Supachitra Chadchawan

Direct-seeded rice offers agronomic and economic advantages, but early-season flooding creates hypoxic conditions around germinating seeds and young seedlings, limiting crop establishment. Understanding genotypic variation in early submergence responses is therefore important for improving tolerance during anaerobic germination (AG) and anaerobic seedling development (ASD). This study aimed to characterize submerged coleoptile elongation in Thai rice germplasm and identify genetic factors associated with this response. We screened 192 Thai indica rice accessions with submergence imposed before or after germination to evaluate AG and ASD responses under naturally varying ambient temperatures. Underwater coleoptile length and elongation index showed substantial genotypic variation, while responses under AG and ASD were only weakly correlated (r = 0.29), indicating that tolerance differs between developmental stages. Across trials, coleoptile elongation under submergence was strongly influenced by the environment, with higher ambient temperature associated with reduced elongation and genotype-dependent sensitivity to the ambient temperature–dissolved oxygen (DO) gradient. Controlled-temperature experiments further showed that elevated temperature was associated with lower DO concentrations and reduced underwater coleoptile elongation. Genome-wide association analysis using mixed-model-adjusted phenotypes identified four quantitative trait loci (QTLs) for coleoptile length and three for elongation index under AG, along with one QTL for coleoptile length under ASD. Integrative analysis of a chromosome 12 QTL combining local linkage disequilibrium, public RNA-seq data, and haplotype variation prioritized OsSWEET13, OsNAM, and OsARF24 as candidate genes for coleoptile elongation under submergence. Together, these findings show that developmental stage, temperature, and genetic background shape submerged coleoptile elongation in Thai indica rice.

Nitrogen availability and salinity are two major environmental factors affecting plant growth and development. Nitrate uptake is strictly regulated through transcriptional networks that balance nutrient assimilation and stress responses. The role of BTB-ZF transcription factors, which have been implicated in various abiotic stress responses, in coordinating nitrate uptake remains largely unknown; specifically, the precise molecular mechanisms through which OsBTBZ1, a BTB-ZF transcription factor from Oryza sativa, confers salt tolerance remain to be fully elucidated. Here, we characterize the function of OsBTBZ1 in Arabidopsis thaliana under nitrate and salt stress conditions. Transcriptomic analysis of the bt3 mutant and revertant lines expressing OsBTBZ1 in the bt3 mutant background indicated a relationship with NRT2.1, which encodes a high-affinity nitrate transporter. The bt3 mutant exhibited severe root growth inhibition under low nitrate and salt stress; however, expression of OsBTBZ1 restored root growth under combined stress, supporting a role for AtBT3 in stress adaptation. Our findings suggest that OsBTBZ1 may contribute to the coordination of nitrate-responsive pathways and root plasticity under stress, potentially through regulation of nitrate transport-related processes, including those associated with NRT2.1. These findings highlight the potential of OsBTBZ1-mediated regulatory mechanisms for improving nitrogen use efficiency and stress tolerance in future crops.

Rice ( Oryza sativa L. ) is a staple food for half of the world's population, and increasing attention has been given to its starch properties in relation to health concerns such as diabetes. Drought stress can limit rice production, particularly in key producing countries including China, India, and Thailand. This study examined the effects of drought on physiological traits and starch properties in five Thai rice varieties that differ in apparent amylose content (AAC): “RD43” (intermediate AAC), “RD69” (low AAC), “Suphanburi 1 (SPR1)” (high AAC), “Hawm Daeng (HD; photoperiod insensitive)” (high AAC), and “Pathumthani 1 (PTT1)” (low AAC). Plants were subjected to 6 days of drought stress at the booting stage, followed by recovery. Drought stress negatively affects physiological responses, such as Soil–Plant Analysis Development (SPAD) values and vegetation indices. Principal component analysis revealed distinct variety‐specific responses and recovery capacities, indicating clear genotype‐dependent differences in drought tolerance. Yield components, including grain weight, total grain weight per plant, and the number of filled grains, were also negatively affected. In addition, drought altered starch properties, particularly AAC. RD43 showed the greatest tolerance to drought stress based on physiological responses, but exhibited the largest change in AAC, suggesting strong drought sensitivity of starch traits. By contrast, SPR1 was more sensitive in physiological responses but maintained relatively stable AAC. We also found a significant correlation between physiological parameters (SPAD, NDVI, SR, G, and SRPI) and AAC. Among these, SRPI showed the strongest relationship with AAC, and a significant correlation coefficient was detected in all cultivars tested ( r = 0.496–0.685, depending on genotype). Lower SPAD values and reflectance indices (NDVI, SR, G, and SRPI) measured during the booting stage were consistently associated with reduced AAC in the final grain, indicating that declines in these parameters correspond to reductions in grain quality. These findings demonstrate how Thai rice varieties differ in their physiological and starch responses to drought and highlight the potential of measuring SPAD and reflectance indices at the booting stage as indicators associated with AAC under drought stress.

The recent development of genome editing technologies using CRISPR/Cas9 has marked a new era in precise genome editing. This study reports on genome editing using seven single-guide RNAs (sgRNAs) to target different positions in the OsGTL1 promoter in rice (Oryza sativa L.). This research focused on identifying CRISPR-edited plants before evaluating the effects of OsGTL1 modification in rice progeny. We successfully developed gene-edited lines that have different types of mutations. Moreover, our study detected at least 35% of genetic chimerism in the first generations of the edited lines. This chimerism resulted in a mosaic of genotypes within an individual plant, suggesting multiple CRISPR-Cas9 events targeting the target region. We successfully identified transgene-free lines in later generations. Various modifications occurred in the targeted region, including large and small deletions, single-base insertions and deletions, and inversions. This study highlights the complex challenges and opportunities of applying CRISPR/Cas9 to improve rice traits, emphasizing the importance of detailed characterization of edited lines to fully understand a gene's function and its pleiotropic effects.

An association of OsCUL3c with salt tolerance has been found by a genome-wide association studies (GWAS) in rice. However, its functions and mechanisms rem

The growth and yield of rice, a major global food crop, are impaired by salt stress. This study aimed to identify quantitative trait loci (QTLs) associated with salt tolerance at the seedling stage. Bulk segregant analysis (BSA) of an F₂ population from a cross between ‘Jao Khao’ (salt-tolerant) and IR29 (salt-susceptible) identified four QTLs on chromosomes 2, 3, 6, and 12. Four markers linked to these QTLs were validated in an F₃ population, showing strong correlations (r = 0.7–0.8) with membrane stability, relative water content, and salt injury scores. Single nucleotide polymorphism (SNP)-by-SNP interactions across parental lines and four additional salt-tolerant and four salt-susceptible varieties revealed significant enrichment of the “plant hormone signal transduction” pathway, identifying LOC_OS03G49990 (OsSLR1) encoding DELLA, as a key gene. Comparative analysis of BSA-predicted QTLs with weighted gene co-expression network analysis-based key genes suggested LOC_Os02g02830 (ubiquitin-conjugating enzyme E2 28) and LOC_Os06g06170 (RING-type E3 ubiquitin transferase) as potential candidate genes. SNP association analysis across ten cultivars identified significant quantitative trait nucleotides on chromosomes 1, 2, 3, and 9, notably involving OsFBOX72 (F-box-type E3 ubiquitin ligase L7). These findings highlight the role of ubiquitination and hormone signalling in salt tolerance, providing potential targets for marker-assisted breeding.

Here, we investigated physiological responses, yield components, starch properties, and starch biosynthesis genes in five Thai rice (Oryza sativa L.) cultivars (SPR1, Hawm Daeng, RD43, RD69, and PTT1) with distinct starch characteristics under salt stress. Salt stress decreased flag leaf greenness (SPAD), normalized difference vegetation index (NDVI) levels, and carotenoid reflectance index 1 (CRI1) levels in all cultivars, resulting in reduced net photosynthesis, transpiration rates, and yield components across all cultivars, with Hawm Daeng and PTT1 being most susceptible. In contrast, RD69 and SPR1 were more tolerant, exhibiting recovered chlorophyll fluorescence levels and total performance index values after 3 days. Salt stress reduced apparent amylose content (AAC) and increased rapidly available glucose (RAG) levels in all cultivars. Granule-bound starch synthase I (GBSSI) expression declined the most in PTT1 and Hawm Daeng. SPAD, NDVI, CRI1, and photosynthetic parameters were correlated with GBSSI expression at the milky and dough stages of grain development. GBSSI expression levels showed little to no correlation with slowly available glucose but correlated with resistant starch levels at the booting stage of grain development. Salt stress affected yield components and rice starch quality, with variations depending on salt susceptibility, which in turn affected GBSSI expression levels during the milky and dough stages of grain development.

Pigmented rice (Oryza sativa L.) is recognized as a source of natural antioxidant compounds, such as flavonoids, oryzanol, tocopherol, and anthocyanin. Because of their nutritional benefits, anthocyanin-enriched or pigmented rice varieties are feasible alternatives for promoting human health. Pigment biosynthesis in rice is a complex process that involves multiple biosynthetic and regulatory genes. This study aimed to identify the genes associated with antioxidant traits in local Thai rice and develop molecular markers for breeding programs. Single nucleotide polymorphisms (SNPs) in 233 rice cultivars, 119,541 SNPs from the promoters, and the first 5 exons of all genes were associated with antioxidant phenotypes determined using 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid), 2,2-diphenyl-1-picrylhydrazyl, ferric reducing antioxidant power, total flavonoid content, and total phenolic content assays through a mixed linear model (MLM) genome-wide association study (GWAS). GWAS analysis detected 336 quantitative trait nucleotides located at 93 loci, 83% of which were consistently mapped to the reported quantitative trait loci of antioxidant traits. Ten loci, including the OsRc gene, were consistently co-associated with all phenotypic traits. Two genetic markers for polymerase chain reaction detection were developed for the OsTT8 gene and the OsRc promoter, both of which were positively correlated with antioxidant properties. These markers can be applied for antioxidant trait selection in rice breeding programs.

Rice is the major crop of Thailand. However, the rice yield is still limited, especially in local cultivars. Fermented chitin (FC) application to soil has been demonstrated to improve rice growth and yield. The application of biostimulants has been proposed to improve both the yield and quality of ‛RD69’ and ‛HGD’ rice varieties. While FC has been suggested as a potential solution, the specific effects of FC on seed quality and quantity remain insufficiently explored. In this study, pot experiments were conducted to determine the effects of FC and FC with rice husk (FC+RH) treatments on the grain quantity and quality of two rice cultivars, ‛RD69’ and ’Hawm Gulahb Deang’ (HGD), which are colored rice varieties with high antioxidant levels. ‛RD69’ has low apparent amylose content (AAC) and a high percentage of rapidly available glucose (RAG), while ‛HGD’ is the local Thai rice with medium AAC and low %RAG. FC and FC+RH were applied as soil supplements at concentrations of 0.01%, 0.1%, and 0.2% (w/w). The supplementation of 0.2% FC+RH resulted in the highest yield of ‛RD69’ (73%) and ‛HGD’ (30%). Although both FC and FC+RH did not significantly affect the AAC content of both cultivars, FC+RH decreased their %RAG. Interestingly, although FC+RH enhanced the antioxidant activity of the seeds of both cultivars, ‛RD69’ was more responsive to the effects of FC and FC+RH treatments than ‘HGD’, as significantly higher antioxidant levels were detected in ‛RD69’ seeds. These findings suggest that FC+RH supplementation can enhance the yield and quality of colored rice.