Molecular Mechanisms Underlying Defense Responses of Potato (Solanum tuberosum L.) to Environmental Stress and CRISPR/Cas-Mediated Engineering of Stress Tolerance

Abstract

Environmental stresses, such as drought, salinity, and pathogen attacks, significantly affect potato growth, development, and yield by disrupting key physiological and biochemical processes. Plant responses to these stresses are mediated by changes in gene expression, transcriptional regulation, and the activity of various functional proteins, all of which contribute to the molecular mechanisms of stress tolerance. Genome editing using the CRISPR/Cas9 system has been effectively used to enhance the resistance of potato to environmental stresses and to improve its nutritional value. This article provides a comprehensive review of recent studies retrieved from academic databases focusing on the effects of various environmental stressors on potato growth, yield, and postharvest storage. It also examines the influence of these stresses on the production of secondary metabolites and their associated molecular pathways. Finally, the review highlights advancements in the application of CRISPR/Cas-based genome editing technologies between 2021 and 2025 to improve stress tolerance and nutritional traits in potato plants.

Keywords: CRISPR/Cas; Solanum tuberosum; defense mechanisms; environmental stresses; secondary metabolites.

Figure 1

Molecular mechanism of StbHLH47, StLike3, StDRO2, and its role in drought and salt stress tolerance. In wild-type potato (left panel), StLike3 is proposed to contribute to sulfur metabolism and oxidative stress responses. StDRO2, a membrane-localized auxin transporter of the DRO1 family, facilitates polar auxin efflux in root tissues, maintaining optimal auxin gradients for gravitropic responses and lateral root emergence. Functional StDRO2 ensures balanced root architecture with moderate depth and branching. StbHLH47 acts as a negative regulator of drought tolerance by suppressing ABA signaling and lignin biosynthesis, leading to weaker cell wall reinforcement, impaired antioxidant defense, and increased susceptibility to membrane damage and chlorophyll loss. In addition, StbHLH47 represses iron uptake genes, resulting in suboptimal Fe(II) accumulation, which limits antioxidant capacity and exacerbates oxidative stress under drought conditions. In CRISPR/Cas9-edited plants (right panel), the overexpression of StLike3 can enhance defense metabolism, while knockout of StbHLH47 derepresses ABA-responsive and lignin biosynthetic pathways, improving cell wall integrity, antioxidant activity, and drought tolerance. Deregulation of iron homeostasis also leads to increased Fe(II) content, which supports chlorophyll stability, efficient photosynthesis, and enhanced ROS scavenging, thereby enhancing overall stress tolerance. Knockout of StDRO2 reduces auxin efflux, leading to intracellular IAA accumulation in root apices. This stimulates lateral root initiation and elongation via ARF-mediated transcriptional cascades, producing a deeper and more branched root system. These architectural changes significantly improve water uptake under drought and confer enhanced tolerance without compromising growth.

Figure 2

Molecular mechanism of ERF3, SR4, DRM6-1, CHL1, NRL1, PM1, DMP2 and their role in resistance to P. infestans. Wild type potato (left panel), which negatively regulates the expression of defense-related genes: ERF3—suppresses defense gene activation downstream of ethylene signaling (ISC1); SR4—represses SA-mediated pathways by inhibiting EDS1 and NDR1; DMR6-1—hydroxylates SA (SA5H), attenuating SA accumulation; CHL1—BR-responsive transcription factor that downregulates immunity under pathogen effector-triggered brassinosteroid signaling; NRL1—mediates proteasomal degradation of the immune regulator SWAP70; and PM1—suppresses PRR signaling at the plasma membrane and negatively modulates the expression of defense-related genes, including StPR1, StPR5, StWRKY7, and StWRKY8. These mechanisms weaken the immune response and facilitate pathogen colonization. StDMP2 encodes an ER-localized DUF679 membrane protein that maintains endoplasmic reticulum (ER) homeostasis and facilitates proper folding and stabilization of immune receptors, such as PRRs and NDR1, thereby enhancing pattern-triggered immunity and hypersensitive response upon Phytophthora recognition. CRISPR/Cas9 knockouts (right panel) of these genes relieve transcriptional repression or eliminate enzymatic activities, resulting in enhanced SA signaling, increased expression of WRKY and pathogenesis-related genes (PR1, PR5), stabilization of immune regulators, and improved recognition of pathogen-associated molecular patterns. By contrast, CRISPR/Cas9-mediated loss-of-function of DMP2 compromises ERQC, reduces PRR and NDR1 accumulation, attenuates immune signaling, and increases susceptibility to P. infestans.

Figure 3

Molecular mechanism of S. tuberosum eIF4E and Potato Virus Y (PVY) genes PI, HC-Pro, P3, CI1, CI2, VPg and their role in resistance to PVY: In the wild-type potato (left panel), infected by PVY, genes encode key viral effectors, including P1, HC-Pro, P3, CI, and VPg. VPg recruits host eIF4E to initiate translation, HC-Pro suppresses RNA interference by sequestering siRNAs, facilitating unchecked viral replication and intercellular movement via P3N-PIPO (P3) and CI (CI1, CI2). This leads to systemic infection and visible disease symptoms. In contrast, the CRISPR/Cas-edited plant (right panel) expresses the multiple targeted guide RNAs from six key genes that specifically recognize and degrade PVY RNA upon infection, preventing the synthesis of viral proteins and halting replication.

Figure 4

Molecular mechanism of GBSS1, SBE1, SBE2, SS5, GWD1, and FtsZ1 genes and their role in tuber characteristics: In wild-type potato (left panel) expressing granule-bound starch synthase 1 (GBSS1), which catalyzes the elongation of linear α-1,4-glucan chains to facilitate amylose production, while starch branching enzymes SBE1 and SBE2 introduce α-1,6 linkages to form the branched amylopectin structure. SS5 functions as a non-catalytic regulator of the granule initiation complex in amyloplasts, ensuring the spatial restriction of nucleation events and the formation of single, uniformly sized granules. GWD1 phosphorylates the C6 hydroxyl of glucans, modulating granule structure and hydration, while FtsZ1 governs plastid division and plastid size, which directly determines starch granule dimensions. CRISPR/Cas9-mediated knockout (right panel) of GBSS1 disrupts amylose synthesis, resulting in amylopectin-rich starch with altered gelatinization properties. Simultaneous targeting of SBE1 and SBE2 modifies amylopectin architecture, increasing apparent amylose content and producing starch with improved industrial utility. CRISPR/Cas9 knockout of StSS5 leads to excessive granule initiation, resulting in multiple small or compound granules and reduced starch yield. Loss of GWD1 function reduces phosphate content in starch, elevates amylose levels, and alters thermal and viscosity properties of tubers, while also delaying tuber initiation. Genome editing of FtsZ1 produces enlarged plastids (“macro-plastids”) that accumulate larger starch granules, significantly increasing final paste viscosity without negatively affecting tuber yield.

Figure 5

Molecular mechanism of the PPO, R2R3-MYB, F3H genes and their role in oxidative stress and secondary metabolism: In wild-type potato tubers (left panel), PPO enzymes encoded by the StPPO gene are produced to catalyze the oxidation of chlorogenic acid to o-quinones upon tissue damage. These reactive intermediates polymerize into melanins, resulting in visible tissue browning and reduced tuber quality. Concurrently, two tandem R2R3-MYB transcription factors regulate the anthocyanin biosynthetic pathway by binding to the promoters of key structural genes (DFR, ANS, UFGT) and recruiting bHLH and WDR cofactors to form the MBW complex, promoting transcription and anthocyanin accumulation in the tuber flesh. F3H catalyzes an essential early step in this pathway by converting flavanones to dihydroflavonols, enabling flux toward anthocyanin biosynthesis and contributing to red and purple pigmentation. CRISPR/Cas9-mediated knockout of StPPO genes (right panel) disrupts PPO activity, preventing quinone formation and subsequent melanin production, thereby reducing tissue browning. Simultaneously, knockout of both tandem R2R3-MYB genes abolishes MBW complex assembly and downstream transcriptional activation of anthocyanin pathway genes. As a result, anthocyanin synthesis is silenced, leading to unpigmented tuber flesh. Complete CRISPR/Cas9 knockout of all F3H alleles likewise terminates anthocyanin biosynthesis by blocking dihydroflavonol production, leading to stable, multigenerational tubers with yellow, unpigmented flesh, while preserving yield and general performance.

Figure 6

Molecular mechanisms of SN2, SP6A, CDF1 genes and their role in the regulation of potato tuberization. In wild-type potato (left panel), SN2 functions as a positive regulator of abscisic acid (ABA) signaling by upregulating the ABA receptor StPYL1 and repressing PP2C, which in turn, activates SnRK2.2/2.3/2.6 kinases and enhances ABI5-mediated transcription, promoting tuber initiation. SP6A encodes a mobile FT-like protein that integrates H₂O₂ signaling with photoperiod and sucrose-responsive pathways. H₂O₂ accumulation induces SP6A expression, repressing StCO, and GA biosynthesis (GA20ox1), while activating StBEL5, StCDPK1, POTH1, and StRboh to drive stolon swelling and tuber formation. CDF1, under short-day conditions, is rhythmically expressed from a 288 bp light- and clock-responsive promoter and represses StCO, thereby derepressing SP6A and activating the tuberization program. Under long-day conditions, CDF1 is destabilized by StFKF1 and StGI, preventing premature tuber formation. CRISPR/Cas9-mediated knockout of StSN2 (right panel) diminishes ABA signal amplification, suppressing ABI5 activation and leading to reduced tuber formation. Disruption of SP6A abolishes H₂O₂ responsiveness, silencing downstream signaling and inhibiting tuber induction. Targeted deletion of cis-elements within the CDF1 promoter reduces its photoperiod-regulated expression amplitude, delaying tuber initiation by ~5–6 days and moderately reducing plant biomass, while maintaining its rhythmic expression pattern.

Figure 7

Molecular mechanism of VInv, AS1, SSR2 genes and their role in tuber characteristics: In wild-type potato (left panel) expressing VInv, which hydrolyzes sucrose to glucose and fructose during cold storage, leading to cold-induced sweetening (CIS) and, upon frying, increased acrylamide formation via Maillard reactions. At the same time, AS1 catalyzes the biosynthesis of asparagine, a key acrylamide precursor. SSR2 encodes the sterol side-chain reductase 2 enzyme that catalyzes the formation of cholesterol precursors for steroidal glycoalkaloid (SGA) biosynthesis. Its activity determines the metabolic flux toward α-solanine and α-chaconine, major toxic SGAs that must be tightly regulated due to food safety concerns. CRISPR/Cas9-mediated knockouts of VInv and AS1 (right panel) significantly reduce sugar and free asparagine levels, respectively, mitigating browning and acrylamide accumulation during processing. CRISPR/Cas9-mediated disruption of SSR2 dramatically reduces total SGA content in tuber tissues, highlighting its utility as a target gene for minimizing glycoalkaloid toxicity.