Article Citation:

Kores J J . Molecular Mechanisms of Plant Adaptation to Abiotic Stress Under

Changing Climates. Journal of Research in Biology (2025) 15(2): 1-24

Journal of Research in Biology

Molecular Mechanisms of Plant Adaptation to Abiotic Stress

Under Changing Climates

Keywords:

Abiotic stress, Climate change, Signal transduction, Transcription factors,

Epigenetics, ABA signaling, Stress tolerance, Crop improvement

ABSTRACT:

Abiotic stresses, including drought, salinity, extreme temperatures,

ﬂooding, and nutrient deﬁciency, represent the most formidable constraints to

global agricultural productivity, collectively accounting for more than 50% of

yield losses in major crop species worldwide. The accelerating pace of climate

change is predicted to intensify the frequency, severity, and co-occurrence of

these stressors, posing unprecedented challenges to food security for a rapidly

growing global population. Plants, as sessile organisms, have evolved an

extraordinarily sophisticated and multilayered repertoire of molecular

mechanisms to perceive, transduce, and respond to adverse environmental

signals. These mechanisms span the entire spectrum of biological organization,

from membrane-localized receptor kinases and second messenger cascades,

through transcriptional reprogramming orchestrated by diverse families of

transcription factors, to post-translational modiﬁcations, epigenetic

remodeling, and non-coding RNA-mediated regulation. This review provides a

comprehensive and integrative synthesis of the current understanding of the

molecular mechanisms underpinning plant adaptation to abiotic stress in the

context of changing climates. This review systematically examine stress

perception and signal transduction, the roles of phytohormones particularly

abscisic acid (ABA), jasmonic acid (JA), ethylene, and melatonin the functions of

major transcription factor families including NAC, WRKY, AP2/ERF, bHLH,

MYB, and HSF, the signiﬁcance of post-translational modiﬁcations such as

ubiquitination and SUMOylation, the emerging roles of epigenetic memory and

stress priming, and the contributions of omics technologies and genome editing

to crop improvement. Special attention is given to quantitative and statistical

dimensions of these processes, as well as to the mathematical frameworks that

describe stress response dynamics. The review concludes by identifying key

knowledge gaps and future research priorities for engineering climate-resilient

crops.

1-24| JRB | 2025 | Vol 15 | No 2

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www.jresearchbiology.com

Journal of Research in Biology

An International

Scientiﬁc Research Journal

Author:

J. Jebasingh Kores

Institution:

Department of Physics,

Pope's College

(Autonomous),

Sawyerpuram 628 251,

Tamil Nadu, India

Corresponding author:

Kores J J

Web Address:

http://jresearchbiology.com/

documents/RA0875.pdf

Dates:

Received: 18 Jan. 2025 Accepted: 19 March 2025 Published: 15 April 2025

Journal of Research in Biology

An International Scientiﬁc Research Journal

ISSN No: Print: 2231 –6280; Online: 2231- 6299

Comprehensive Review

Kores et al., 2025

2 Journal of Research in Biology (2025) 15(2): 1-24

1. Introduction

1.1 The Global Challenge of Abiotic Stress Under

Climate Change

The intersection of rapid climate change and the

imperative to sustain global food security represents one

of the defining scientific and societal challenges of the

twenty-first century. Abiotic stresses encompassing

drought, high salinity, extreme heat, freezing

temperatures, flooding, heavy metal toxicity, and nutrient

deficiency are estimated to affect more than 90% of rural

farmland at some point during the growing season (Atak

et al., 2023), and collectively reduce the average yield of

major crops by more than 50% (Gandhi & Oelmüller,

2023; Sasi et al., 2018). These losses are not uniformly

distributed; they disproportionately affect smallholder

farmers in tropical and subtropical regions, where the

impacts of climate change are most acute (Antoniou et

al., 2017).

Global warming and associated climatic perturbations are

predicted to exacerbate the frequency and severity of

abiotic stress events (Lagiotis et al., 2023). Extreme

weather episodes, including intense rainfall, prolonged

drought, and more frequent heat and cold waves, are

becoming increasingly common (Primo-Capella et al.,

2022). In the current state of global warming, the impact

of abiotic stressors on crops has increased significantly

and will only continue to rise (Patel et al., 2023). Some

estimates suggest that ongoing global warming and

climate change will further aggravate the effects of abiotic

stressors on plants (Atak et al., 2023). The consequences

for agricultural systems are profound: abiotic stresses lead

to more than 50% of yield losses in most plant species

(Gandhi & Oelmüller, 2023), and the genetic basis of

plant adaptation to abiotic stress remains poorly

understood even in genomic model species such as rice

(Vigueira et al., 2016).

Plants, by virtue of their sessile nature, cannot escape

adverse environmental conditions and have therefore

evolved a broad range of molecular mechanisms to

respond to complex networks of environmental signals.

These mechanisms activate multiple pathways, modulated

by different responsive genes, which in some cases confer

tolerance to the pressure exerted by stressor factors

(Ambrosino et al., 2020). Understanding these

mechanisms at the molecular level is not merely an

academic exercise; it is a prerequisite for the rational

engineering of stress-tolerant crops capable of sustaining

productivity under the climatic conditions projected for

the coming decades (Moshelion & Altman, 2015).

1.2 Scope and Organization of This Review

This review systematically examines the molecular

mechanisms of plant adaptation to abiotic stress, with

particular emphasis on developments reported through

2025. We begin with an overview of stress perception and

early signal transduction, proceed through the major

signaling cascades and transcriptional regulatory

networks, address post-translational and epigenetic

mechanisms, and conclude with a discussion of omics-

enabled discoveries and biotechnological strategies for

crop improvement. Throughout, we integrate quantitative

and statistical data where available and highlight areas of

nuance or disagreement in the literature. A summary of

major abiotic stresses and their associated molecular

responses is provided in Table 1.

Kores et al., 2025

3 Journal of Research in Biology (2025) 15(2): 1-24

Table 1. Major Abiotic Stress Types and Corresponding Molecular Responses

Abiotic

Stress

Key Molecular

Signals

Major Pathways Representative

Genes/Proteins

References

Drought ABA

accumulation, Ca²⁺

spikes

ABA signaling,

stomatal regulation

PYR/PYL/RCAR,

SnRK2, ABF

(Luo et al., 2018; Fidler et

al., 2022)

Salinity Ionic imbalance

(Na⁺/K⁺), ROS

Ion transport,

antioxidant defense

KUP transporters,

SOD, APX

(Chakraborty et al., 2023;

Hernández-Bueno et al.,

2021)

Heat Protein

denaturation, ROS

Heat shock response HSFs, HSPs (Jin et al., 2020; Singh et

al., 2019)

Cold Membrane rigidity,

Ca²⁺ influx

MAPK cascade,

CBF pathway

CRLK1, CBF/DREB (Li et al., 2017)

Flooding Hypoxia, ethylene

signaling

ERF-mediated

transcription

ERFs, ACS genes (Huang et al., 2025; Islam

et al., 2020)

Nutrient

deficiency

Metabolic

imbalance

Hormonal +

transcriptional

regulation

PSTOL1, COR

proteins

(Vigueira et al., 2016;

Govta et al., 2024)

2. Stress Perception and Early Signal Transduction

2.1 Receptor-Like Kinases (RLKs) as Primary Stress

Sensors

The perception of abiotic stress signals at the cell surface

is a critical first step in the plant stress response. Receptor-

like kinases (RLKs) constitute one of the largest gene

families in plant genomes and serve as primary sensors of

diverse environmental cues, hormonal signals, and stress

stimuli (Li et al., 2017). RLKs are characterized by an

extracellular domain for ligand perception, a

transmembrane domain, and an intracellular kinase

domain for signal transduction (Gandhi & Oelmüller,

2023). The RLK superfamily includes members such as

leucine-rich repeat RLKs (LRR-RLKs), mannose-binding

lectin RLKs (MRLKs), and lectin RLKs (LecRLKs), all

of which have been shown to mediate cellular responses

to various environmental cues (Li et al., 2017).

Despite the enormous size of the RLK family, only a

handful of studies have shed light on the role of RLKs in

abiotic stress responses and the potential mechanisms

underlying RLK-mediated abiotic stress tolerance. A

deeper understanding of kinase signaling cascades in

responses to fluctuating environmental conditions such as

drought, heat, cold, or salt is paramount to engineer stress-

tolerant crops (Gandhi & Oelmüller, 2023). In rice, the

LRR-RLK gene FON1 increased drought tolerance of

transgenic rice plants through phosphorylating key

components of the ABA signaling pathway and activating

the ABA signal. Another well-studied example is CRLK1,

a calcium-regulated RLK, which modulated cold

tolerance through phosphorylating MAP kinases in plants,

promoted expression of cold stress response genes, and

ultimately regulated plant adaptation to cold stress (Li et

al., 2017).

Kores et al., 2025

4 Journal of Research in Biology (2025) 15(2): 1-24

The energy-dependent transmembrane receptor-like

kinases (RLKs) also recognize priming elicitors and,

when activated, regulate the transcription of abiotic stress

defense genes (Lagiotis et al., 2023). This dual role in

primary stress perception and stress memory underscores

the centrality of RLKs in plant stress adaptation.

2.2 Calcium Signaling and Calcium-Dependent

Protein Kinases (CPKs)

Calcium ions (Ca²⁺) serve as universal second messengers

in plant stress signaling, with transient increases in

cytosolic Ca²⁺ concentration representing one of the

earliest cellular responses to virtually all abiotic stresses.

Calcium-dependent protein kinases (CPKs, also known as

CDPKs) are a plant-specific family of serine/threonine

kinases that directly sense Ca²⁺ signals through their

calmodulin-like domain and transduce them into

downstream phosphorylation events (Atif et al., 2019).

CPKs show their role against biotic and abiotic stress

tolerance upon interaction with specific calcium signals.

With respect to abiotic stresses, CPKs are involved in

drought, salinity, heat, and cold stress response signaling

by regulating ABA-responsive transcriptional factors and

ion channel regulation. Some Arabidopsis CPKs (e.g.,

CPK13) is also involved in potassium ion (K⁺) channel

regulation and other ion transportation in guard cells.

CPK11, induced by hydrogen peroxide (H₂O₂), regulates

and controls the activity of superoxide dismutase (SOD)

and ascorbate peroxidase (APX) production induced by

the ABA signaling pathway. CPK activity confirmed by

global expression analyses shows that several CPK

members are expressed differentially under varying ABA,

salinity, drought, and heat and cold levels. The change in

the expression of CPK genes indicates the role of CPKs in

plant adaptation against abiotic stress environments (Atif

et al., 2019).

2.3 G-Protein Signaling

Heterotrimeric G-proteins, comprising Gα, Gβ, and Gγ

subunits, are important components of plant stress

signaling networks. The signaling mechanisms in plants

during low and high temperature, drought, and salinity are

different and yet related to each other, with G-proteins

playing a role in integrating these diverse signals. In

Arabidopsis, the G-protein coupled receptor GCR1 and

the Gα subunit GPA1 mediate responses to multiple

abiotic stresses. GCR1 acts as a negative regulator of

GPA1-mediated ABA responses in Arabidopsis guard

cells. In tobacco, transgenic lines overexpressing Gα and

Gβ from pea revealed the role of Gα in salinity and high

temperature stress response, while Gβ was linked to heat

tolerance. Recent studies in Arabidopsis revealed that G-

proteins are also involved in growth under salt stress, as

well as cellular senescence and cell division in rice and

maize (Chakraborty et al., 2015).

2.4 MAP Kinase Cascades

Mitogen-activated protein kinase (MAPK) cascades are

evolutionarily conserved signal transduction modules that

relay stress signals from the cell surface to the nucleus.

The canonical MAPK cascade consists of a MAP kinase

kinase kinase (MAPKKK), a MAP kinase kinase

(MAPKK), and a MAP kinase (MAPK), operating in a

sequential phosphorylation relay. The calcium-regulated

RLK CRLK1 modulates cold tolerance through

phosphorylating MAP kinases in plants (Li et al., 2017),

illustrating the integration of Ca²⁺ and MAPK signaling in

stress responses. MAPK cascades are also activated by

drought, salinity, and oxidative stress, and their outputs

include the phosphorylation and activation of

transcription factors that drive stress-responsive gene

expression (Gandhi & Oelmüller, 2023).

2.5 Mathematical Framework for Signal Transduction

Dynamics

The dynamics of stress signal transduction can be

modeled mathematically using systems of ordinary

Kores et al., 2025

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differential equations (ODEs). In the case of a simplified

two-component signaling system involving a receptor (R)

and a response regulator (RR), the activation kinetics can

be described as follows:

𝑑𝑅

∗

𝑑𝑡

=𝑘

on

𝑆𝑅− 𝑘

off

𝑅

∗

𝑑𝑅𝑅

∗

𝑑𝑡

=𝑘

cat

𝑅

∗

𝑅𝑅− 𝑘

phos

𝑅𝑅

∗

Here, 𝑆represents the concentration of the stress signal,

𝑅and 𝑅

∗

denote the inactive and active receptor

concentrations, while 𝑅𝑅and 𝑅𝑅

∗

represent the inactive

and active response regulator concentrations. The

parameters 𝑘

on

and 𝑘

off

are the activation and deactivation

rate constants, respectively, 𝑘

cat

is the catalytic rate

constant for response regulator phosphorylation, and

𝑘

phos

is the dephosphorylation rate constant.

At steady state, the concentration of the active receptor is

given by:

𝑅

ss

∗

=

𝑘

on

𝑆𝑅

total

𝑘

on

𝑆 +𝑘

off

This mathematical framework demonstrates how the

amplitude and duration of the stress signal (𝑆) influence

the magnitude of the downstream response. Additionally,

feedback mechanisms, represented by 𝑘

phos

, modulate the

attenuation of the signal. This principle is particularly

relevant to understanding the dose-dependent and time-

dependent nature of plant stress responses, as observed in

studies by Atif et al. (2019) and Gandhi & Oelmüller

(2023). An integrated overview of stress perception and

signal transduction pathways is illustrated in Figure 1.

Figure 1. Integrated Model of Abiotic Stress Signal Transduction

3. Phytohormone Signaling in Abiotic Stress

Responses

3.1 Abscisic Acid (ABA): The Master Stress Hormone

Abscisic acid (ABA) is the central phytohormone

mediating plant responses to abiotic stress, particularly

drought, salinity, and cold (Luo et al., 2018; Fidler et al.,

2022). ABA biosynthesis is rapidly induced by water

deficit and other osmotic stresses, and the resulting

increase in ABA concentration triggers a cascade of

molecular events that collectively promote stress

tolerance. Abiotic stress (such as cold, drought, salinity,

and heat) results in strong increases in ABA level, and this

accumulation promotes stress tolerance in various plant

species. Exogenous ABA application has been shown to

enhance plant abiotic stress tolerance through a series of

physiological and biochemical changes (Luo et al., 2018).

3.1.1 The PYR/PYL/RCAR Receptor System

The molecular basis of ABA perception was elucidated

with the discovery of the PYR/PYL/RCAR family of

soluble ABA receptors. In many abiotic stresses, such as

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drought, salinity, or cold, the activation of many

molecular mechanisms depends on the ABA content in the

tissues. Endogenous changes in ABA concentration

enable the initiation of a signaling cascade, the activation

of which depends on the binding of ABA by appropriate

receptor proteins (Fidler et al., 2022). Upon ABA

binding, PYR/PYL/RCAR receptors inhibit type 2C

protein phosphatases (PP2Cs), which in turn releases and

activates SNF1-related protein kinase 2s (SnRK2s).

Activated SnRK2s phosphorylate downstream targets

including ABA-responsive element binding factors

(ABFs/AREBs), which drive the expression of ABA-

responsive genes.

The ABF/AREB/ABI5 family members are widely

implicated in plant responses to abiotic stresses (e.g.,

drought, salinity, cold) and developmental regulations.

Arabidopsis ABF/AREB/ABI5 gene expression is

coordinately induced by light signals, ABA, and multiple

abiotic stresses (drought, high salinity, and cold), forming

a multi-layered stress response network. Beyond these

signals, PmABFs in Prunus mume can also be activated

by exogenous hormones (e.g., gibberellins, ethylene) and

hypoxia stress, implying roles in broader physiological

adaptation (Zhang et al., 2025).

3.1.2 ABA-Mediated Stomatal Regulation

One of the most critical responses to drought mediated by

abscisic acid (ABA) is the regulation of stomatal aperture.

When plants experience water deficit, ABA is perceived

by guard cells, initiating a signaling cascade that leads to

the activation of anion channels (such as SLAC1) and

outward-rectifying K⁺ channels (such as GORK). This

results in the efflux of anions and K⁺ from guard cells,

causing water to exit the cells, reducing guard cell turgor,

and ultimately leading to stomatal closure. This process

minimizes water loss through transpiration and helps the

plant conserve water during stress.

In Arabidopsis, the calcium-dependent protein kinase

CPK13 plays a pivotal role in this regulatory network by

inhibiting inward-rectifying K⁺ channels (KAT1 and

KAT2) in guard cells. By suppressing K⁺ influx, CPK13

further promotes stomatal closure and exemplifies the

integration of Ca²⁺ and ABA signaling pathways in guard

cell function (Atif et al., 2019).

The quantitative relationship between stomatal

conductance (𝑔



) and ABA concentration can be

described by a Hill function:𝑔



=𝑔

,max

⋅













ABA



where:

 𝑔

,max

is the maximum stomatal conductance in

the absence of ABA,

 𝐾



is the ABA concentration at which

conductance is reduced to half its maximum

(reflecting sensitivity),

 𝑛 is the Hill coefficient, indicating the steepness

and cooperativity of the response.

This sigmoidal dose-response model accurately captures

how stomatal conductance decreases as ABA

concentration increases and has been empirically

validated across multiple plant species (Fidler et al.,

2022).

3.1.3 ABA-Independent Stress Signaling

While ABA-dependent pathways are central to drought

and osmotic stress responses, ABA-independent

pathways also contribute significantly to stress tolerance.

For example, SNAC3, a NAC transcription factor,

functions as a positive regulator of drought, heat, and

oxidative stress response through an ABA-independent

pathway (Yuan et al., 2019). This highlights the

complexity and redundancy of plant stress signaling

networks.

3.2 Jasmonic Acid (JA) in Abiotic Stress Tolerance

Jasmonic acid (JA) and its bioactive conjugate jasmonoyl-

isoleucine (JA-Ile) are lipid-derived phytohormones with

well-established roles in biotic stress responses that have

more recently been recognized as important regulators of

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abiotic stress tolerance (Li et al., 2017). JA regulates

freezing tolerance controlled by the CBF pathway, where

JAZ proteins physically interact with and inhibit ICE1 and

ICE2 transcription factors to reduce expression of the cold

regulon. Genetic analysis with various JA biosynthesis

and response mutants has shown that JA is required for

basal thermotolerance. JA also enhances salt stress

tolerance in wheat by increasing antioxidant levels in

order to reduce the effects of ROS stimulated by high

salinity conditions (Gonzalez et al., 2017).

Recent studies have highlighted that JA plays an

important role in the regulation of abiotic stress tolerance

under osmotic stress conditions. JAs regulate gene

expression involved in stress responses through up-

regulating expression of antioxidant enzymes and

eliciting plant secondary metabolism. In a global gene

expression analysis of cassava seedlings, 50 differentially

expressed genes (DEGs) associated with "response to JA

stimulus" signaling pathways were significantly enriched

under both cold and drought stress (Li et al., 2017),

underscoring the broad relevance of JA signaling across

multiple stress types.

3.3 Ethylene Signaling in Stress Adaptation

Ethylene is a gaseous phytohormone synthesized from

methionine via the Yang cycle, with 1-

aminocyclopropane-1-carboxylate (ACC) as the

immediate precursor. The ACC synthase (ACS) gene

family encodes the rate-limiting enzymes in ethylene

biosynthesis and is differentially regulated by abiotic

stresses. In cotton plants, the expression patterns of

GhACS10 and GhACS12 change under various abiotic

stresses, including cold, heat, drought, and salinity. In

sugarcane, ACS2 and ACS3 respond to low-nitrogen stress

by regulating ethylene biosynthesis, contributing to stress

tolerance and sugar accumulation. These findings

highlight the central role of ACS genes in regulating

ethylene signaling in response to environmental stimuli

(Huang et al., 2025).

Ethylene-response transcription factors (ERFs) are key

downstream effectors of ethylene signaling and have been

shown to play important roles in regulating gene

expression during submergence and other abiotic stresses

(Islam et al., 2020). The AP2/ERF transcription factor

family, which includes both DREB/CBF and ERF

subfamilies, is one of the most extensively studied TF

families in the context of abiotic stress (Mosa et al.,

2017).

3.4 Melatonin as an Emerging Stress Regulator

Melatonin (N-acetyl-5-methoxytryptamine) has emerged

as a pleiotropic molecule with diverse roles in plant stress

response and growth regulation (Gao et al., 2023;

Antoniou et al., 2017). An evolutionarily conserved

molecule, melatonin participates in improving plant

abiotic stress tolerance to cold, heat, high salinity,

drought, heavy metals, waterlogging, global warming,

and UV-B. It can regulate plant vegetative and

reproductive growth, including seed germination,

vegetative growth, root induction, tropism,

photosynthesis, stem strength, leaf water/CO₂ exchange,

root development, flowering, fruit quality, ripening, and

senescence (Gao et al., 2023).

Melatonin systemically ameliorates drought stress-

induced damage in Medicago sativa plants by modulating

nitro-oxidative homeostasis and proline metabolism

(Antoniou et al., 2017). Priming with melatonin is a

rapidly emerging field in plant stress physiology and crop

stress management, serving as an attractive alternate tool

for improving plants' abiotic stress tolerance. Melatonin

also alleviates fungal, bacterial, viral, phytophthora

blight, and nematode diseases in plants by regulating plant

immunity and pathogen pathogenicity (Gao et al., 2023),

illustrating its role at the interface of abiotic and biotic

stress responses. The interactions among major

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8 Journal of Research in Biology (2025) 15(2): 1-24

phytohormones in abiotic stress responses are

summarized in Figure 2.

Figure 2. Phytohormone Crosstalk in Abiotic Stress

Responses

4. Transcription Factor Networks in Abiotic Stress

Responses

Transcription factors (TFs) are proteins that specifically

bind to 5′ upstream DNA regions and ensure target gene

expression at a certain time and space; they are vital for

the normal development of an organism, as well as for

routine cellular functions (Zhang et al., 2017). Some TFs

interact with cis-elements in the promoter regions of

several stress-related genes and thus up-regulate the

expression of many downstream genes, resulting in the

imparting of abiotic stress tolerance. Protein kinases and

TFs correspond to the most regulated genes under abiotic

stress, suggesting that cold and drought stress signal

transduction pathways overlap at several points (Li et al.,

2017). The following sections systematically review the

major TF families involved in abiotic stress responses.

The major transcription factor families involved in abiotic

stress responses are summarized in Table 2.

Table 2. Key Transcription Factor Families in Abiotic Stress Tolerance

TF

Family

Key Functions Stress Types Example Genes References

NAC Regulation of drought &

oxidative stress genes

Drought,

salinity, cold

ONAC066,

SNAC3

(Yuan et al., 2019; Cao et

al., 2017)

WRKY W-box binding, stress gene

activation

Drought, heat,

salinity

OsWRKY45,

WRKY53

(Zhang et al., 2017; Song

et al., 2009)

AP2/ERF DREB/CBF-mediated

transcription

Cold, drought,

heat

DREB2B (Mosa et al., 2017)

HSF Heat stress signaling, HSP

regulation

Heat, oxidative

stress

HSFA2 (Qiao et al., 2015; Singh

et al., 2019)

bHLH Gene regulation under stress Drought AtbHLH17 (Zhang et al., 2017)

MYB Regulation of secondary

metabolism

Drought,

salinity

MYB TFs (Fujita et al., 2011)

HD-Zip Development + ABA signaling Drought,

salinity

HD-Zip TFs (Patel et al., 2023)

4.1 NAC Transcription Factors

NAC (NAM, ATAF1/2, CUC2) domain proteins

constitute the largest plant-specific transcription factor

family and play important roles in plant development and

regulation of abiotic stress tolerance. These proteins have

received attention as major regulators in various stress

signaling pathways and have been found to improve the

abiotic stress tolerance of different crops through genetic

Kores et al., 2025

9 Journal of Research in Biology (2025) 15(2): 1-24

engineering. As transcriptional factors, NAC domain

proteins contain a highly conserved DNA-binding domain

in the N-terminal and a diverse transcription activation or

repression domain in the C-terminal.

Numerous NAC domain proteins from different crops

have been reported to play a positive role in stress

responsiveness and regulation of abiotic stress tolerance.

For example, the pumpkin NAC transcription factor

CmNAC1 significantly improves the tolerance of

Arabidopsis to salt, drought, and cold stress, with ectopic

expression (EE) lines showing better growth performance

and higher survival ratios under stress conditions (Cao et

al., 2017). In rice, the NAC transcription factor

ONAC066 functions as a positive regulator of drought

and oxidative stress response. Transgenic rice lines

overexpressing stress-related NAC TFs exhibited

significant improvement of abiotic stress tolerance under

severe stress conditions without any adverse effect on

yield, or even with yield increase, providing a promising

potential for application of these stress-related NAC TFs

in improvement of abiotic stress tolerance in crops.

Interestingly, ONAC095 negatively regulates drought

response but oppositely acts as a positive regulator of cold

response in rice, illustrating the context-dependent and

sometimes opposing roles of individual NAC TFs in

different stress responses. In most cases, ABA-mediated

signaling pathways, stomatal movement, and root system

architecture were found to be involved in NAC-mediated

improvement of abiotic stress tolerance in transgenic

plants (Yuan et al., 2019).

4.2 WRKY Transcription Factors

WRKY transcription factors are named for the conserved

WRKYGQK amino acid sequence in their DNA-binding

domain and bind with high affinity to the W-box cis-

acting element ((C/T)TGAC(T/C)) in the promoters of

stress-responsive genes Zhang et al., 2014). WRKY

proteins are emerging as key regulators in abiotic stress

defense responses. A majority of WRKY family members

are differentially induced by drought, high salinity, cold,

and heat. Many rice WRKY genes are inducible by

drought, high salinity, cold, and heat stresses.

Overexpression of OsWRKY45, OsWRKY11, TcWRKY53,

and GmWRKY13/21/54 altered drought tolerance, dry

heat tolerance, osmotic stress tolerance, and multiple

abiotic stress tolerance of transgenic plants, respectively.

Additionally, LtWRKY21 was induced by drought and

salinity stress, CaWRKY1 protein was thought to function

in cold adaptation, and HvWRKY38 protein was involved

in cold-, drought-, and ABA-responses. Overexpression

of OsWRKY08 improves osmotic stress tolerance in

Arabidopsis (Song et al., 2009). In maize, WRKY

transcription factors responding to Pb stress have been

characterized, with TtWRKY28 up-regulated under

oxidative stress. Over-expression of these TFs up-

regulates downstream target genes and improves abiotic

stress tolerance (Zhang et al., 2017).

4.3 AP2/ERF Transcription Factors

The AP2/ERF (APETALA2/Ethylene Response Factor)

superfamily is one of the largest and most functionally

diverse TF families in plants, encompassing the DREB

(Dehydration-Responsive Element Binding), CBF (C-

repeat Binding Factor), and ERF subfamilies. Abiotic

stresses such as drought, salinity, cold, heat, and

mechanical wounding regulate many genes, and this often

occurs at the transcriptional level in which several genes

are activated in response to different abiotic stresses. In

the promoter regions, transcription factors interact with

cis-elements of several stress-related genes, which leads

to the upregulation of many downstream genes causing

abiotic stress tolerance (Mosa et al., 2017).

The overexpression of Dehydration-Responsive Element-

Binding Protein 2 (EsDREB2B), which exhibits

transactivation activity of a GAL4-containing reporter,

increases the tolerance to multiple abiotic stress factors

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10 Journal of Research in Biology (2025) 15(2): 1-24

including drought, salinity, cold, heat, heavy metals, and

mechanical wounds in yeast (Zhang et al., 2017).

Molecular characterization of two AP2/ERF transcription

factor genes from Egyptian tomato cultivar (Edkawy) has

revealed their roles in mediating responses to multiple

abiotic stresses (Mosa et al., 2017).

4.4 Heat Shock Transcription Factors (HSFs)

Heat shock transcription factors (HSFs) are particularly

involved in the heat stress response and are important

regulators in the sensing and signaling of heat stress.

Recent studies have also shown that HSFs are involved in

plant growth and development, as well as in responses to

other abiotic stresses such as cold, salt, and drought. In

Pyrus bretschneideri and five other Rosaceae species,

genome-wide identification revealed a large and diverse

HSF family with members showing differential

expression under multiple stress conditions (Qiao et al.,

2015).

HSFA2 is associated with ABA-mediated heat stress

tolerance in tall fescue and Arabidopsis. ABA can regulate

the expression of several small HSPs (sHsps) in maize

leaves when imposed to combined drought and heat

stresses (Singh et al., 2019). Heat shock proteins (HSPs)

are known as target genes for TFs responding to heat

stress. Heat stress changes the way genes are involved in

signaling pathways, as well as transcriptional control and

the expression of heat shock proteins at the molecular

level (Jin et al., 2020). In Syzygium cumini, the heat shock

transcription factor (Hsf) regulates oxidative stress

response by directly sensing reactive oxygen species

(ROS) (Chakraborty et al., 2023).

4.5 bHLH and MYB Transcription Factors

Basic helix-loop-helix (bHLH) transcription factors are

involved in diverse aspects of plant development and

stress responses. TF AtbHLH17 is up-regulated under

drought stress in Arabidopsis, and its over-expression up-

regulates downstream target genes and improves abiotic

stress tolerance (Zhang et al., 2017). The MYB

(myeloblastosis) transcription factor family is one of the

largest TF families in plants, with members involved in

responses to drought, cold, salinity, and oxidative stress.

MYB binding sites (MBS) are among the cis-regulatory

elements identified in the promoters of stress-responsive

genes.

4.6 HD-Zip Transcription Factors

The homeodomain-leucine zipper (HD-Zip) class of TFs

has highly conserved homeodomain (HD) and leucine

zipper (Zip) motifs. The HD-Zip class of TFs interacts

with abscisic acid-regulated developmental networks,

positioning them at the interface of developmental and

stress-responsive signaling. HD-Zip TFs have been

implicated in responses to drought, salinity, and other

abiotic stresses, and represent potential targets for crop

improvement (Patel et al., 2023).

4.7 Quantitative Aspects of Transcription Factor

Networks

The transcriptional reprogramming of plants under abiotic

stress is a remarkable phenomenon, characterized by the

activation of complex regulatory networks involving

transcription factors (TFs). These TFs play a pivotal role

in modulating gene expression, enabling plants to adapt to

environmental challenges such as drought, heat, and cold.

For instance, in cassava seedlings subjected to cold and

drought stress, global gene expression analysis revealed

that protein kinases and TFs were among the most

regulated genes, with 50 differentially expressed genes

(DEGs) associated with "response to JA stimulus"

signaling pathways significantly enriched under both

stress conditions (Li et al., 2017). Similarly,

transcriptome analyses in lentil under heat stress

identified novel genes and regulatory networks linked to

heat tolerance mechanisms (Singh et al., 2019). In rice,

transcriptomic studies of seeds developing under heat

stress uncovered critical heat-responsive genes involved

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in regulatory mechanisms (Islam et al., 2020), while

meta-expression analyses under abiotic stress conditions

identified 264 cold or heat stress-responsive plastid-

related genes, illustrating the breadth of transcriptional

reprogramming (Rane et al., 2021).

The mathematical relationship between TF binding

affinity and gene expression can be described using a

thermodynamic model. For a gene regulated by a single

TF, the binding site occupancy (𝜃) is given by:

𝜃=

TF/𝐾



1 + TF/𝐾



where TF represents the concentration of the transcription

factor, and 𝐾



is the dissociation constant for TF-DNA

binding. The gene expression level can then be expressed

as:

Expression =Basal + Max ⋅ 𝜃

=Basal + Max ⋅

TF/𝐾



1 + TF/𝐾



Here, Basal is the basal expression level of the gene,

and Max is the maximum inducible expression level. This

model predicts that genes with lower 𝐾



values

(indicating higher TF binding affinity) will be more

sensitively induced at lower TF concentrations. Such

hierarchical activation of stress-responsive genes aligns

with experimental observations, where genes with high-

affinity TF binding sites are activated earlier or at lower

stress levels. This quantitative framework provides

valuable insights into the dynamics of transcriptional

regulation during abiotic stress, highlighting the critical

role of TFs in orchestrating plant stress responses (Zhang

et al., 2017).

5. Post-Translational Modifications in Stress Signaling

5.1 Ubiquitination and the 26S Proteasome

Ubiquitination is a reversible post-translational

modification in which ubiquitin, a 76-amino acid protein,

is covalently attached to target proteins, typically marking

them for degradation by the 26S proteasome. This system

plays critical roles in regulating the abundance and

activity of key stress signaling components. The

ubiquitin-proteasome system (UPS) modulates the

stability of transcription factors, signaling kinases, and

hormone receptors, thereby controlling the amplitude and

duration of stress responses (Singh et al., 2022).

5.2 SUMOylation and the SUMO Stress Response

Small ubiquitin-like modifier (SUMO) proteins are

conjugated to target proteins in a process called

SUMOylation, which modulates protein activity,

localization, and interactions. Hyper-SUMOylation under

acute heat, cold, high salinity, drought, oxidative stress,

and nutrient deficiency marks the conserved SUMO stress

response (SSR) in plants. SIZ1-mediated SUMOylation

positively responds to salt and drought-induced osmotic

stress; enhances metal stress tolerance and light signaling;

and regulates N, P, and ROS homeostasis in plants.

SUMOylation regulates heat stress positively at

transcriptional, post-transcriptional, and translational

levels.

The mutated AtSIZ1, a SUMO ligase, resulted in

compromised tolerance to cold and drought, early

flowering, and phosphate starvation symptoms,

demonstrating the pleiotropic importance of

SUMOylation in plant stress adaptation. The conservation

of the SUMO stress response across diverse stress types

suggests that SUMOylation serves as a general stress-

responsive regulatory mechanism (Singh et al., 2022).

5.3 Phosphorylation Cascades

Protein phosphorylation is the most prevalent post-

translational modification in stress signaling, with kinases

and phosphatases acting as molecular switches that

control the activity of signaling components (Gandhi &

Oelmüller, 2023). CPKs phosphorylate ABA-responsive

transcription factors and ion channels in response to Ca²⁺

signals (Atif et al., 2019). RLKs phosphorylate MAP

kinases and other downstream effectors in response to

stress perception (Li et al., 2017). The interplay between

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phosphorylation and dephosphorylation events

determines the net output of stress signaling cascades and

the magnitude of the transcriptional response (Atif et al.,

2019).

5.4 Cyclophilins and Protein Folding

Cyclophilins are peptidyl-prolyl cis-trans isomerases

(PPIases) that catalyze the isomerization of peptide bonds

preceding proline residues, facilitating protein folding and

assembly. In plants, cyclophilin A (CyPA) was involved

in signal transduction mechanisms regulating various

abiotic stresses via phosphoprotein cascades, Ca²⁺, and

other secondary signaling molecules. A new class of

cyclophilin, OsCyP-25, from rice (Oryza sativa L.) was

upregulated in response to different abiotic stresses

including salinity, cold, heat, and drought. The cyclophilin

A homologue from Piriformospora indica (PiCyPA) is

likely to be a part of the general cellular stress response to

multiple abiotic stresses, which is conserved in

prokaryotes, fungi, and plants (Trivedi et al., 2013).

6. Reactive Oxygen Species (ROS) Signaling and

Antioxidant Defense

6.1 ROS as Stress Signals and Damaging Agents

Reactive oxygen species (ROS), including superoxide

(O₂⁻), hydrogen peroxide (H₂O₂), and hydroxyl radicals

(•OH), are produced as inevitable byproducts of aerobic

metabolism and are generated in excess under virtually all

abiotic stress conditions. Abiotic stresses that restrict CO₂

availability because of stomatal closure facilitate the

generation of ROS molecules in chloroplasts. ROS serve

a dual role: at low concentrations, they act as signaling

molecules that activate stress-responsive gene expression;

at high concentrations, they cause oxidative damage to

proteins, lipids, and nucleic acids (Sasi et al., 2018).

The heat shock transcription factor (Hsf) in Syzygium

cumini regulates oxidative stress response by directly

sensing ROS (Chakraborty et al., 2023), illustrating the

direct coupling between ROS levels and transcriptional

responses. CPK11, induced by H₂O₂, regulates and

controls the activity of SOD and APX production induced

by the ABA signaling pathway (Atif et al., 2019),

demonstrating the integration of ROS and Ca²⁺ signaling

in antioxidant defense.

6.2 Antioxidant Enzyme Systems

Plants possess a sophisticated enzymatic antioxidant

defense system comprising SOD, catalase (CAT), APX,

glutathione reductase (GR), and peroxidases

(Hernández-Bueno et al., 2021). To survive under

conditions that consist of growing levels of abiotic stress,

plants alter their metabolism by activating signal cascades

and regulatory proteins such as transcription factors and

heat shock factors, which activate and modify the

antioxidant defense system. This response acts to help

maintain homeostasis and synthesize and accumulate

compatible solutes (Patel et al., 2023).

Peroxidases have been shown to enhance stress tolerance.

A versatile peroxidase from the fungus Bjerkandera

adusta confers abiotic stress tolerance in transgenic

tobacco plants, demonstrating that heterologous

expression of antioxidant enzymes can improve plant

stress tolerance. Plants have a large number of peroxidase

isozymes, which are encoded by multigenic families

(Hernández-Bueno et al., 2021).

6.3 Glyoxalase System and Methylglyoxal

Detoxification

Methylglyoxal (MG) is a cytotoxic byproduct of

glycolysis that accumulates under abiotic stress

conditions. The glyoxalase pathway, comprising

glyoxalase I (Gly I) and glyoxalase II (Gly II), detoxifies

MG using glutathione as a cofactor. Expression of

glyoxalase genes, as well as enzyme activity, have been

reported to be altered in response to various abiotic, biotic,

hormonal, and chemical treatments. Overexpression of

MG-detoxifying glyoxalase pathway provides significant

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abiotic stress tolerance by resisting the excess

accumulation of MG in transgenic tobacco and tomato

plants. Both glyoxalase enzymes and methylglyoxal level

are considered as biomarkers for plant stress tolerance

(Islam & Ghosh, 2018).

7. Osmotic Adjustment and Compatible Solute

Accumulation

7.1 Proline and Other Osmolytes

Under osmotic and drought stress conditions, plants

synthesize and accumulate a diverse array of low-

molecular-weight organic solutes collectively termed

compatible solutes or osmolytes that confer protection

against cellular dehydration without disrupting normal

metabolic functions (Patel et al., 2023). Among these,

proline is perhaps the most extensively characterized; its

rapid accumulation is orchestrated primarily through

upregulation of the Δ¹-pyrroline-5-carboxylate synthetase

(P5CS) pathway and concurrent suppression of proline

dehydrogenase, resulting in substantial cytoplasmic

proline pools that contribute to turgor maintenance and

enzyme stabilization (Zhang et al., 2014). Beyond

proline, glycine betaine synthesized via the choline

oxidation pathway stabilizes thylakoid membranes and

protects the photosynthetic apparatus under high-salinity

and temperature stress, while trehalose and mannitol serve

dual roles as osmoprotectants and reactive oxygen species

(ROS) scavengers, collectively sustaining cellular redox

homeostasis during prolonged stress exposure (Antoniou

et al., 2017). The thermodynamic basis of osmotic

adjustment is described by the van 't Hoff equation for

osmotic potential:

Ψ

S

= −(n/V) · R · T

where Ψ

S

is the osmotic (solute) potential (MPa), n is the

number of moles of solute, V is the volume of solvent (L),

R is the universal gas constant (8.314 × 10⁻³

L·MPa·mol⁻¹·K⁻¹), and T is the absolute temperature (K).

This relationship illustrates that increasing intracellular

solute concentrations lowers Ψ

S

, thereby maintaining a

favorable water potential gradient for continued water

uptake from the surrounding soil matrix. Importantly, the

effectiveness of osmolyte-mediated adjustment is

contingent not only on solute concentration but also on

compartment-specific accumulation, with chloroplastic

and cytosolic pools playing distinct protective roles

(Fidler et al., 2022). Collectively, the coordinated

induction of proline, glycine betaine, trehalose, and

mannitol biosynthesis pathways represents a highly

conserved and multifaceted adaptive strategy that

underpins plant resilience to water-deficit environments,

and their manipulation via genetic engineering or priming

treatments holds considerable promise for improving crop

performance under climate-change-associated abiotic

stresses (Patel et al., 2023).

7.2 Betaine Synthesis

Another gene used to develop abiotic stress-tolerant crops

is the betaine synthesis (betA) gene, derived from either

E. coli or Rhizobium meliloti, which encodes choline

dehydrogenase. Betaine accumulation contributes to

osmotic adjustment and also protects macromolecular

structures under stress conditions (Patel et al., 2023).

7.3 Ion Homeostasis Under Salinity Stress

Salinity stress imposes both osmotic and ionic stress on

plants. The ionic component results from the

accumulation of Na⁺ and Cl⁻ ions to toxic levels in the

cytoplasm. Plants maintain ion homeostasis through the

activity of ion transporters and channels, including the

KUP K⁺ transporter family, which is involved in

potassium deficiency and salt and drought stress response

(Chakraborty et al., 2023). ABA-mediated signaling

promotes the expression of ion transporters that exclude

Na⁺ from the cytoplasm or compartmentalize it in the

vacuole. Research on rice seeds presoaked with ABA

showed enhanced salinity tolerance through the

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suppression of Na⁺ and Cl⁻ levels, lowering Na⁺/K⁺ ratios,

as well as increasing soluble sugar content (Luo et al.,

2018).

8. Non-Coding RNAs in Abiotic Stress Regulation

8.1 MicroRNAs (miRNAs)

MicroRNAs (miRNAs) are small (~21 nucleotide) non-

coding RNAs that regulate gene expression post-

transcriptionally by guiding the RNA-induced silencing

complex (RISC) to complementary target mRNAs,

resulting in their cleavage or translational repression

(Zhang et al., 2014; Patel et al., 2024). Numerous

miRNAs have been identified as potential targets for

enhancing tolerance to abiotic stress, particularly cold,

heat, salinity, and drought. For example, miRNAs were

reported to be involved in tolerance against drought

(miRNA156 and miR393), salt (miR319 and miR393),

and temperature stress (miR9748, miR169, and miR1320)

(Patel et al., 2024).

In potato, deep sequencing identified novel and conserved

miRNAs related to drought stress, including miRNAs

targeting WRKY transcription factors. WRKY

transcription factors can bind with high affinity to the W-

box cis-acting element, permitting signal transduction to

regulate the expression of stress-related genes, resulting

in plant stress tolerance (Zhang et al., 2014). In

Ammopiptanthus nanus, conserved and lineage-specific

miRNAs contributed to the cold stress response by

regulating ROS homeostasis and stress signaling by

negatively regulating the corresponding targets (Zhu et

al., 2023).

8.2 Long Non-Coding RNAs (lncRNAs)

Long non-coding RNAs (lncRNAs) are transcripts longer

than 200 nucleotides that lack significant protein-coding

potential but play important regulatory roles in gene

expression. Combined lncRNA and mRNA expression

profiles identified lncRNA–miRNA–mRNA modules

regulating the cold stress response in Ammopiptanthus

nanus. A. nanus showed high levels of tolerance to

drought, high salinity, high temperature, cold, and

freezing stresses, and was used as an important material

for studying the stress tolerance mechanism of woody

plants. Researchers have carried out a number of studies

using physiological and biochemical methods,

transcriptomics, proteomics, and other omics techniques

to analyze the abiotic stress tolerance mechanism and

identify stress tolerance-related genes in A. nanus (Zhu et

al., 2023).

8.3 Cell-Penetrating Peptides and miRNA Delivery

Cell-penetrating peptides (CPPs) offer a potential solution

for improving plant tolerance to abiotic stress through the

delivery of peptides and miRNAs. Several signaling

peptides that play important roles in plant responses to

abiotic stress have been identified and used to increase

stress tolerance in plants. This emerging technology

represents a novel approach to modulating stress-

responsive miRNA levels in planta without the need for

stable genetic transformation (Patel et al., 2024).

9. Epigenetic Mechanisms and Stress Memory

9.1 DNA Methylation

DNA methylation is a heritable epigenetic mark that plays

important roles in regulating gene expression, transposon

silencing, and genome stability. DNA methylation has

been previously involved in the regulation of stress

response genes, which may allow plants to

transgenerationally adapt to stress conditions (Lagiotis et

al., 2023). The intensity and duration of the abiotic stress

stimulus (priming) can variably affect the intra

9.2 Histone Modifications

Histone modifications, including acetylation,

methylation, phosphorylation, and ubiquitination,

regulate chromatin accessibility and gene expression.

Chromatin remodeling has been associated with a number

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of plant responses to abiotic signals, including cold, heat,

drought, and salinity. Photon irradiance-dependent

alterations in histone acetylation and global chromatin

compaction have been recorded, illustrating the

integration of light and stress signaling at the chromatin

level. Since many developmental and environmental

responses are known to be regulated by epigenetics, it is

predicted that reprogramming of the epigenome will be a

substantial factor in crop breeding and cultivar

development (Moshelion & Altman, 2015).

9.3 Stress Priming and Epigenetic Memory

Stress priming refers to the phenomenon whereby a prior

exposure to a mild or sublethal stress enhances the plant's

ability to tolerate a subsequent, more severe stress.

Climate change and global warming exacerbate abiotic

stress incidents, which are predicted to become more

frequent and severe within the century, posing a serious

challenge for crop cultivation and production. To cope

with such adverse environmental conditions, plants can

reprogram their regular development at the expense of

reproductive potential, favoring stress response

mechanisms.

The overall molecular mechanism of priming-mediated

responses against salt stress involves energy-dependent

transmembrane receptor-like kinases (RLKs), which

recognize the priming elicitors and, when activated,

regulate the transcription of abiotic stress defense genes.

In Lolium perenne, short-term epigenetic salt

stress/recovery treatments could change the

transcriptional response to subsequent abiotic stress,

inducing transcriptional and metabolic changes and

improving plants' stress response via inhibiting

physiological damage (such as cell membrane stability

and ROS) regulated by trainable genes (Lagiotis et al.,

2023). Abiotic stress might induce epigenetic changes as

well, and epigenetic regulators might have an adaptive

advantage although we must consider a negative impact

on crop yield by preventing the plant from growing to its

full potential (Moshelion & Altman, 2015).

10. Cross-Stress Signaling and Stress Crosstalk

10.1 Molecular Basis of Stress Crosstalk

Plants in natural environments are rarely exposed to a

single abiotic stress in isolation; rather, they typically

encounter multiple stresses simultaneously or

sequentially (Rane et al., 2021; Ambrosino et al., 2020).

The signal transduction genes and stress-tolerance genes

often demonstrate overlapping functionalities when plants

are subjected to abiotic stressors. For example, ethylene-

response transcription factors and GA pathway regulators

that are stress-responsive in heat stress were also reported

to play important roles in regulating gene expression

during submergence (Islam et al., 2020).

Global gene expression analysis of cassava seedlings

revealed that cold and drought stress signal transduction

pathways overlap at several points, with protein kinases

and TFs corresponding to the most regulated genes. The

important RLK group, which includes members like

LRR-RLK, MRLK, and LecRLK, has been previously

shown to be involved in mediating the cellular response

to various environmental cues, hormonal signals, and

stress perception (Li et al., 2017). The signaling

mechanisms in plants during low and high temperature,

drought, and salinity are different and yet related to each

other (Chakraborty et al., 2015).

10.2 Chloroplast-Mediated Stress Responses

Chloroplasts are not only the sites of photosynthesis but

also important sensors and integrators of abiotic stress

signals. The metabolites synthesized in chloroplasts

protect plants from abiotic and biotic stresses, including

heat, cold, drought, salt, light, and pathogens. Through

meta-expression analyses under abiotic stress conditions,

264 cold or heat stress-responsive plastid-related genes

were identified in rice. The significance of the function of

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16 Journal of Research in Biology (2025) 15(2): 1-24

chloroplast-related genes in response to climate change

has not been well studied in crops (Rane et al., 2021),

representing an important knowledge gap.

10.3 Secondary Metabolites in Stress Adaptation

Secondary metabolites are produced and regulated in

response to various abiotic and biotic stresses, and aid in

better survival of the plants. In Syzygium cumini, various

biotic and abiotic stress tolerance response genes

displayed multiple signatures of adaptive evolution.

Among the major genes with multiple signatures of

adaptive evolution (MSA) involved in abiotic stress

tolerance responses, ABF regulates the expression of

ABA-responsive genes to provide salinity, drought, and

osmotic stress tolerance; MPAO facilitates oxidative

burst-mediated programmed cell death; KUP K⁺

transporter family is involved in potassium deficiency and

salt and drought stress response; and LOX confers abiotic

(drought, salinity, etc.) and biotic stress tolerance

(Chakraborty et al., 2023).

11. Omics Approaches to Dissecting Abiotic Stress

Responses

11.1 Transcriptomics

Transcriptomic approaches, including microarray analysis

and RNA sequencing (RNA-seq), have revolutionized our

understanding of the global gene expression changes that

occur during abiotic stress (Ambrosino et al., 2020).

Transcriptome analysis may provide an overview of novel

genes and regulatory networks linked with heat tolerance

mechanisms in lentil (Singh et al., 2019). In rice seeds

developing under heat stress, transcriptomic data-driven

discovery revealed vital roles of heat-responsive genes in

regulatory mechanisms (Islam et al., 2020). Comparative

transcriptome analysis has uncovered different heat stress

responses in heat-resistant and heat-sensitive jujube

cultivars (Jin et al., 2020).

Bioinformatics resources for plant abiotic stress responses

have expanded enormously in the omics era. Abiotic

stresses, such as heat and cold, drought, salinity, and

flooding, dramatically affect plant growth and crop yield,

and extensive studies have been focused on understanding

the molecular basis of abiotic stress response and the

research for improved, productive plants adapted for

stress tolerance (Ambrosino et al., 2020).

11.2 Genomics and Genome-Wide Association Studies

(GWAS)

Genome-wide approaches have enabled the identification

of quantitative trait loci (QTLs) and candidate genes

associated with abiotic stress tolerance. The genetic basis

of plant adaptation to abiotic stress remains poorly

understood, even in genomic model species such as rice.

Identification of stress tolerance genes is often limited to

mutant lines or a relatively few individuals used in

mapping populations, and wider analysis of natural allelic

variants in cultivated and wild populations is rare

(Vigueira et al., 2016).

In bread wheat, nitrogen deficiency tolerance was

conferred by introgression of a QTL derived from wild

emmer, with several candidate genes associated with

abiotic stress identified within the QTL interval. These

include genes encoding cold-regulated protein (COR) for

plant adaptation to cold and drought stress tolerance,

pentatricopeptide repeat proteins involved in resistance to

abiotic stress including salinity, drought, and cold, and the

HKMT protein that influences chromatin and DNA

methylation under stress (Govta et al., 2024).

Long-term balancing selection at the Phosphorus

Starvation Tolerance 1 (PSTOL1) locus in wild,

domesticated, and weedy rice (Oryza) illustrates how

natural selection has shaped allelic diversity at stress

tolerance loci. Abiotic stresses, such as drought, high

salinity, and low soil nutrient levels, negatively impact

crop production worldwide and are predicted to increase

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in coming decades due to climate change (Vigueira et al.,

2016).

11.3 Proteomics and Metabolomics

Proteomics and metabolomics provide complementary

layers of information about the molecular responses to

abiotic stress. Researchers have carried out a number of

studies using physiological and biochemical methods,

transcriptomics, proteomics, and other omics techniques

to analyze the abiotic stress tolerance mechanism and

identify stress tolerance-related genes (Zhu et al., 2023).

Unraveling the genetic, epigenetic, transcriptomic, and

metabolomic bases of stress tolerance mechanisms/traits

is crucial for breeding climate-resilient or abiotic stress-

tolerant crop varieties (Rane et al., 2021).

11.4 Genome Sequencing and Adaptive Evolution

Genome sequencing of Syzygium cumini (jamun) revealed

adaptive evolution in secondary metabolism pathways

associated with its medicinal properties and stress

tolerance. Various biotic and abiotic stress tolerance

response genes displayed multiple signatures of adaptive

evolution in S. cumini (Chakraborty et al., 2023). High-

throughput phenotyping and advances in bioinformatics

allow researchers to screen for key genomic features that

contribute to abiotic stress tolerance (Patel et al., 2023).

12. Biotechnological Strategies for Engineering Stress-

Tolerant Crops

12.1 Transgenic Approaches

Transgenic technology has been widely used to

overexpress stress-related genes in crop plants, with

numerous examples of improved stress tolerance. A long

list of transgenic plants with a myriad of exogenous genes

has been shown to display improved tolerance to drought,

salt, cold, heat, and oxidative stresses (Hernández-

Bueno et al., 2021). Transgenic rice lines overexpressing

stress-related NAC TFs exhibited significant

improvement of abiotic stress tolerance under severe

stress conditions without any adverse effect on yield, or

even with yield increase (Yuan et al., 2019).

The betaine synthesis (betA) gene, derived from either E.

coli or Rhizobium meliloti, which encodes choline

dehydrogenase, has been used to develop abiotic stress-

tolerant crops (Patel et al., 2023). Overexpression of MG-

detoxifying glyoxalase pathway provides significant

abiotic stress tolerance by resisting the excess

accumulation of MG in transgenic tobacco and tomato

plants (Islam & Ghosh, 2018). A versatile peroxidase

from the fungus Bjerkandera adusta confers abiotic stress

tolerance in transgenic tobacco plants (Hernández-

Bueno et al., 2021).

12.2 CRISPR/Cas9 and Genome Editing

CRISPR/Cas9 and related genome editing technologies

offer unprecedented precision in modifying stress-related

genes and regulatory elements. Climate change and

extensive agriculture practice have provoked water

scarcity, severe droughts, and soil salinity around the

world; therefore, major efforts are required to improve

abiotic stress tolerance in plants, either by classic genetics

or genetic manipulation techniques using transgenic,

CRISPR/Cas9, or oligonucleotide-directed mutagenesis

tools (Hernández-Bueno et al., 2021). Methods of crop

improvement and applications towards fortifying food

security include CRISPR-based approaches targeting key

genomic features that contribute to abiotic stress tolerance

(Patel et al., 2023).

12.3 Marker-Assisted Selection and Conventional

Breeding

Conventional breeding and marker-assisted selection

(MAS) remain important tools for improving abiotic

stress tolerance in crops. Seed companies are investing

enormous effort into developing crops with higher

tolerance to drought, heat, cold temperatures, and salinity.

Recent studies have identified a large number of genetic

and molecular networks underlying plant adaptation to

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adverse environmental growth conditions (Moshelion &

Altman, 2015). However, abiotic tolerance mechanisms

in crop plants are limited and have largely failed to bridge

the gap between theoretical research and crop breeding

(Rane et al., 2021).

12.4 Grafting and Rootstock-Mediated Stress

Tolerance

Grafting is widespread to improve plant performance in

terms of yield, quality, and resilience to abiotic and biotic

stresses. The use of tolerant rootstocks to different abiotic

stresses, such as drought, salinity, and drastically rising or

decreasing temperature, is becoming indispensable in this

global climate change era. The influence of rootstocks on

many scion biology aspects is well-established, and

molecular aspects of root-to-shoot and/or shoot-to-root

signaling events are starting to be known and show how

grafting triggers differential responses between the scion

and rootstock. Comparative transcriptomic analyses of

citrus cold-resistant vs. sensitive rootstocks suggest a

relevant role of ABA signaling in triggering cold scion

adaptation (Primo-Capella et al., 2022). Current

biotechnological approaches for improving abiotic stress

tolerance are summarized in Table 3.

Table 3. Biotechnological Strategies for Enhancing Abiotic Stress Tolerance

Strategy Mechanism Example

Application

Advantages References

Transgenic

overexpression

Introduce stress-

responsive genes

NAC TF

overexpression in rice

High

specificity

(Yuan et al., 2019)

CRISPR/Cas9 Targeted genome

editing

Editing stress-related

loci

Precision

breeding

(Hernández-Bueno

et al., 2021)

Marker-assisted

selection

QTL-based breeding PSTOL1

introgression

Field

applicability

(Vigueira et al.,

2016)

Glyoxalase

engineering

MG detoxification Transgenic

tobacco/tomato

ROS reduction (Islam & Ghosh,

2018)

Antioxidant enzyme

engineering

ROS scavenging Peroxidase expression Enhanced

tolerance

(Hernández-Bueno

et al., 2021)

Grafting Rootstock-mediated

signaling

Citrus cold tolerance Non-GMO

strategy

(Primo-Capella et

al., 2022)

13. Crop-Specific Adaptations to Abiotic Stress

13.1 Cereals

Cereals, including rice, wheat, maize, and barley, are the

most important food crops globally and are severely

affected by abiotic stresses. The adaptation and tolerance

of major cereals and legumes to important abiotic stresses

have been extensively reviewed. In wheat, the

chloroplast-localized membrane protein TaRCI has been

characterized for its role in heat, drought, and salinity

stress tolerance, and could be a potential candidate for

gene manipulation for improving stress tolerance in crop

plants (Rane et al., 2021). In rice, numerous stress-related

genes and regulatory networks have been characterized,

including NAC TFs, WRKY TFs, CPKs, and RLKs (Atif

et al., 2019; Song et al., 2009).

13.2 Legumes

Kores et al., 2025

19 Journal of Research in Biology (2025) 15(2): 1-24

Legumes, including soybean, lentil, and Medicago sativa,

are important sources of protein and are also severely

affected by abiotic stresses (Rane et al., 2021). In

soybean, genome-wide dissection and expression

profiling of unique glyoxalase III genes revealed

differential patterns of transcriptional regulation under

abiotic stress (Islam & Ghosh, 2018). In lentil,

transcriptome analysis identified novel genes and

regulatory networks linked with heat tolerance

mechanisms (Singh et al., 2019). Melatonin systemically

ameliorates drought stress-induced damage in Medicago

sativa plants by modulating nitro-oxidative homeostasis

and proline metabolism (Antoniou et al., 2017).

13.3 Triticale and Other Cereals

Triticale has been found to tolerate some abiotic stress

conditions better than other cereal species. For instance,

triticale was reported to be more drought tolerant than

durum wheat, and its salinity tolerance was better than

wheat and even similar to barley. Some estimates suggest

that over 90% of rural farmland was affected by abiotic

stressors at some point during the growing season (Atak

et al., 2023), underscoring the importance of developing

stress-tolerant varieties of all major crops.

14. Integrative Models of Plant Stress Response

14.1 Systems Biology Approaches

The complexity of plant stress responses, involving

thousands of genes, proteins, and metabolites interacting

in dynamic networks, necessitates systems biology

approaches for their comprehensive understanding. Plants

display an amazing diversity and, owing to their sessile

nature, they evolved a broad range of molecular

mechanisms to respond to complex networks of

environmental signals, which activate multiple pathways,

modulated by different responsive genes. Bioinformatics

resources for plant abiotic stress responses have expanded

enormously in the fast-evolving omics era (Ambrosino et

al., 2020).

14.2 Network Analysis and Gene Regulatory Networks

Gene regulatory network (GRN) analysis has been used to

identify key regulatory hubs and modules in plant stress

responses. Transcriptomic data-driven discovery of global

regulatory features of rice seeds developing under heat

stress revealed complex regulatory networks involving

transcription factors, signaling kinases, and hormone

pathways (Islam et al., 2020). A protein-to-protein

interaction network analysis associated with high

temperature stress is expected to provide the basis for

studying molecular mechanisms by which chloroplasts

will respond to different abiotic stresses under changing

climatic scenarios (Rane et al., 2021).

14.3 Mathematical Modeling of Stress Tolerance

Mathematical modeling provides a quantitative

framework for understanding and predicting plant stress

responses. A general model for plant stress tolerance can

be expressed using the Tolerance Index (TI), which

quantifies the relative performance of plants under stress

compared to optimal conditions:

𝑇𝐼=

𝑌



𝑌



× 100

where 𝑌



represents plant yield (or any relevant

performance metric) under stress conditions, and

𝑌



represents the corresponding yield under non-

stress (control) conditions. This index provides a

percentage-based measure of tolerance, with higher

values indicating greater resilience.

To account for multiple simultaneous stresses, the

model can be extended as follows:

𝑇𝐼



= 

𝑌

,

𝑌













where 𝑛is the total number of stress factors, 𝑌

,

is the

yield under the 𝑖-th stress condition, and 𝑤



is the weight

assigned to each stress based on its relative importance.

Kores et al., 2025

20 Journal of Research in Biology (2025) 15(2): 1-24

The weights allow differential contributions of individual

stresses to the overall tolerance index.

More sophisticated models incorporate the dynamics of

stress signaling, gene expression, and metabolic responses

using systems of ODEs or stochastic differential equations

(SDEs), enabling the prediction of stress tolerance

phenotypes from molecular data (Atif et al., 2019; Gandhi

& Oelmüller, 2023).

15. Future Perspectives and Research Priorities

15.1 Understanding Multi-Stress Responses

A major challenge for future research is to understand how

plants respond to multiple simultaneous stresses, which is

the condition most commonly encountered in agricultural

settings (Ambrosino et al., 2020). The signal

transduction genes and stress-tolerance genes often

demonstrate overlapping functionalities when plants are

subjected to abiotic stressors. Unraveling the genetic,

epigenetic, transcriptomic, and metabolomic bases of

stress tolerance mechanisms/traits is crucial for breeding

climate-resilient or abiotic stress-tolerant crop varieties

(Rane et al., 2021).

15.2 Translating Molecular Knowledge to Crop

Improvement

Despite significant advances in understanding the

molecular mechanisms of plant stress tolerance, abiotic

tolerance mechanisms in crop plants are limited and have

largely failed to bridge the gap between theoretical

research and crop breeding. Some success has been

achieved in understanding the crop tolerance mechanisms

to abiotic stresses, and a few of them have been explored

for crop improvement. Future research should focus on

translating molecular knowledge into practical breeding

strategies, leveraging the power of genomics,

transcriptomics, and genome editing (Patel et al., 2023;

Moshelion & Altman, 2015).

15.3 Epigenomics and Transgenerational Stress

Memory

The role of epigenetic mechanisms in stress memory and

transgenerational adaptation is an emerging and rapidly

evolving field. DNA methylation has been previously

involved in the regulation of stress response genes, which

may allow plants to transgenerationally adapt to stress

conditions. Future research should investigate the

mechanisms by which stress-induced epigenetic changes

are established, maintained, and erased, and how they

contribute to adaptive evolution (Lagiotis et al., 2023;

Moshelion & Altman, 2015).

15.4 Emerging Technologies

Emerging technologies, including single-cell

transcriptomics, spatial transcriptomics, and advanced

genome editing tools, offer new opportunities for

dissecting the molecular mechanisms of plant stress

responses at unprecedented resolution. Omics approaches

have now been extensively studied and integrated to

decipher the molecular mechanisms leading to abiotic

stress tolerance in plants. Cell-penetrating peptides offer

a potential solution for improving plant tolerance to

abiotic stress through the delivery of peptides and

miRNAs (Patel et al., 2024), representing a novel and

potentially transformative approach to crop improvement.

16. Conclusion

Plant adaptation to abiotic stress under changing climates

is a complex, multilayered process involving the

coordinated action of stress perception systems, signal

transduction cascades, transcriptional regulatory

networks, post-translational modifications, epigenetic

mechanisms, and metabolic adjustments. Abiotic stresses

collectively account for more than 50% of yield losses in

major crop species, and the accelerating pace of climate

change is predicted to intensify these losses. The

molecular mechanisms reviewed here from RLK-

Kores et al., 2025

21 Journal of Research in Biology (2025) 15(2): 1-24

mediated stress perception; and CPK-mediated Ca²⁺

signaling, through ABA, JA, ethylene, and melatonin

signaling, to the transcriptional regulatory networks

orchestrated by NAC, WRKY, AP2/ERF, HSF, and other

TF families, and the post-translational regulatory layers of

ubiquitination, SUMOylation, and phosphorylation,

collectively constitute a sophisticated and highly

integrated stress response system.

Epigenetic mechanisms, including DNA methylation,

histone modifications, and non-coding RNA-mediated

regulation, add further layers of complexity and provide

mechanisms for stress memory and transgenerational

adaptation. Omics technologies have dramatically

accelerated the pace of discovery in this field, and

biotechnological strategies including transgenic

overexpression, CRISPR/Cas9 genome editing, and

marker-assisted selection offer promising avenues for

translating molecular knowledge into climate-resilient

crops.

Despite these advances, significant knowledge gaps

remain, particularly regarding the molecular basis of

multi-stress responses, the mechanisms of

transgenerational epigenetic inheritance, and the

translation of laboratory findings to field-level crop

improvement. Addressing these gaps will require

integrated, interdisciplinary approaches combining

molecular biology, systems biology, computational

modeling, and plant breeding. The development of

climate-resilient crops capable of sustaining productivity

under the abiotic stress conditions projected for the

coming decades is not merely a scientific challenge but an

urgent societal imperative.

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