated with these traits through genome-wide association analyses; and (3) Characterize the physiology of haplotypes carrying favorable loci for tolerance to heat stress.
Project Methods
The study will use a Heat-MAGIC population with similar days to headings and a broader variability in yield, grain quality, and nutrition for phenotyping. To execute the proposed interdisciplinary objectives, the natural field environment, the field-based heat tents and growth chamber facilities at Mississippi State University (MSU, Mississippi State, Mississippi), USDA-ARS Dale Bumpers National Rice Research Center (DBNRRC, Stuttgart, Arkansas), and the International Rice Research Institute (IRRI, Los Baños, Philippines) will be used.Aim 1: Phenotype Heat-MAGIC population for heat stress tolerance.Field phenotyping for HS tolerance: The Heat-MAGIC population of similar flowering dates will be evaluated for two years for heat stress tolerance at IRRI, Philippines (Years 1 and 2) and USDA-ARS DBNRRC, Stuttgart (Years 2 and 3). Based on the historical weather data for observed monthly maximum air temperatures, two planting dates will be used: early planting as a control and late planting as heat stress trials based on temperature regimes to coincide with the reproductive and grain-filling stages at each phenotyping site. At IRRI, early planting (non-stress) will be seeded during November and transplanted during December to avoid heat stress during grain filling. For the late planting, seeding will be done during January and transplanted during February, thus allowing reproductive and grain-filling stages to be exposed to heat stress between late April and mid-May. Likewise, at DBNRRC, Stuttgart, the early planting trial (control) will be drill-seeded one month early (the first or second week of April) to avoid heat stress during flowering and grain filling. The late planting trial will be planted in the last week of May, allowing reproductive and grain-filling stages to occur Mid to late July. Heat stress impact on rice will be quantified by collecting physiology, agronomic, and quality data across locations. The approach will enable effective comparisons by ensuring comparable heat stress for the same planting across years and locations.Controlled conditions and field-based tent phenotyping for heat stress tolerance: The same population will be phenotyped for the same traits during the grain-filling stage using the plant growth facility at IRRI (Years 1 and 2) and custom-designed field-based heat-tent at MSU, Mississippi (Year 3). At IRRI, two sets of materials will be grown following a completely randomized design with three replications. At heading (primary tiller panicle fully emerged out of the flag leaf sheath), replicated plants (300 lines x 5 replications = 1,500 pots) will be subjected to heat stress (40/23oC, day/night, from flowering until maturity) to quantify the impact of heat stress on rice grain yield, quality, and nutrition. An equal number of plants (1,500) will be maintained under control conditions throughout the crop growth cycle and treated as control (32/23oC, day/night). The same population will be phenotyped (Year 3) for the same traits during the grain-filling stage using the three custom-designed field-based heat-tent facilities at MSU. Once plants reach anthesis on the primary tiller, heat stress will be imposed by moving tents on the targeted plots until maturity. The thermostat will be automated to induce a maximum temperature of 40oC. When temperatures exceed the set temperature inside the heat tents, the end walls will be programmed to open to avoid excess heating. Three areas of the same size will be randomly assigned as replicated controls. Air temperature will be recorded throughout the experiment using data loggers.Data collection and analysis: Physiological traits such as canopy temperature and pigment data will be measured across all screening activities during mid-grain filling. Agronomic traits such as days to heading, plant height, panicle number, yield, and 100-seed weight will be recorded. Replicated samples from each line will be analyzed for quality (amylose, chalkiness, and milling percentage) and grain size (length and width, mm). Grain samples from IRRI trials will used to measure iron and zinc content using XRF-Bruker S2 Ranger. Weather data will be recorded across locations.Aim 2: Map genetic loci associated with yield and grain micronutrients under heat stress The polished founder genomes and sequence read data for the Heat-MAGIC lines will be analyzed to impute missing calls and identify recombination points and haplotype blocks. Using established methods, generated phenotypic (Aim 1) and high-density SNP data will be used for genome-wide association analysis (GWA) to detect genetic loci associated with rice grain yield, quality, and nutrition under heat stress. GWA performed on each trait, treatment, environment, and relative indices will be used to identify common and treatment-specific loci. Phenotype data generated across locations and years will be used to identify contrasting haplotypes. Treatment-specific genetic loci or haplotypes with favorable alleles for tolerance and vice versa for the susceptible group will be selected for physiological characterization at MSU using a field-based facility.Aim 3: Physiological characterization of haplotypes under heat stressCharacterizing selected haplotypes helps ascertain the physiological and biochemical processes (network of traits) associated with heat stress tolerance in rice. Contrasting lines identified from Aims 1 and 2 will be characterized along with regional checks, such as Rex and Thad at MSU (Year 4). The study will use custom-designed tents to reconfirm the phenotypic performance of haplotypes under field conditions. Three areas of the same size will be randomly assigned as controls. All the lines will be replicated three times following a split-plot randomized complete block design. Once plants reach anthesis on the primary tiller, heat stress will be imposed by moving heat tents on the targeted plots until maturity. Stress-induced changes to the plant processes, such as photosynthetic efficiency, stomatal conductance, transpiration, and fluorescence, will be measured using LICOR-600 and canopy temperature using the thermal infrared camera at 7 and 14 days after stress. Stress injury to leaves (electrolyte leakage and chlorophyll stability assays) will be performed to assess the biophysical properties of tolerant and sensitive lines. At maturity, dry weights, seed number, seed weight, 100-seed weight, and harvest index will be determined. Grains harvested at maturity will be used to assess the effects of heat treatment on seed quality and nutrients. Finally, all the physiological and biochemical parameters will be correlated with the yield and quality to determine critical parameters associated with favorable haplotype under heat stress. Candidate loci/SNPs will be shortlisted to initiate breeder-friendly assay.