Climate change increases the frequency of repeated environmental stresses, such as drought and extreme temperatures, which have an impact on declining crop productivity. This study aims to analyze the effectiveness of epigenetic stress memory engineering in improving the adaptability of plants to climate disturbances that occur repeatedly. The study used an experimental approach on 120 rice plants divided into treatment and control groups. Data were collected through measurements of growth, chlorophyll content, water use efficiency, and expression of epigenetic markers, then analyzed using variance analysis (ANOVA). The results showed that plants that received epigenetic stress memory treatment had higher stress tolerance, more stable growth, and better water use efficiency than the control group. These findings indicate that epigenetic stress memory engineering has the potential to be an innovative strategy to improve plant resilience in the face of increasingly intense climate change.
Climate change is one of the biggest challenges in the global agricultural sector as it causes an increase in the frequency of environmental disturbances such as drought, extreme temperatures, salinity, and rainfall instability that have a direct impact on crop productivity. The World Food Organization points out that climate change patterns have affected food production systems in various countries and increased the risk of long-term food security. In Indonesia, the agricultural sector is among the most vulnerable to climate change because most food production still depends on the conditions of agroecosystems that are sensitive to weather variability (Sekaranom et al., 2021). This impact can be seen through a decrease in the productivity of food crops, changes in the planting season, an increase in attacks by plant pest organisms, and an increased risk of crop failure in various areas of agricultural centers (Amalia & Sitompul, 2024).
The increasingly intensive phenomenon of climate change demands the development of agricultural technologies that not only focus on increasing production yields, but also on the ability of plants to maintain adaptation to repeated environmental stresses. Various studies show that plants have biological mechanisms that allow adaptive responses to environmental stress to occur through physiological, molecular, and genetic changes. In this context, the concept of epigenetic stress memory is beginning to gain attention because it plays a role in storing biological information from previous stress exposure so that plants are able to respond more quickly and effectively when facing similar stress in the next period (Li et al., 2025).
Studies on agricultural adaptation to climate change in Indonesia generally still focus on conventional agronomic strategies such as modification of planting patterns, the use of tolerant varieties, land conservation, and water resource management. Research conducted by Nafi'Azizi et al. (2025) shows that rice farmers in Bojonegoro Regency carry out various adaptation strategies through changes in planting schedules and the selection of varieties that are more resistant to uncertain climatic conditions. Similar results were also found by Atasa et al. (2024) who explained that horticultural farmers are making adjustments to cultivation patterns in response to climate change. However, the approach still focuses on the cultivation management level and has not explored much of the plant's internal biological mechanisms that have the potential to increase stress resilience in a sustainable manner.
At the molecular level, developments in plant epigenetics suggest that environmental stress can trigger changes in gene expression through DNA methylation mechanisms, histone modification, and non-coding RNA regulation without altering the main DNA makeup of plants. This mechanism allows the formation of stress memory that can be inherited temporarily or across generations, thereby increasing the plant's adaptation capacity to the next stress. Li et al. (2025) explain that optimizing plant stress responses through the regulation of physiological and molecular mechanisms has the potential to be an important strategy in dealing with the challenges of global climate change. Thus, the epigenetic approach opens up new opportunities in the development of sustainable agrotechnology that is more adaptive to recurrent climate disruptions.
Although research on climate change and agricultural adaptation has progressed quite rapidly, there is still a significant research gap. Most of the research in Indonesia focuses on social, economic, and aquaculture management aspects in dealing with climate change (Harahap, 2025; Nafi'Azizi et al., 2025), while studies that specifically integrate the concept of epigenetic stress memory with plant resilience enhancement strategies are still very limited. Previous research has discussed the impact of climate change on crop productivity (Prasetyo, 2023; Ramadhan et al., 2024) without examining how epigenetic mechanisms can be used as an adaptive technology that is applicable in modern agricultural systems.
Another research gap lies in the lack of studies linking epigenetic stress memory engineering with the development of adaptive agricultural technologies in conditions of recurrent climate disturbances. Some international research has shown that plants are able to retain molecular traces of previous stressful experiences thereby increasing tolerance to subsequent stressors (Li et al., 2025). However, the implementation of this concept in the context of tropical agrotechnology, especially in strategic commodities in Indonesia, has not been widely explored. This condition shows the need for research that integrates the perspective of plant epigenetics with the need for agricultural adaptation to climate change.
Based on these problems, this study aims to analyze the potential of epigenetic stress memory engineering in improving the adaptability of plants to recurrent climate disturbances. This study is focused on identifying the physiological and molecular responses of plants after experiencing repeated stress treatment and evaluating the effectiveness of epigenetic stress memory mechanisms in improving plant tolerance to extreme environmental conditions. Through this approach, it is hoped that a more comprehensive understanding of the relationship between epigenetic engineering and plant resilience to climate change will be obtained.
This research is expected to make a theoretical contribution in the form of strengthening the concept of plant adaptation based on epigenetics in the study of modern agrotechnology and expanding the development of plant physiology and biotechnology. Practically, the results of the research can be the basis for the development of cultivation and plant breeding technologies that are more adaptive to climate change, thereby supporting increased agricultural productivity and sustainable food security. In addition, this research can be a reference for policymakers in formulating agricultural adaptation strategies based on scientific innovation to deal with increasingly complex climate risks.
Climate change has become a major factor affecting the stability of global agricultural systems through increased frequency of droughts, floods, extreme temperatures, and crop season uncertainty. These conditions cause a decrease in crop productivity, physiological disorders, and an increased risk of crop failure in various strategic food commodities. In Indonesia, the impact of climate change is increasingly felt in the agricultural sector because most food crop production is still highly dependent on natural environmental conditions that are vulnerable to weather changes (Sekaranom et al., 2021). Research by Ramadhan et al. (2024) shows that climate change contributes to a decrease in rice productivity through increased environmental stress that affects vegetative and generative growth of plants. This condition shows that the development of plant adaptation strategies is an urgent need to support sustainable food security.
In addition to affecting productivity, climate change also increases the intensity of environmental disturbances that occur repeatedly. According to Amalia and Sitompul (2024), repeated stresses such as seasonal drought and extreme temperature fluctuations cause plants to experience more complex physiological stress than a single stress. Therefore, the approach to agricultural adaptation is no longer enough to rely only on conventional cultivation techniques, but requires a deeper understanding of the biological mechanisms of plants in maintaining resistance to environmental stress.
In modern plant physiology, the concept of stress memory describes the ability of plants to retain biological information from previous stressful experiences so that they are able to respond more effectively when facing the same stress in the future. This mechanism allows plants to make physiological, biochemical, and molecular adjustments that increase their chances of survival under unstable environmental conditions (Li et al., 2025).
International research shows that plants that have experienced drought stress have a faster response to subsequent stresses through increased water use efficiency, activation of defense genes, and stabilization of cellular metabolism (Li et al., 2025). The mechanism shows that plants not only react passively to the environment, but also have adaptive abilities that are dynamic. In the context of climate change, stress memory is one of the biological approaches that has the potential to support the development of plants that are more resistant to repeated environmental disturbances.
The development of epigenetics provides a new understanding of how plants regulate responses to environmental stressors without altering the main DNA sequence. Epigenetics refers to changes in gene expression that are affected by mechanisms such as DNA methylation, histone modification, and non-coding RNA regulation. The mechanism allows plants to adjust the activity of certain genes in response to environmental changes (Li et al., 2025).
In modern agricultural research, epigenetics is seen as one of the important factors that support the formation of stress memory in plants. When plants experience recurrent stress, the epigenetic changes that occur can maintain certain gene expression patterns so that the response to subsequent stress becomes faster and more efficient. Thus, epigenetics not only plays a role in the process of momentary adaptation, but also contributes to increasing plant resilience in the long term.
Epigenetic stress memory engineering is an approach that utilizes epigenetic mechanisms to increase the adaptive capacity of plants to extreme environmental conditions. This concept is growing as the need for agricultural technology that is able to deal with climate change in a sustainable manner increases. Through manipulation or stimulation of certain stress responses, plants can build biological memories that strengthen tolerance to repetitive stress (Li et al., 2025).
In the field of agrotechnology, epigenetic stress memory engineering has the potential to be an alternative to conventional crop breeding. This approach allows for increased stress tolerance without having to make permanent genetic changes to the plant. Therefore, this strategy is considered more flexible and has a great opportunity to be applied to various agricultural commodities that face environmental pressures due to climate change.
Studies on agricultural adaptation in Indonesia still mostly focus on agronomic and socio-economic aspects. Nafi'Azizi et al. (2025) explained that farmers carry out various forms of adaptation through changes in planting patterns, the use of more tolerant varieties, and more efficient irrigation management. Similar findings are also described by Atasa et al. (2024) who show that horticultural farmers are making adjustments to cultivation techniques in response to climate uncertainty.
Although such strategies have been shown to help reduce production risks, most studies still place plants as passive objects that depend on cultivation interventions. Studies that explore the intrinsic capabilities of plants through epigenetic mechanisms are still relatively limited. In fact, understanding the biological adaptation capacity of plants can open up opportunities for the development of more sustainable and efficient agricultural technology.
Based on various previous studies, there is a fairly clear research gap. Research related to climate change in Indonesia mostly discusses adaptation strategies based on agricultural management, while studies on epigenetic stress memory engineering are still very limited. In addition, research linking epigenetic stress memory to increased plant adaptations to recurrent climate disturbances in tropical agricultural systems has not been widely found.
This research seeks to fill this gap by integrating the perspective of plant epigenetics into the development of adaptive agrotechnology. The main focus of the research is directed at the analysis of the relationship between epigenetic stress memory engineering and improved plant adaptability to recurrent climate disturbances. Thus, this research not only expands the study of plant physiology, but also provides a scientific basis for the development of agricultural technology based on stress resistance.
This study uses an experimental quantitative approach with a Completely Randomized Design (CRD) design to analyze the effect of epigenetic stress memory engineering on the adaptation of rice plants to recurrent climatic disturbance conditions. The experimental approach was chosen because it allows testing of the cause-and-effect relationship between the treatment given and the plant's response in a controlled manner (Li et al., 2025).
The study population is rice plants (Oryza sativa L.) that are cultivated under controlled environmental conditions. The sample consisted of 120 rice plants selected using simple random sampling and divided into two groups, namely the treatment group (60 plants) and the control group (60 plants). The number of samples is considered adequate to obtain reliable and representative experimental results (Wahyuni et al., 2024).
Data were collected using plant physiological and molecular measurement instruments. The observed parameters included plant height, biomass, chlorophyll content, water use efficiency, and expression of epigenetic markers using the quantitative Polymerase Chain Reaction (qPCR) method. The validity of the instrument is guaranteed through the calibration of the tool, while reliability is obtained through repeated measurements on each parameter (Li et al., 2025). The observed molecular parameters included the relative expression of the OsDREB2A gene as a marker of drought response, the OsHSP70 gene as a marker of high temperature tolerance, as well as the relative level of DNA methylation as an early indicator of the involvement of epigenetic mechanisms in the formation of stress memory. Gene expression analysis was carried out using the quantitative Polymerase Chain Reaction (qPCR) method. DNA methylation measurements are used as an initial approach to identify the likelihood of epigenetic regulatory changes due to repeated stress exposure.
The research began with the preparation of seeds and planting media, followed by the provision of epigenetic stress memory engineering treatment through the induction of drought stress and high temperature in a controlled manner. After the recovery period, the plant is given a re-grip to form a stress memory. Next, physiological and molecular parameters were measured, then all data were tabulated for analysis. Treatment was carried out through three cycles of drought and high temperature stress interspersed with recovery periods. This approach is used to induce the formation of physiological and molecular stress memories in plants. After the last cycle is completed, measurements of physiological and molecular parameters are carried out to evaluate the plant's adaptive response to recurrent stress.
Data were analyzed using IBM SPSS Statistics 27 and R Studio. The analysis began with a normality and homogeneity test, then continued with an Analysis of Variance (ANOVA) to test the differences between the treatment and control groups. If significant differences are found, a follow-up test of Tukey HSD is carried out at a significance level of 5% (Ghozali, 2023).
The study involved 120 rice plants consisting of 60 plants in the epigenetic stress memory engineering treatment group and 60 plants in the control group. After experiencing three cycles of repeated environmental stress in the form of drought and high temperatures, the treatment group showed a higher survival rate than the control group. A total of 55 plants (91.7%) in the treatment group were able to survive until the end of the observation period, while in the control group only 47 plants (78.3%) survived.
Analysis of physiological parameters showed significant differences between the treatment group and the control group. Plants in the treatment group had higher plant height, chlorophyll content, and biomass than the control group after repeated stress periods. The results of ANOVA showed that all physiological parameters had a significance value of less than 0.05 which indicated a significant difference between the two groups.
Water use efficiency is one of the main indicators in evaluating the adaptability of plants to climate change. The results showed that the treatment group had a higher water use efficiency than the control group. The difference was statistically significant (p=0.001), suggesting that the treated plants were able to maintain growth with more efficient use of water during periods of stress.
Testing of the expression of epigenetic markers using qPCR analysis showed increased stress response gene activity in the treatment group. Some genes related to drought tolerance and high temperatures showed higher levels of expression than the control group. The results of qPCR analysis showed that the expression of the OsDREB2A and OsHSP70 genes in the treatment group was significantly increased compared to the control group. In addition, the increase in DNA methylation levels relatively indicates the involvement of epigenetic regulatory mechanisms in the plant's response to recurrent stress.
Hypothesis testing was carried out using a one-way ANOVA with a significance level of 5%. The test results showed that epigenetic stress memory engineering had a positive effect on increasing plant adaptation to recurrent climate disturbances. Treatments also improve plant tolerance through changes in physiological and molecular responses, as well as contribute to growth stability and resource use efficiency.
| Groups | Number of Plants | Survival | Percentage (%) |
|---|---|---|---|
| Treatment | 60 | 55 | 91.7 |
| Controls | 60 | 47 | 78.3 |
| Parameter | Treatment (Mean ± SD) | Control (Mean ± SD) | p-value |
|---|---|---|---|
| Plant height (cm) | 86.4 ± 5.7 | 78.2 ± 6.4 | 0.001 |
| Dry biomass (g) | 31.8 ± 3.2 | 26.1 ± 3.8 | 0.000 |
| Chlorophyll content (SPAD) | 42.7 ± 3.6 | 36.9 ± 4.1 | 0.002 |
| Groups | Water Use Efficiency (g/L) |
|---|---|
| Treatment | 4.85 ± 0.41 |
| Control | 3.71 ± 0.38 |
| Molecular Markers | Treatment | Control | p-value |
|---|---|---|---|
| OsDREB2A (drought response) | 2.84 | 1.00 | 0.000 |
| OsHSP70 (high temperature tolerance) | 2.37 | 1.00 | 0.001 |
| Relative DNA methylation | 1.92 | 1.00 | 0.003 |
| Hypothesis | Results | Verdict |
|---|---|---|
| H1 | p = 0.001 | Accepted |
| H2 | p = 0.000 | Accepted |
| H3 | p = 0.002 | Accepted |
The results of the study show that the induction of stress memory through repeated drought and high temperature stress has a positive influence on the adaptability of rice plants in dealing with environmental disturbances that occur repeatedly. These findings can be seen from the increased survival rate of plants, improved physiological parameters, increased water use efficiency, and increased molecular responses related to stress tolerance. In general, the treatment group performed better than the control group on almost all of the observed indicators. These results indicate that previous stress experiences are able to form adaptive responses that increase plant readiness to face the next environmental stress.
The survival rate of the plants in the treatment group reached 91.7%, higher than the control group which only reached 78.3%. These findings suggest that the induction of stress memory contributes to increased plant tolerance to unfavorable environmental conditions. According to Chakim et al. (2023), rice genotypes that have tolerance to drought are generally able to maintain physiological activity better than susceptible genotypes when facing recurrent stress. This ability allows plants to maintain metabolic balance and maintain growth despite being in less favorable environmental conditions.
The increase in plant height, dry biomass, and chlorophyll content in the treatment group showed that the induction of stress memory not only affected the ability to survive, but was also able to maintain the vegetative growth of the plant. The better height of the plant indicates that cell division and elongation activities are still going on optimally despite the stress. Higher dry biomass indicated that the plants were able to maintain the accumulation of photosynthesis results and assimilate distribution more effectively than the control group. The higher chlorophyll content in the treatment group is one of the important indicators in this study. According to Putri et al. (2022), chlorophyll content can be used as an indicator of plant tolerance to drought because it is directly related to photosynthesis ability. Plants that experience drought stress generally show a decrease in chlorophyll content due to disruption of chloroplast structure and increased oxidative stress.
The higher water use efficiency in the treatment group showed that the plants were able to produce better growth with more economical water use. According to Sujinah and Ali (2021), one of the main mechanisms of drought tolerance in rice plants is the ability to optimize water use through stomata regulation, reduced transpiration rate, and increased metabolic efficiency. Thus, the high value of water use efficiency in the treatment group indicates that the plants are able to utilize water resources more effectively during the stress period.
At the molecular level, increased expression of the OsDREB2A gene as a marker of drought response, the OsHSP70 gene as a marker of high temperature tolerance, as well as an increase in DNA methylation markers suggest that the induction of stress memory affects the plant's internal regulatory system. The increased expression of both genes indicated that the treated plants had a better response capacity in the face of drought stress and high temperatures than the control group. These findings suggest that the adaptation of plants to repetitive stress does not only occur at the physiological level, but also involves changes in molecular regulation that support increased stress tolerance.
In addition, an increase in DNA methylation markers suggests the possible involvement of epigenetic mechanisms in the formation of plant adaptive responses. Epigenetic changes allow plants to regulate the expression of certain genes more quickly when facing the same stress in the following period. Thus, the results of this study show that the induction of stress memory not only results in physiological changes, but also has the potential to influence molecular regulatory systems that support increased plant tolerance to environmental changes.
Overall, the results of this study reinforce the findings of Widiantari (2024) who stated that the success of plant adaptation to drought stress is greatly influenced by the plant's ability to maintain growth, photosynthetic activity, and water use efficiency. Therefore, stress memory induction has the potential to be an innovative approach to increase the resilience of rice crops to increasingly uncertain climate change.
Although all research hypotheses are supported by empirical data, there are several factors that have the potential to influence the results of the study. Plant genetic factors, stress intensity, duration of stress exposure, and microenvironmental conditions during the study can affect the magnitude of the physiological and molecular responses that arise. In addition, this research was conducted on controlled environmental conditions so that it does not fully represent the complexity of the actual field conditions.
The study also has limitations in the molecular aspect because the analysis is still limited to some gene markers and DNA methylation. As a result, the epigenetic mechanisms underlying the formation of stress memories have not been comprehensively explained. Therefore, further research needs to use more comprehensive molecular approaches, such as extensive genome methylation analysis, transcriptome expression, and cross-generational observations to evaluate the sustainability of adaptive responses formed due to stress memory induction.
Based on the results of the study, it can be concluded that the induction of stress memory through repeated drought and high temperature stress has a positive effect on the adaptability of rice plants. The treatments given have been shown to improve plant survival rates, maintain vegetative growth, improve chlorophyll content and water use efficiency, and strengthen molecular responses demonstrated by increased expression of genes related to stress tolerance and DNA methylation markers. These findings suggest that previous stress experiences can form adaptive responses that help plants cope with environmental pressures more effectively.
As a practical implication, stress memory induction has the potential to be one of the innovative approaches in the development of adaptive agriculture technologies to support plant resilience to the impacts of climate change. However, the involvement of epigenetic mechanisms demonstrated through increased DNA methylation markers in this study still requires further verification using a more comprehensive molecular approach. Therefore, further research is recommended to test the effectiveness of this approach on different rice varieties and different field conditions, as well as to conduct cross-generational observations to evaluate the stability and possible inheritance of adaptive responses formed due to stress memory induction.
Future studies should investigate the transgenerational inheritance of stress memory and employ advanced multi-omics approaches to identify key molecular mechanisms regulating stress adaptation in rice under diverse environmental conditions.