Water and food security are the most alarming concerns because of rapid climate change, and both are vulnerable to climate variability. Reports indicate that by the 21st century’s end, irregular, erratic rainfall patterns and an average global temperature of 1.4°C–5.8°C will have resulted in limited surface water availability for irrigation in field crops, resulting in drought and a reduction in agricultural yield (Misra, 2014; Sandhu et al., 2018). Furthermore, storm surges may influence freshwater availability, altering the quality of the surface irrigation water by making it saline or alkaline. Rice, a staple in millions of households, is a multiple daily meal in Asia and South America. As a cost-effective, high-calorie grain, the rice crop is a major contributor to fulfilling daily diets globally. Reports estimate that the production of rice crops will double in the next decade to satisfy the needs of an ever-growing rice-consuming population, and this must be done with less land and without depleting natural resources such as water (Sandhu and Kumar, 2017). Existing high-yielding cultivars of rice are sensitive to drought during the reproductive phase, significantly affecting grain yield. Breeding efforts to develop such varieties began more than two decades ago, utilizing both conventional and molecular approaches to integrate drought-tolerant traits into new and existing rice varieties (Bernier et al., 2007). Several studies have attempted to develop tolerant lines that do not yield under drought stress (Kumar et al., 2014; Vikram et al., 2015; Baisakh et al., 2020).

Combining the high-yield traits of irrigated rice with drought-tolerant traits from upland rice cultivators offers the potential to develop better abiotic tolerant rice varieties. Secondary drought tolerance, relative water content, canopy temperature, leaf area, and root growth were not decisive in determining grain yield under water-stress conditions. On the other hand, the grain yield-contributing traits under drought at the reproductive stage demonstrated their significance as the most reliable and efficient for selecting drought-tolerant rice genotypes (Swain et al., 2014; Vikram et al., 2015). Therefore, identification and introgression of drought QTLs is a practical approach for breeding high-yielding drought-tolerant rice (Collins et al., 2008; Kumar et al., 2008). The first reported drought QTL on chromosome 12 (qDTY_12.1 ) was used in drought-tolerant upland and lowland rice with increased grain yield (Bernier et al., 2009; Mishra et al., 2013) because of its consistent tolerance over multiple generations (Bernier et al., 2007). Similarly, qDTY_1.1 , identified on chromosome 1 in the Nagina 22 variety under drought conditions, contributes to grain yield (Vikram et al., 2011; Ghimire et al., 2012; Bhattarai and Subudhi, 2018). Drought QTL qDTY_2.3 (Yadaw et al., 2013) from the background variety Vandana interacted with the major QTL qDTY_12.1 .

The effects of the identified QTLs are not universal; only a few robust QTLs work in several backgrounds, but not all. Due to epistatic interactions, the same favorable QTLs in one background may not be favorable to another genetic background. The QTL’s instability in effects across different populations QTL × genetic background interaction (Q × G) and across environments QTL × environmental interaction (Q × E) has always been the bottleneck for the successful deployment of identified QTLs in molecular breeding (Courtois et al., 2003; Lafitte et al., 2004; Bernier et al., 2008; Collins et al., 2008; Yadav et al., 2019). Although many QTL reports are available on drought tolerance, novel QTLs from exotic landraces in different genetic backgrounds linked to grain yield during the reproductive stage of drought stress are limited. Therefore, an attempt was made to develop the mapping population of an exotic drought-tolerant (Chao Khaw) landrace from Loas and a drought-sensitive variety (Kasturi) to identify any novel or previously reported drought QTLs.

Rice is a highly susceptible to drought stress at the reproductive stage, which leads to yield losses compared to other cereals, such as wheat, maize, sorghum, and pearl millet. Unlike traditional cultivars cultivated in specific rice ecosystems before the Green Revolution, modern high-yielding varieties have replaced adaptable varieties. However, the newly introduced varieties lack drought tolerance (Bernier et al., 2008; Kumar et al., 2014). Over the past two decades, the impact of climate change has intensified and become visible. Research on drought tolerance breeding has accelerated, leading to the discovery of many drought QTLs/genes.

For successful drought-tolerant breeding programs and subsequent drought-tolerant varieties, breeders need to identify droughts with significant and consistent effects across diverse environments and genetic backgrounds. Identifying QTLs/genes is crucial for integrating these findings into breeding programs. The International Rice Research Institute led this initiative. Over the past decade, IRRI has discovered several grain yield-related QTLs, such as qDTY_1.1 , qDTY_2.1 , qDTY_3.1 , and qDTY_12.1 , utilizing SSR markers (Solis et al., 2018). Farmers from Southeast Asian countries, particularly in India, Nepal, Malaysia, and Lao PDR, widely cultivate improved lines developed using mega varieties such as Swarna, Swarna-Sub1, IR64, Samba Mahsuri, Vandana, Anjali, Kalinga III, MTU1010, Savitri, MR219, and TDK1-Sub1 (Kumar et al., 2020). However, drought yield QTL is a quantitative and complex trait. Phenotypic variation explained (PVE) by the identified QTL is often limited, generally below 40%. In addition, many drought-yield QTLs show limited or no expression in other varietal backgrounds and environmental conditions. Therefore, breeders must explore novel and previously reported QTLs from new genetic backgrounds and donors to enhance their widespread application in global and national breeding programs.

This study was designed to identify QTLs/genes for yield under reproductive drought stress in a population derived from an exotic landrace from Laos and an aromatic variety, Kasturi. We provided three stress cycles during the crop duration to the two seasons of the drought trials to expose the mapping population to the maximum drought conditions. In addition, we sowed the drought trials late to adjust in such a way as to avoid the rainfall period, distinguishing between drought-tolerant and drought-sensitive lines. Bernier et al. (2007) classified lowland drought screening experiment results based on yield reductions as mild (30%), moderate (31%–65%), and severe drought (65%–85%). Kasturi experienced nearly 80% reduction in both stress trials in the drought-sensitive parent. This reduction in Kasturi yield validates the severity of the two stress trials. With an average population yield reduction exceeding 60%, these conditions were ideal for selecting drought-tolerant lines and differentially expressing lines for QTL mapping in drought-tolerant breeding. The observed high heritability, surpassing 80% for all traits at the reproductive stage under drought stress conditions, indicates a vast genetic influence on these traits. The high heritability enhances the reliability and significance of QTL mapping efforts, providing precise insights into the genetic factors that determine the yield and yield-attributing traits of drought stress. The effectiveness of yield drought QTLs is further exemplified by the successful incorporating of these favorable qDTY alleles into high-yielding rice varieties.

In the context of marker-assisted breeding (MAB), genetic mapping of the reproductive stage will facilitate the breeding of cultivars suitable for drought-prone environments. While numerous drought QTLs, various yield QTLs under drought stress, and various yield QTLs under reproductive-stage drought stress have been identified for the marker-assisted breeding program, the study identified a gap in QTLs from an exotic landrace controlling different traits related to drought stress tolerance. The mapping of QTLs linked to reproductive stage grain yield traits in the evaluated F_2:3 mapping population, characterized by wide variations in ten morpho-physiological traits during stress, addresses this gap.

Genotyping of the F_2:3 population using 721 SSR primers revealed 89 polymorphic markers, contributing to the construction of a comprehensive linkage map covering 2,118.29 cM with an average distance of 23.80 cM. In our study, several key traits associated with grain yield were identified across various chromosomes, providing better insight into enhancing the productivity of rice under drought conditions. A total of 13 QTL loci related to drought tolerance traits distributed on chromosomes 1, 3, 7, 8, 10, and 11 may provide important genetic resources for future breeding. A consistent major QTL for yield, qDTY_1.1 , was identified on the chromosome in 2016WS and 2016WS. Earlier studies by Ghimire et al. (2012) and Vikram et al. (2011) reported qDTY_1.1 on chromosome 1. Another major QTL, qDTY_8.1 , was identified on chromosome 8, which aligns with the results reported by Prakash et al. (2019). The study revealed that the QTLs for drought-related traits in rice overlap on chromosome 8 and positively influence the grain yield and harvest index. It is also noteworthy that the genomic region overlapped by qDHI_1.1 and qDTY_1.1 on chromosome 1, while qDTY_8.1, qDSPF_8.1 , and qDBM_8.1 , on chromosome 8. The study identified promising lines with the high yielding are carrying the consistent QTLs under both non -stress and drought stress conditions ( Table 4 ). The genes within the identified QTL region and their influence on yield were considered candidate genes. qDTY_1.1 is associated with genes such as Os01g41450.1, Os01g41510.1, Os01g41550.1, Os01g41834.1, Os01g41900.1, Os01g42960.1, Os01g43150.1, and Os01g43180.1. Similarly, five candidate genes (Os08g0518800, Os08g0518900, Os08g0519300, Os08g0487800, and Os08g0500700) were identified on chromosome 8.

Linking QTLs to the underlying genes in mapping studies is crucial for the effective use of QTL regions. Hence, it is necessary to investigate whether other genes of interest are present in a particular QTL region. This study reports the genetic complexity of QTLs by clustering gene expression. Advances in genomics have facilitated the critical role of candidate genes in abiotic stress tolerance in plants (Sreenivasulu et al., 2007; Vij and Tyagi, 2007; Urano et al., 2010). Many transcription factors, enzymes, and stress-responsive element-binding factors are responsible for various stresses (abiotic) across multiple plant species (Pottorff et al., 2014). Although several QTLs influence tolerance in rice under drought stress, understanding the complex molecular mechanisms and linking each QTL to its underlying genes remains challenging. Although each gene has a different expression, more than 300 unique subtracted cDNA sequences covering diverse cellular activities and functional genes have been reported. Detailed bioinformatics analyses revealed that the drought tolerance mechanisms of the three rice lines were associated with different numbers and types of deferentially expressed genes. This suggests that various genes govern tolerance via distinct biochemical mechanisms. The most differentially expressed genes under drought conditions could contribute to drought tolerance, and QTLs show high correspondence among genomic regions (Fu et al., 2007). We observed two genes in the QTL region of chromosome 8 that aligned with the phenylpropanoic biosynthesis pathway. These genes are activated in response to stress conditions such as drought, heavy metal exposure, salinity, high/low temperatures, and ultraviolet radiation. This activation leads to the accumulation of diverse phenolic compounds with an inherent capability to scavenge harmful reactive oxygen species, among other functions. Three genes were identified to play essential roles in the amino acid biosynthesis pathway, which have been suggested by many researchers for drought conditions. On chromosome 1, all seven genes identified under functional ontologies were characterized as genes that can respond to abiotic stress and biotic stimuli.

In conclusion, this study identified key stable drought yield QTLs utilizing a drought-tolerant exotic landrace. The study also identified QTLs linked to the genomic regions that can serve as a valuable genetic resource for developing drought-tolerant rice varieties. These QTLs can be integrated into the present drought breeding program to develop improved varieties.

The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.

(i) The plant materials used in this study were sourced from the International Rice Research Institute (IRRI) gene bank, an independent nonprofit research and educational institute. The IRRI holds the authority to collect and preserve rice germplasm globally for research purposes, and the materials used in this study have been documented and acquired through appropriate channels. (ii) Our experimental research and field studies on cultivated or wild plants strictly adhered to pertinent institutional, national, and international guidelines and legislation. It is ensured that all activities related to the collection of plant materials comply with the regulations. Specifically, the IRRI Rice GenBank operates according to the provisions set forth by the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA), thus affirming its commitment to responsible and ethical practices in genetic resource management and research.