Changing climate and growing global population are significant concerns for rice (Oryza sativa L) production (Manasa et al., 2023). Climate change disturbs the consistency and intensity of hydrological occurrences, threatening crop yield and food security. Primary regions experiencing these effects include South and Southeast Asia, Sub-Saharan Africa, and Latin America, covering both uplands and shallow rainfed lowlands (Radha et al., 2023). In order to address the challenge of feeding an anticipated global population of nine billion by 2050, we must substantially enhance rice production. To put this into perspective, the current yield stands at 104 million tons, and our target is to generate an additional 160 million tons of rice (www.FAO.org). Amid the changing climate, almost half of the rice cultivation regions are impacted, leading to a 42% decrease in yield worldwide due to various abiotic stresses (Muthu et al., 2020).

Rice is life for millions of farmers and is considered a staple food for over a billion people in the world. Rice cultivation primarily thrives in tropical and subtropical climates, which are mainly affected by drought, salinity, and submergence. On a global scale, 90% of rice production and consumption takes place in Asia (Adhikari et al., 2019). When subjected to drought, crops face a significant reduction in yield, particularly when the stress coincides with the reproductive stage (Garrity and O'Toole, 1994; Oladosu et al., 2020; Verma et al., 2014). Despite Asia being the major producer, approximately 34 Mha of rainfed lowland and 8 Mha of upland rice cultivable area are annually impacted by drought resulting in a yield reduction of 13% to 35% (Panda et al., 2022). Enhancing drought tolerance poses a challenge due to the unpredictable nature of drought stress and the complex response mechanisms of plants (Takahashi et al., 2020). Likewise, salinity is a widespread problem in both coastal and marginal inland environments, limiting rice production in 30% of rice growing area, encompassing 45 million hectares of irrigated land and 32 million hectares of dry land worldwide (Singh et al., 2016; FAO, 2018; Ravikiran et al., 2018). The elevated salt levels disrupt water and nutrient absorption by the roots, causing an imbalance in the plant’s metabolism, ultimately resulting in decreased plant growth, leading to a yield loss of up to 35% (Farooq et al., 2015). Although rice is a semi-aquatic plant, it is well-suited for stagnant conditions due to its well-established aerenchyma, enabling oxygen transportation through the roots. However, recurrent flooding in lowland and deep-water rice regions, impacts an area of 12–14 million hectares in India, leading to a yield loss of up to 32% (Oladosu et al., 2020). The ability of tolerance to endure submergence relies on its carbohydrate levels (Alpuerto et al., 2016).

Utilizing natural genetic resources is the primary avenue for advancing stress resilience in rice cultivation (Marone et al., 2021). Studying natural variation not only helps us comprehend the genetic mechanisms underpinning tolerance during crucial growth stages but also advances our understanding of the associated physiological process (Ismail and Horie, 2017). Traditional rice landraces possess a robust genetic foundation that offers enhanced adaptability and protection against various biotic and abiotic stresses (Binodh et al., 2023). Therefore, landraces play a vital role as integral plant genetic resources, holding immense potential as donors for developing multiple stress tolerance. Significant advancements have been made in the past few decades leading to the identification of recognized donors, such as N22 for drought (Vikram et al., 2016), Pokkali for salinity (Singh and Sengar, 2014), and FR13A for submergence (Xu et al., 2006). Currently, due to changing climatic conditions, crops in stress-affected areas are expected to face a combination of abiotic stresses rather than single stresses (Slama et al., 2015; Wani et al., 2016). Thus, breeding for tolerance to a single abiotic stress may be risky, as plant responses to combined stresses differ from individual stress responses. When rice seedlings encounter various abiotic stresses during their initial growth phase, issues may arise due to suboptimal crop establishment, decreased length of roots and shoots, reduced leaf area, and early seedling death (Krishnamurthy et al., 2016). Hence, seedling stage tolerance to multiple abiotic stresses is crucial for better crop establishment, robust vegetative growth, and ultimately higher yield. To tackle this, a trait-based breeding approach in crop improvement programs is more effective than focusing on yield-based breeding (Paleari et al., 2017). Numerous studies have indicated the use of PEG-6000 for drought tolerance (Binodh et al., 2023), sodium chloride (NaCl) for salinity adaptation (Kakar et al., 2019), and the maintenance of a water level ranging from 90 cm to 120 cm for submergence tolerance (Samanta et al., 2022) were employed for quick screening during the seedling stage to identify promising candidates with stress tolerance.

Recent advancements in crop genetics have led to the creation of molecular tools that assist in faster and more efficient breeding techniques. Examining genetic diversity and population structure is valuable for identifying superior breeding materials and enhancing breeding efficiency. The use of DNA-based markers resulted in the identification of markers linked to QTLs or genic regions of particular traits, making the breeding process quicker and more precise to select preferred plants more rapidly (Singh et al., 2015). Several studies have highlighted specific quantitative trait loci (QTLs) linked to stress tolerance. During the reproductive stage of drought stress, several yield QTLs such as qDTY 1.1, qDTY 2.1, qDTY 3.1, and qDTY 12.1 were found to be closely associated with particular markers, including RM104 (Ghimire et al., 2012), RM2634 (Muthu et al., 2020), RM168 (Dixit et al., 2014), and RM28166 (Mishra et al., 2013). Moreover, RM3412 is found to be associated with the saltol region of seedling stage salinity (Krishnamurthy et al., 2016), and ART5 is found to be associated with the sub1 region for submergence (Sarkar and Bhattacharjee, 2011). In the present era, rapid changes in climatic conditions emphasize the need for developing broad-spectrum genetic resistance in rice. This genetic resistance, with its inbuilt tolerance to these stresses, offers an economically viable and sustainable option to improve rice productivity under multiple stress conditions. Despite considerable efforts through traditional breeding approaches, molecular introspection of genetic diversity could reveal more precise information about the genetic variation, which would be helpful for genetic improvement breeding by identifying multiple abiotic stress tolerance. Therefore, this study aimed to evaluate the physiological responses and genetic diversity residing among the landraces, prerelease cultures, and cultivars to multiple abiotic stresses in order to identify potential donors to be employed in climate-resilient breeding programs.

In total, 41 diverse rice genotypes, including native landraces of Tamil Nadu, prerelease lines, and cultivars were evaluated independently for three different abiotic stress tolerance involving respective tolerant checks, viz., IR64Drt1 for drought possessing qDTY 2.2 and qDTY 4.1 QTL (Binodh et al., 2023), FL478 for salinity having saltol QTL (Muthu et al., 2020), and FR13A for submergence having Sub1 QTL (Xu et al., 2006), whereas IR64 for drought and salinity and IR42 for submergence were used as susceptible checks ( Supplementary Table 1 ). The present investigation was carried out in the Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, during Kharif and Rabi 2022–2023.

Rapid changes in climatic conditions have a significant impact on rice yield, and global food demand is increasingly affected by various abiotic stresses (Ramankutty et al., 2018). In the future development of crops, especially within the context of changing climatic conditions, the focus has shifted toward enhancing climate resilience in the creation of climate-smart crops to ensure food and nutritional security (Salgotra and Chauhan, 2023). Multifaceted abiotic stress tolerance takes on substantial importance in high-yield breeding initiatives. Consequently, there is a need to explore physiological variations and genetic diversity at earlier stages (Muthu et al., 2020). This effort aligns with the primary goal of enhancing the capacity for stress resilience and productivity, particularly given the dynamic shifts in environmental conditions. In this study, a diverse panel of rice genotypes, including prerelease lines, cultivars, and landraces, underwent screening under drought, salinity, and submergence conditions to evaluate their performance and identify potential donors for climate-resilient variety development.

The present study demonstrates that the resultant reduction in seedling growth parameters, viz., plant biomass and RGI, in both seasons leads to a depletion of dry matter content when the rice genotypes are exposed to subsequent stresses like drought, salinity, and submergence. Under all stress conditions, there was a significant reduction in plant biomass over the season of about 13.253% under drought, 16.466% under salinity, and 26.104% under submergence. Likewise, the relative growth index also showed reductions of 36.900%, 42.00%, and 75.600% under drought, salinity, and submergence, respectively. Similarly, Zhao et al. (2014) reported a 46.700% and 56.800% decline in biomass in FL478 and IR64 under salinity stress conditions. The degree of response of genotypes to stress-induced changes in plant growth varies due to a combination of factors, including genetic variations, duration of stress exposure, and developmental stages (Mundada et al., 2020). The seedling biomass obtained under various stress conditions was employed to derive stress-tolerant indices like DTI, STI, and FTI and was subsequently used for identifying tolerant genotypes. Significant divergence in the values of DTI, STI, and FTI indicted wide diversity among the studied genotypes. Generally, higher values of the stress-tolerant index imply their tolerance nature. As per the finding of Muthuramu and Ragavan (2020), the genotypes (viz., Norungan, APD19002, Anna (R) 4, Arupatham samba, Varigarudan samba, Mattaikar, Ponmani samba, CO53, and Poongar) with a high DTI value and superiority over the tolerant check IR64Drt1 indicate their ability to grow under limited water conditions. Likewise, the genotypes viz., Arupatham samba, CO53, and Norungan exhibited superiority compared to the tolerant check FL478, whereas APD19002, Mattaikar, and Varigarudan samba were identified with STI values exceeding 1 in both seasons. High STI signifies their potential to be grown in salt-affected areas. Higher values of FTI in the genotypes, viz., Arupatham samba, Mattaikar, APD19002, and Varigarudan samba, were found to be on par with the tolerant check FR13A, indicating their ability to withstand flooding situations. The study revealed that the genotypes, viz., Mattaikar, APD19002, Varigarudan samba, and Arupatham samba, were found to be multiple stress tolerant ( Figure 10 ). Hence, these genotypes can be employed as potential donors in the development of climate-resilient varieties.

Leaf photosynthesis is an important process in plants and is highly sensitive to various abiotic stresses (Sharma et al., 2020). The results revealed that a gradual reduction in PN was also accompanied by a decrease in e and gs in rice seedlings. Under stress conditions, on average, the PN decreased by about 16.394% in drought, 17.434% in salinity, and 50.322% in submergence. Likewise, gs and e were found to be drastically reduced under stress conditions. This suggests that stomatal closure upon stress imposition is the major limiting parameter, resulting in declining photosynthesis. This is in accordance with the previous findings of Yamori et al. (2020), where they showed how stomatal conductance affects photosynthesis in rice under changing light conditions using wild-type (WT) rice (Oryza sativa L. cv. Taichung 65) and the slac1 mutant (defective in the OsSLAC1 gene) with a modified stomatal regulation gene (SLAC1 knockout). Overall, the findings show a considerable impact of drought, salinity, and submergence on key leaf gas exchange parameters, indicating a compromised physiological performance of the plants under these stress conditions in both seasons. The RWC and CCI were highly affected under stress conditions. According to Polash et al. (2018), the accumulation of both organic (proline) and inorganic (K+) osmolytes may play a role in stress alleviation by retaining water in the cells. Fluorescence parameters, viz., Fm and Fv/Fm, are excellent ways to evaluate the potential of PSII (Faseela et al., 2020). Under all the stress conditions, we observed an increase in Fo values whereas the Fm and Fv/Fm showed a declining trend, suggesting the alteration of PSII activity and photo-inhibition under various stress conditions. Similar results were obtained by Muhammad et al. (2021) for drought, Tsai et al. (2019) for salinity, and Elanchezhian et al. (2015) for submergence. The ability of genotypes to uphold photosynthetic rate and PSII activity determines their tolerance potentiality (Sarkar and Ray, 2016; Pradhan et al., 2019). As a result, the genotypes Mattaikar, Arupatham samba, Varigarudan samba, and Vadakathi samba were identified with higher PSII activity under stress conditions, ultimately leading to better photosynthesis and growth. Based on our experiments, it appears that physiological efficiency is the most indicative parameter for distinguishing genotype responses. Genotypes exhibiting higher physiological efficiency are more likely to tolerate stress conditions, whereas those with lower physiological efficiency are more susceptible.

SSR markers tightly linked to QTLs are amazing molecular tools for the genetic profiling of rice accessions and the identification of tolerant genotypes under multiple abiotic stress conditions. In this study, the genetic diversity of 41 rice genotypes was evaluated by employing 30 markers associated with the target trait. A substantial level of polymorphism was identified in the majority of the SSR markers. A similar result was found in Ram et al. (2007), who assessed genetic diversity and revealed the considerable allelic variability among SSR markers encompassing rice germplasm into cultivars, landraces, and wild relatives, providing valuable insights into genetic variability for future utilization. Based on marker profiling, the SSR primer RM8094, RM1287, RM2634, RM22, RM10694, and RM140 displayed higher values for PIC, MI, and RP, suggesting the potential of further utilization of these markers in investigating genetic diversity of rice accessions. Likewise, Lokeshkumar et al. (2023) identified three landraces (Kuttimanja, Tulasimog, and IET-13713I) as salt-tolerant with strong correlations in morphological and physiological traits under various conditions. Similarly, based on molecular analysis of the Saltol region, the markers viz., AP3206F, RM10793, and RM3412b, located close to the SKC1 gene (11.23–12.55 Mb), displayed new alleles in tolerant lines like Kuttimanja, IET-13713I, and Tulasimog, suggesting their potential as candidates for novel genomic regions associated with salinity tolerance, whereas using high-yielding indica rice variety as a donor to developing multiple stress-tolerant rice variety through marker-assisted selection by Ali et al. (2017).

The average genetic distance among the genotypes was 0.443, suggesting an elevated magnitude of genetic diversity among the studied rice genotypes, and maximal genetic similarity was observed in the pairwise comparison between germplasm IR64 and Upumolagai. Whereas, the landraces are more genetically diverse than prerelease lines and cultivars. Despite diverse genotypes, rice landraces and cultivars exhibit tolerance to drought, salinity, and submergence. An earlier study of a diverse panel of 148 rice accessions, including 47 cultivars, 59 landraces from Taiwan, and 42 from other countries revealed five subpopulations. Genetic diversity ranked higher in wild rice than in landraces and cultivars. These landraces exhibited significant genetic diversification, offering a valuable reservoir for future rice breeding (Hour et al., 2020). All genotypes were grouped into two major and seven subclusters by the Jaccard cluster analysis ( Figure 9 ). Furthermore, the identification of tolerant groups was done using their respective tolerant and susceptible checks. Eight rice genotypes, such as CB22504, CB17561, CB17597, CB17502, Vadakathi samba, Varigarudan samba, Mattaikar, and ADT54, were identified to be multiple abiotic stress tolerant as they are grouped together with all the tolerant checks, viz., Anna (R) 4 and IR64Drt1 (drought), FL478 (salinity), and FR13A (submergence). A similar grouping pattern was observed in aromatic rice landraces under multiple abiotic stress conditions by Behera et al. (2023). Genotypic diversity attributed to stress tolerance QTLs varies among varieties and is highly affected by the environment (Gaballah et al., 2021). Results from this study identified that the salt-tolerant check (FL478) and submergence-tolerant check (FR13A) are genetically close. It was also reported that FR13A can be a donor for novel alleles, and FR13A can be a donor for new alleles imparting salinity and drought resistance. An earlier study showed that Porteresia coarctata, a wild relative of rice, exhibits high salinity and submergence tolerance. Through transcriptome analysis encompassing 375 million reads, 152,367 unique transcripts, including stress-responsive genes and 2,749 transcription factors, were identified. Likewise, key pathways in amino acid and hormone biosynthesis, secondary metabolite biosynthesis, carbohydrate metabolism, and cell wall structures contribute to stress tolerance (Garg et al., 2014). These findings provide insight into the genetic mechanisms of Porteresia’s tolerance, offering potential strategies for engineering salinity and submergence tolerance in rice. An earlier study reported that genetic network induced in response to submergence and drought tolerance might share some common transcriptional factors at the gene expression level (Fukao et al., 2011), and engineering common transcription factors can ultimately lead to higher multiple stress tolerance (Manna et al., 2021). The genotypes that are identified as genetically close to IR64Drt1, FL478, and FR13A can be used as potential donors for developing climate resilience cultivars (Muthu et al., 2020).

STRUCTURE analysis revealed a very broad genetic base (K = 2) while employing different SSR markers linked to multiple abiotic stress-tolerant QTLs. The higher K value obtained in this study depicts the diverse nature of the population ( Figure 8A ). Our results were in comparison with the earlier reports of Kimwemwe et al. (2023), who assessed the genetic diversity and population structure of 94 rice genotypes using DArT-based SNP markers. We observed an average PIC of 0.25, identified five subpopulations (K = 5), and found a high average Euclidean genetic distance of 0.87, indicating the existence genetic diversity. The level of genetic diversity found in our study may help to select and conserve rice landraces. Thus, the rice landraces associated with multiple abiotic stress tolerance may be used as parental material in rice breeding to manage rice production in a changing climate.

Marker-assisted breeding programs emphasize the importance of establishing strong marker-trait associations in order to effectively utilize specific markers for trait enhancement (Lakshmi et al., 2021). The genetic associations among 13 polymorphic drought-linked markers and two plant growth parameters, viz., plant biomass and relative shoot length, analyzed using a single-marker analysis revealed RM211 and RM212 are closely associated with plant biomass under water-limiting conditions whereas RM551 was closely linked to relative shoot length under water-limiting conditions. Likewise, Salunkhe et al. (2011) reported that RM212, RM302, RM8085, and RM3825 exerted a substantial influence on drought-resistant traits. Similarly, the marker-trait association employing eight salinity-linked polymorphic markers identified RM10694 to be closely linked to plant biomass and relative shoot length under saline conditions. The results are in concordance with Kumari et al. (2019) and Volkova (2017), in which they stated the markers, viz., RM302, RM8094, RM10665, RM10694, RM10748, and RM10825, can be employed in validating QTLs for salinity tolerance. The single marker analysis employing seven submergence-linked markers identified RM219 and RM21 to be significantly associated with plant biomass under submergence, whereas ART5 was found to be associated with relative shoot length under submergence. It is worth noting that similar markers (RM219, RM21, and ART5) were reported to be closely linked to submergence, as per earlier findings of Islam et al. (2008); Biswas et al. (2013), and Muthu et al. (2020). Therefore, the abovementioned marker-trait associations could be employed in the identification of tolerant lines in future breeding programs aimed at developing multiple abiotic stress-tolerant varieties.

In the face of climate change and global warming, developing and utilizing genotypes with tolerance to multiple abiotic stresses is of great significance, as it has the potential to boost food production and ensure the stability of rice cultivation. The findings of this study present an opportunity to improve rice cultivars with multiple abiotic stress tolerance, as these germplasms exhibit a wider genetic diversity related to traits enabling them to withstand challenges like drought, salinity, and submergence. Genotypic analysis involving 30 SSR markers revealed substantial genetic similarity among all the studied rice genotypes, indicating a significant level of genetic diversity within the population. STRUCTURE analysis revealed a broad genetic base (K = 2), further emphasizing the suitability of these rice genotypes for coping with environmental stresses. The marker-trait associations suggest that markers RM211, RM212, RM10694, RM219, RM21, and ART5 could be useful for evaluating trait-specific multiple abiotic stress tolerance. The genotypes APD19002, Mattaikar, Varigarudan samba, and Arupatham samba are considered important genetic resources as they exhibit multiple stress tolerance making them a potential donor to be employed in stress resilience breeding.

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

KP: Data curation, Methodology, Software, Visualization, Writing – original draft. RP: Conceptualization, Investigation, Methodology, Resources, Supervision, Writing – review & editing. SM: Investigation, Resources, Writing – review & editing. MR: Writing – review & editing. SS: Data curation, Software, Writing – review & editing. AS: Investigation, Writing – review & editing.