Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.

Dirty panicle disease is one of the most important diseases that can cause yield losses in rice production. Despite the severity of the disease, the molecular basis of resistance to the pathogen is poorly understood. Using QTL-seq with an F₂ population, we identified three genomic regions on chromosomes 1, 9, and 10, namely qDP1, qDP9, and qDP10. These regions are significantly associated with resistance to dirty panicle disease caused by two fungal pathogens, Bioplaris oryzae and Cirvularia lunata. qDP1 was significantly associated only with resistance to B. oryzae, whereas qDP9 and qDP10 were significantly associated with both B. oryzae and C. lunata. We also developed KASP markers for each QTL detected and validated them in the F₂ population. The markers were able to explain phenotypic variation in a range of 5.87–15.20%. Twelve potential candidate genes with annotated functions as resistance-related genes were proposed. These candidate genes include those encoding RLK, MATE, WAK, NBS-LRR, subtilisin-like protease, and ankyrin repeat proteins. The results of this study provide insights into the genetic mechanism of dirty panicles in rice and will be useful for future breeding programs for dirty panicle resistance. This is the first report of QTLs associated with resistance to dirty panicle disease in rice.

Rice is a staple food crop that plays a pivotal role in global food security, feeding more than half of the world’s population. Soil salinity is one of the most important global problems affecting rice productivity. Salt stress at the seedling stage inhibits root growth, impairs nutrient and water uptake, and affects overall plant vigor, resulting in poor establishment and reduced growth. Therefore, acquiring salt tolerance, especially at the seedling stage, is critical for successful rice production in salinity-affected areas. In this study, 160 RILs derived from a cross between Pokkali and KDML105 were evaluated for their salt tolerance at the seedling stage. QTL-seq analysis with this population identified nine QTLs associated with salt tolerance. Through a comprehensive examination of the effects of coding sequence variants of the 360 annotated genes within the QTLs and gene expression under salt stress, 47 candidate genes were prioritized. In particular, Os01g0200700 (metallothionein-like protein) and Os12g0625000 (O-acetylserine (thiol)lyase) were suggested as potential candidates based on annotated functions and expression data. The results provide valuable insights for improving rice productivity and resistance under salt stress conditions during the critical seedling stage.

The impact of increasing drought periods on crop yields as a result of global climate change is a major concern in modern agriculture. Thus, a greater understanding of crop physiological responses under drought stress can guide breeders to develop new cultivars with enhanced drought tolerance. In this study, selected chromosome segment substitution lines of KDML105 (KDML105-CSSL) were grown in the Plant Phenomics Center of Kasetsart University in Thailand under well-watered and drought-stressed conditions. Physiological traits were measured by observing gas exchange dynamics and using a high-throughput phenotyping platform. Furthermore, because of its impact on plant internal gas and water regulation, stomatal morphological trait variation was recorded. The results show that KDML105-CSS lines exhibited plasticity responses to enhance water-use efficiency which increased by 3.62%. Moreover, photosynthesis, stomatal conductance and transpiration decreased by approximately 40% and plant height was reduced by 17.69%. Stomatal density tended to decrease and was negatively correlated with stomatal size, and stomata on different sides of the leaves responded differently under drought stress. Under drought stress, top-performing KDML105-CSS lines with high net photosynthesis had shorter plant height and improved IWUE, as influenced by an increase in stomatal density on the upper leaf side and a decrease on the lower leaf side.

Rice (Oryza sativa L.) ‘KDML105’ is the most popular aromatic rice originating in Thailand. This cultivar is highly susceptible to abiotic stresses, especially drought and salt stress during the seedling stage. The objective of this study was to investigate the photosynthetic performance in response to drought and salt stress of four improved breeding lines, specifically CSSL94 and CSSL103 (containing drought-tolerant quantitative trait loci: DT-QTLs) and RGD1 and RGD4 (containing a salt-tolerance gene, SKC1), with ‘KDML105’ (susceptible) and DH103 (tolerant to drought and salt stress) as the controls. Rice seedlings were grown for 21 days in hydroponic solutions and then exposed to salt stress (150 mM NaCl) or drought stress (20% PEG6000) for 10 days. The results indicated that when subjected to drought and salt stress, all rice lines/cultivar exhibited significant reductions in net photosynthesis rate (PN), stomatal conductance (gs), transpiration rate (E), the maximal quantum yield of PSII photochemistry (Fv/Fm), the effective quantum yield of PSII photochemistry (Fv’/Fm’), photosynthetic pigments, and SPAD readings, whereas water use efficiency (WUE) and non-photochemical quenching (NPQ) increased. Compared with ‘KDML105’, CSSL94, and CSSL103 were more tolerant to both drought and salinity, showing less reduction in all photosynthetic parameters. For RGD1 and RGD4, it was confirmed that these lines had a higher level of salt tolerance than ‘KDML105’ based on better photosynthetic performance under salt stress, demonstrating that these lines were also more tolerant to drought stress.

Rice is a staple food for more than half of the world’s population. However, the pervasive problem of salinity is severely undermining rice production, especially in coastal and low-lying areas where soil salinization is widespread. This stress, exacerbated by climate change, necessitates the development of salt-tolerant rice varieties to ensure food security. In this study, an F_2:3 population (n = 454) from a cross of KDML105 and its chromosome segment substitution line (CSSL) was used to identify genomic regions associated with salt tolerance at the seedling stage. Using the QTL-seq approach, a QTL significantly associated with salt tolerance was identified on chromosome 1. Annotation of candidate genes in this region revealed the potential regulators of salt tolerance, including MIKC-type MADS domain proteins, calmodulin-binding transcription factors, and NB-ARC domain-containing proteins. These and other identified genes provide insights into the genetic basis of salt tolerance. This study underscores the importance of using advanced genomics tools and CSSL populations in the study of complex traits such as salt tolerance in rice. Several candidate genes identified in this study could be used in further studies on molecular or physiological mechanisms related to the salt response and tolerance mechanism in rice. Additionally, these genes could also be utilized in plant breeding programs for salt tolerance.