Enhancing Crop Resilience: The Role of Plant Genetics, Transcription Factors, and Next-Generation Sequencing in Addressing Salt Stress

Abstract

Salt stress is a major abiotic stressor that limits plant growth, development, and agricultural productivity, especially in regions with high soil salinity. With the increasing salinization of soils due to climate change, developing salt-tolerant crops has become essential for ensuring food security. This review consolidates recent advances in plant genetics, transcription factors (TFs), and next-generation sequencing (NGS) technologies that are pivotal for enhancing salt stress tolerance in crops. It highlights critical genes involved in ion homeostasis, osmotic adjustment, and stress signaling pathways, which contribute to plant resilience under saline conditions. Additionally, specific TF families, such as DREB, NAC (NAM, ATAF, and CUC), and WRKY, are explored for their roles in activating salt-responsive gene networks. By leveraging NGS technologies-including genome-wide association studies (GWASs) and RNA sequencing (RNA-seq)-this review provides insights into the complex genetic basis of salt tolerance, identifying novel genes and regulatory networks that underpin adaptive responses. Emphasizing the integration of genetic tools, TF research, and NGS, this review presents a comprehensive framework for accelerating the development of salt-tolerant crops, contributing to sustainable agriculture in saline-prone areas.

Keywords: crop improvement; genetic transcription factors (TFs); next-generation sequencing (NGS); salt stress; salt tolerance.

Figure 1

Salt stress effects on the growth and development of rice and wheat plants.

Figure 2

Pathways involved in salt stress response in plants: distinct mechanisms for ionic and osmotic stress. This figure illustrates the complex network of signaling pathways activated in plants under salt stress. It highlights the key roles of signaling molecules such as calcium ions (Ca²⁺), reactive oxygen species (ROS), phospholipids, and phytohormones in regulating cellular adaptations. The figure distinguishes between ionic and osmotic stress responses, showing how plants maintain ion balance, osmotic homeostasis, and cellular integrity. It also emphasizes the involvement of cytoskeletal dynamics, cell-wall modification, metabolic adjustments, and growth regulation that, together, enhance plant salt tolerance.

Figure 3

Salinity stress signaling pathways. This figure illustrates the molecular mechanisms underlying salinity stress signaling in plants. Salt stress is initially perceived by specific receptors or sensors on the plasma membrane (Step 1), which activate intracellular signaling cascades (Step 2). These cascades involve the generation of secondary messengers, such as calcium ions (Ca²⁺), reactive oxygen species (ROS), and cyclic AMP (cAMP). These molecules play crucial roles in amplifying and transmitting the salt stress signal to downstream effectors. In the cytosol, the mitogen-activated protein kinase (MAPK) pathway and calcium-dependent protein kinase (CDPK) pathway (including other pathways) are activated. These signaling pathways facilitate the phosphorylation of key proteins and transcription factors (TFs), including WRKY, NAC, DREB, MYB, and SOS, which are responsible for regulating salt stress-inducible genes (Step 3). These TFs modulate gene expression to restore ion homeostasis, regulate osmotic balance, and initiate antioxidant responses. The right panel of the figure highlights these regulatory pathways. MAPKs primarily regulate stress-responsive gene expression, while CDPKs act as calcium sensors, linking Ca²⁺ signaling to transcriptional changes. These processes culminate in the expression of salt tolerance genes, enabling the plant to adapt to saline conditions (Step 4). This mechanism ensures physiological and biochemical adjustments to mitigate salt stress impacts.