Plant growth-promoting rhizobacteria (PGPR) offer a sustainable alternative to chemical fertilizers in rice production, yet the mechanisms underlying multifunctional growth promotion by individual strains remain insufficiently characterized. In this study, strain ST2023006 was isolated from sugarcane rhizosphere and systematically characterized through phenotypic assays and whole-genome sequencing. The strain was identified as Pseudomonas chlororaphis based on morphological, physiological, biochemical, and multilocus sequence analyses. It exhibited tolerance to temperature (25-37 ℃), pH (5.0-9.0), and salinity (≤2% NaCl). ¹⁵N isotope dilution analysis revealed nitrogen fixation contribution rates of 13.4% and 9.72% to rice roots and shoots, respectively. Pot experiments demonstrated that inoculation significantly promoted growth in two rice varieties, increasing plant height by up to 86.6%, while enhancing root surface area, root volume, and biomass accumulation. In vitro antagonism against Rhizoctonia solani and quantitative IAA analysis (59.44 µg·mL⁻¹) provided experimental support for genome-predicted biocontrol and IAA production traits. Whole-genome sequencing revealed genes potentially associated with nitrogen fixation (nifU, fixI), nutrient mobilization (potassium/zinc solubilization, siderophores), phytohormone synthesis (IAA), stress tolerance (heavy metal resistance, heat/cold shock proteins), and complete biosynthetic gene clusters for the antifungal compounds pyrrolnitrin, phenazine, and hydrogen cyanide. These findings indicate that P. chlororaphis ST2023006 is a promising multifunctional PGPR candidate with demonstrated plant growth-promoting effects and experimentally supported genomic potential for biocontrol.

Background: High-temperature stress can cause serious abiotic damage that limits the yield and quality of rice. Heat tolerance during the flowering stage of rice is a key trait that can guarantee a high and stable yield under heat stress. Heat tolerance is a complex trait that is regulated by numerous quantitative trait loci (QTLs); of which, however, few underlying genes have been fine mapped and cloned.Results: In this study, the F_2:3 population derived from a cross between Huanghuazhan (HHZ), a heat-tolerant indica cultivar, and 9311, a heat-sensitive indica rice variety, were used to map the QTLs for heat tolerance during the flowering stage of rice. The F_2:3 lines were treated under 38 °C from 9:30 am to 3:30 pm continuously for 3 days in a phytotron, and spikelet fertility was assessed. A new major QTL, qHTT8, controlling heat tolerance was located on chromosome 8 using the bulked-segregant analysis (BSA)-seq method. The QTL qHTT8 was determined to be located in the 355500–4520000 bp region, with a size of 0.965 Mb. The candidate region of qHTT8 on chromosome 8 contained 65 predicted genes. Ten putative predicted genes were found to be associated with abiotic stress tolerance. In future studies, the backcross population will be constructed to fine map and validate the effect of qHTT8.Conclusion: The information obtained in this study is useful for the fine mapping and cloning of qHTT8 and breeding heat-tolerant varieties of rice using marker-assisted selection.