Strategies to develop climate-resilient chili peppers: transcription factor optimization through genome editing

Abstract

Chili peppers (Capsicum spp.), a globally significant crop revered for their nutritional, economic, and cultural importance, are increasingly imperiled by the converging burdens of climate-induced abiotic stresses, including drought, heat, and salinity, and relentless biotic assaults from pathogens and insect herbivores. These overlapping stressors not only destabilize yield but also compromise the metabolic intricacy responsible for the accumulation of health-promoting secondary metabolites. Although Capsicum exhibits remarkable genetic and phytochemical diversity, the integrated transcriptional, metabolic, and epigenetic frameworks that underpin its stress resilience remain poorly delineated. This review synthesizes recent advances in decoding core transcription factor families, such as CaNAC, CaWRKY, and CaMYB, that serve as pivotal regulators of osmotic adjustment, reactive oxygen species detoxification, hormonal crosstalk, and secondary metabolite biosynthesis under stress conditions. We further highlight how multi-omics-guided gene discovery, when paired with CRISPR/Cas-mediated genome editing, enables precise reprogramming of key regulatory loci to enhance adaptive responses. Emerging innovations, including base editing, prime editing, and novel nucleases like Cas12a and Cas13d, are expanding the functional genome-editing landscape, while the integration of morphogenic regulators and genotype-independent transformation platforms is beginning to circumvent long-standing obstacles in Capsicum genetic engineering. Lastly, we propose a transformative framework that converges transcription factor modulation, multi-omics strategies, precision phenotyping, and next-generation genome editing to accelerate the development of climate-resilient Capsicum cultivars with optimized metabolic traits. This strategic convergence of molecular insight and biotechnological innovation offers a robust foundation for building next-generation chili pepper varieties capable of withstanding intensifying environmental and pathogenic pressures, ultimately safeguarding yield, nutritional quality, and agricultural sustainability in the face of global climate change.

Keywords: Capsicum stress tolerance; CRISPR/Cas9; Genome editing; Multi-omics; Transcription factors.

Fig. 1

Transcription factor engineering and genome editing strategies for developing climate-resilient chili plants. A Chili peppers (Capsicum spp.) are routinely challenged by an array of biotic (pathogens, insects, and herbivores) and abiotic (heat, cold, flooding, drought, and imbalance of nutrients or salts) stresses that threaten their growth and productivity. Despite these adversities, chili peppers deploy intricate molecular networks orchestrated by signaling cascades to mount robust stress responses. B Stress resilience begins with the detection of external signals by receptors or sensors located on the cell wall or plasma membrane. These sensors translate external stimuli into intracellular signals, initiating a cascade of events that amplify and relay the signal internally. This process often engages reactive oxygen species (ROS), calcium ions (Ca²⁺), and phytohormones such as abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and ethylene (ETH), which serve as secondary messengers. Signal transduction pathways are further modulated by protein kinases (PKs) and phosphatases (PPPs), with two central cascades—the mitogen-activated protein kinase (MAPK) and calcium-dependent protein kinase (CDPK) pathways—playing pivotal roles in stress signaling. These cascades ultimately converge on transcription factors (TFs), the master regulators of gene expression. Activated TFs bind to cis-regulatory elements (CREs) within promoter regions of stress-responsive genes, driving transcriptional reprogramming. Key TF families such as CabZIP, CaMYB, CaNAC, CaWRKY, and CaDREB coordinate stress adaptation by modulating genes involved in osmotic balance, ROS detoxification, and other protective mechanisms. C This molecular choreography culminates in the expression of stress-resilient phenotypes, bolstering the plant’s capacity to withstand environmental pressures. Through these transcriptional signaling networks, coupled with emerging dCas9-based regulatory systems such as CRISPRko (knock out), CRISPRi (interference), and CRISRPa (activation), chili peppers exemplify the remarkable plasticity of plant stress adaptation, underscoring the potential for biotechnological innovations to further enhance resilience. PM plasma membrane, TFs Transcription factors, CRE cis-regulatory element, Pol II RNA polymerase II, bZIP Basic Leucine Zipper, MYB myeloblastosis viral oncogene homolog, NAC/WRKY NAM, ATAF1/2, and CUC2, DREB Dehydration responsive element-binding, CRISPR/Cas Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein

Fig. 2

Schematic illustration for engineering climate-smart and metabolite-rich Capsicum. A, B The Cultivated Capsicum species exhibit extensive morphologic and agronomic diversity, primarily in Central and South America (Liu et al. 2023). The landraces are great sources for conservation and breeding programs. Future Capsicum improvement requires a comprehensive understanding of its biology, extending beyond individual traits to a system-level perspective. C The genomic and phenomics selection process will provide the foundation for molecular design, D whereas in-silico approaches facilitate the application of stress-resilient alleles and genes, aiding in the dissection of gene networks that regulate responses to diverse environmental factors, including biotic and abiotic stresses, and metabolite content of chili cultivars. E Targeting transcription factors (TFs) is one of the key strategies for climate-smart and nutrient-rich chili peppers. Rewiring of TFs also contributes to the modulation of major secondary metabolites in Capsicum. F CRISPR-mediated modification of TFs will enable the precise engineering of these traits at the genetic and molecular level. G The TFs involved in the capsaicinoids biosynthesis pathway (Islam et al. 2023b) have great potential for future CRISPR targets for H capsaicin improvement. Pinkish-colored baubles represent various transcription factors known to regulate genes involved in capsaicin biosynthesis and accumulation. Dashed magenta arrows indicate the enzymatic steps of shikimate and fatty acid metabolic pathways. PAL- Phenylalanine ammonia lyase, C4H-Cinnamate 4-hydroxylase, 4CL−4-Coumaroyl-CoA ligase, HCT Hydroxycinnamoyl transferase, COMT-Caffeoyl-CoA O-methyltransferase, pAMT-Putative aminotransferase, and CS/PUN1-Capsaicin Synthase/Pun1 (AT3) Acyl transferase). Transcription factor genes such as ERF Ethylene Responsive Factor, MYB-v-Myb myeloblastosis viral oncogene homolog, bHLH-basic helix-loop-helix, BCAT-Branched-chain amino acid transferase, BCKDH-Branched-chain α-ketoacid dehydrogenase, ACS-Acyl-CoA synthetase, KAS-Ketoacyl-ACP Synthase, ACL-Acyl carrier protein, FAT-Fatty acid thioesterase