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Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops,...
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Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Crop Physiology and Crop Production".

Deadline for manuscript submissions: 20 October 2025 | Viewed by 6688

Special Issue Editors

Dr. Peng Zhang

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou 310006, China
Interests: abiotic stress tolerance; GWAS; rice molecular breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Hanhua Tong

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou 310006, China
Interests: crop abiotic stress resistance; crop nutrient utilization; rice breeding
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Dezhi Wu

E-Mail Website
Guest Editor
College of Agronomy, Hunan Agricultural University, Changsha 410128, China
Interests: crop biotechnology; genomics; molecular mechanism of crop salt tolerance; ion transporters
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Abiotic stress caused by either natural or human activities has become a great threat to sustainable agricultural production in the world, such as drought, salinity, high or low temperature, nutrient deficiency, and heavy metal stresses. It is a big challenge to produce enough crop food to feed the growing global population. Abiotic stresses seriously affect crop growth and development, eventually leading to yield loss. Under abiotic stress condition, crops may suffer from osmotic and oxidative stress, photosynthetic and metabolic damage, nutrient imbalance, and ion toxicity. To deal with these stresses, crops have developed a series of tolerance mechanisms, including osmotic adjustment through compatible solutes in the cytoplasm, reactive oxygen species (ROS) scavenging system through anti-oxidative enzymes, and nutrient homeostasis through membrane channels and transporters. However, the progress in developing tolerant crops is significantly hampered by the complexity of the physiological and genetic mechanisms of abiotic stress tolerance.

Dr. Peng Zhang
Dr. Hanhua Tong
Prof. Dr. Dezhi Wu
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • abiotic stress
  • crop physiology
  • gene mining
  • genetic regulation
  • metabolomics
  • molecular response
  • proteomics
  • transcriptomics

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Related Special Issues

Published Papers (7 papers)

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Research

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16 pages, 3903 KB  
Article
Identification of Salt Tolerance-Related NAC Genes in Wheat Roots Based on RNA-Seq and Association Analysis
by Lei Zhang, Aili Wei, Weiwei Wang, Xueqi Zhang, Zhiyong Zhao and Linyi Qiao
Plants 2025, 14(15), 2318; https://doi.org/10.3390/plants14152318 - 27 Jul 2025
Viewed by 470
Abstract
Excavating new salt tolerance genes and utilizing them to improve salt-tolerant wheat varieties is an effective way to utilize salinized soil. The NAC gene family plays an important role in plant response to salt stress. In this study, 446 NAC sequences were isolated [...] Read more.
Excavating new salt tolerance genes and utilizing them to improve salt-tolerant wheat varieties is an effective way to utilize salinized soil. The NAC gene family plays an important role in plant response to salt stress. In this study, 446 NAC sequences were isolated from the whole genome of common wheat and classified into 118 members based on subgenome homology, named TaNAC1 to TaNAC118. Transcriptome analysis of salt-tolerant wheat breeding line CH7034 roots revealed that 144 of the 446 TaNAC genes showed significant changes in expression levels at least two time points after NaCl treatment. These differentially expressed TaNACs were divided into four groups, and Group 4, containing the largest number of 78 genes, exhibited a successive upregulation trend after salt treatment. Single nucleotide polymorphisms (SNPs) of the TaNAC gene family in 114 wheat germplasms were retrieved from the public database and were subjected to further association analysis with the relative salt-injury rates (RSIRs) of six root phenotypes, and then 20 SNPs distributed on chromosomes 1B, 2B, 2D, 3B, 3D, 5B, 5D, and 7A were correlated with phenotypes involving salt tolerance (p < 0.0001). Combining the results of RT-qPCR and association analysis, we further selected three NAC genes from Group 4 as candidate genes that related to salt tolerance, including TaNAC26-D3.2, TaNAC33-B, and TaNAC40-B. Compared with the wild type, the roots of the tanac26-d3.2 mutant showed shorter length, less volume, and reduced biomass after being subjected to salt stress. Four SNPs of TaNAC26-D3.2 formed two haplotypes, Hap1 and Hap2, and germplasms with Hap2 exhibited better salt tolerance. Snp3, in exon 3 of TaNAC26-D3.2, causing a synonymous mutation, was developed into a Kompetitive Allele-Specific PCR marker, K3, to distinguish the two haplotypes, which can be further used for wheat germplasm screening or marker-assisted breeding. This study provides new genes and molecular markers for improvement of salt tolerance in wheat. Full article
(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)
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18 pages, 2659 KB  
Article
Salt Stress Responses of Different Rice Varieties at Panicle Initiation: Agronomic Traits, Photosynthesis, and Antioxidants
by Yusheng Li, Yuxiang Xue, Zhuangzhuang Guan, Zhenhang Wang, Daijie Hou, Tingcheng Zhao, Xutong Lu, Yucheng Qi, Yanbo Hao, Jinqi Liu, Lin Li, Haider Sultan, Xiayu Guo, Zhiyong Ai and Aibin He
Plants 2025, 14(15), 2278; https://doi.org/10.3390/plants14152278 - 24 Jul 2025
Viewed by 492
Abstract
The utilization of saline–alkali land for rice cultivation is critical for global food security. However, most existing studies on rice salt tolerance focus on the seedling stage, with limited insights into tolerance mechanisms during reproductive growth, particularly at the panicle initiation stage (PI). [...] Read more.
The utilization of saline–alkali land for rice cultivation is critical for global food security. However, most existing studies on rice salt tolerance focus on the seedling stage, with limited insights into tolerance mechanisms during reproductive growth, particularly at the panicle initiation stage (PI). Leveraging precision salinity-control facilities, this study imposed four salt stress gradients (0, 3, 5, and 7‰) to dissect the differential response mechanisms of six rice varieties (YXYZ: Yuxiangyouzhan, JLY3261: Jingliangyou3261, SLY91: Shuangliangyou91, SLY138: Shuangliangyou138, HLYYHSM: Hualiangyouyuehesimiao, and SLY11:Shuangliangyou111) during PI. The results revealed that increasing salinity significantly reduced tiller number (13.14–68.04%), leaf area index (18.58–57.99%), canopy light interception rate (11.91–44.08%), and net photosynthetic rate (2.63–52.42%) (p < 0.001), accompanied by reactive oxygen species (ROS)-induced membrane lipid peroxidation. Integrative analysis of field phenotypic and physiological indices revealed distinct adaptation strategies: JLY3261 rapidly activated antioxidant enzymes under 3‰ salinity, alleviating lipid peroxidation (no significant difference in H2O2 or malondialdehyde content compared to 0‰ salinity) and maintaining tillering and aboveground biomass. SLY91 tolerated 7‰ salinity via CAT/POD-mediated lipid peroxide degradation, with H2O2 and malondialdehyde contents increasing initially but decreasing with escalating stress. These findings highlight genotype-specific antioxidant strategies underlying salt-tolerance mechanisms and the critical need for integrating phenomics–physiological assessments at reproductive stages into salt-tolerance breeding pipelines. Full article
(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)
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16 pages, 1108 KB  
Article
Effects of Modified Biochar on Growth, Yield, and Quality of Brassica chinensis L. in Cadmium Contaminated Soils
by Guojun Pan, Shufang Geng, Liangliang Wang, Jincheng Xing, Guangping Fan, Yan Gao, Xin Lu and Zhenhua Zhang
Plants 2025, 14(4), 524; https://doi.org/10.3390/plants14040524 - 8 Feb 2025
Cited by 1 | Viewed by 1233
Abstract
Cadmium (Cd) pollution in farmland soil leads to excessive Cd in vegetables, which can be transferred to humans through the food chain, posing a significant threat to human health, and requires urgent measures to combat it. Modified biochar may have the potential to [...] Read more.
Cadmium (Cd) pollution in farmland soil leads to excessive Cd in vegetables, which can be transferred to humans through the food chain, posing a significant threat to human health, and requires urgent measures to combat it. Modified biochar may have the potential to remediate Cd pollution in farmland soils. In this experiment, bulk biochar (YC) derived from reed straw or modified biochar by ball milling (Q) either alone or combined with a combination of several passivation agents {potassium hydroxide (K), attapulgite (A), calcium magnesium phosphate fertilizer (M), and polyacrylamide (P)} was applied to soils polluted with Cd, to investigate the growth, yield, and quality of pakchoi (Brassica chinensis L.). The results showed that bulk biochar (YC) provided pakchoi with plenty of nitrogen, phosphorus, and potassium, while passivation agents enhance macronutrient accumulation. Compared to YC, modified biochar improved pakchoi yields and nutritional quality. Among them, concentrations of nitrates in pakchoi significantly decreased by 51.8% and 51.0%, while vitamin C levels increased by 29.6% and 19.0%, respectively, in QKAMP and QKAM treatments. The contents of Cd in pakchoi significantly decreased by 21.6% and 18.6%, respectively, in QKAMP and QKAM treatments. The implementation of QKAMP led to the cadmium contents in edible vegetables being lower than the maximum stipulated content as defined by the national standard, but QKAM failed to accomplish it. In conclusion, QKAMP effectively reduced the bioavailability of Cd in the middle to slightly Cd-polluted alkaline soils, making it a suitable soil amendment to improve the yield and quality and mitigate Cd accumulation in vegetables. Full article
(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)
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18 pages, 7504 KB  
Article
Effects of Nitrogen Fertilizer Types and Planting Density on the Yield and Nitrogen Use Efficiency of Salt-Tolerant Rice Under Salt Stress Conditions
by Tingcheng Zhao, Jianbo Wang, Rongyi Li, Pengfei Zhang, Xiayu Guo, Yucheng Qi, Yusheng Li, Shenghai Cheng, Junchao Ji, Aibin He and Zhiyong Ai
Plants 2025, 14(4), 501; https://doi.org/10.3390/plants14040501 - 7 Feb 2025
Cited by 1 | Viewed by 1345
Abstract
Soil salinization poses a serious threat to global food security, as high Na+ contents in soils hinder nitrogen use efficiency (NUE), affecting the growth and yield of crop plants. The present study aims to explore the effects of different nitrogen fertilizer types [...] Read more.
Soil salinization poses a serious threat to global food security, as high Na+ contents in soils hinder nitrogen use efficiency (NUE), affecting the growth and yield of crop plants. The present study aims to explore the effects of different nitrogen fertilizer types viz., NO3− (N1) and NH4+ (N2) and planting densities, viz., D1: 30 × 10 cm, D2: 20 × 20 cm, and D3: 30 × 20 cm, on growth and development, nitrogen absorption and utilization, and yield formation. The salt-tolerant rice variety ‘Jingliangyou 3261’ was exposed to 0.3% salt irrigation water. Results revealed that N2 substantially improved the rice yield by increasing the number of effective panicles and the rate of grain-setting compared to N1. In addition, the N2 also increased leaf chlorophyll content, dry matter accumulation, antioxidant enzyme activity such as superoxide dismutase, peroxidase, and catalase activity and reduced the content of malondialdehyde. In comparison with N1, the N2 treatment resulted in an increase of 12.21%, 31.89%, and 37.53% in total nitrogen accumulation, nitrogen recovery efficiency (NRE), and nitrogen agronomic efficiency (NAE), respectively. This increase can be attributed to enhanced leaf nitrogen metabolic enzyme activity, including nitrate reductase and glutamine synthetase, and a more robust root system. Under N1 and N2 conditions, compared to D3, D1 resulted in an increase in the number of tillers but decreased the percentage of productive tillers, the grains per panicle, the grain-filling rate, and the thousand-grain weight, thereby reducing yield. Additionally, the D3 treatment also significantly improved NRE and NAE compared to the D1 treatment. Therefore, the rational selection of nitrogen fertilizer type (N2) and planting density (D3) is crucial for improving the yield and nitrogen use efficiency of salt-tolerant rice. This would broaden the scope of agricultural solutions for saline soils, potentially improving food security in regions where soil salinization is a widespread issue. Full article
(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)
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Review

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18 pages, 2123 KB  
Review
Epitranscriptomic Control of Drought Tolerance in Rice: The Role of RNA Methylation
by Xiaoru Fan, Yong Zhang, Pengyuan Gu and Misbah Naz
Plants 2025, 14(13), 2002; https://doi.org/10.3390/plants14132002 - 30 Jun 2025
Viewed by 610
Abstract
Drought stress is a predominant abiotic constraint adversely affecting global rice (Oryza sativa) production and threatening food security. While the transcriptional and post-transcriptional regulation of drought-responsive pathways has been widely investigated, the emerging field of epitranscriptomics, particularly RNA chemical modifications such [...] Read more.
Drought stress is a predominant abiotic constraint adversely affecting global rice (Oryza sativa) production and threatening food security. While the transcriptional and post-transcriptional regulation of drought-responsive pathways has been widely investigated, the emerging field of epitranscriptomics, particularly RNA chemical modifications such as N6-methyladenosine (m6A), adds a new dimension to gene regulation under stress. The most prevalent internal modification in eukaryotic messenger RNA influences RNA metabolism by interacting dynamically with enzymes that add, remove, or recognize the modification. Recent studies in rice reveal that m6A deposition is not static but dynamically regulated in response to water-deficit conditions, influencing transcript stability, splicing, nuclear export, and translation efficiency of key drought-responsive genes. This review critically synthesizes current findings on the distribution and functional implications of m6A and other epitranscriptomic marks (e.g., 5-methylcytosine [m5C], pseudouridine [Ψ]) in modulating rice responses to drought. We discuss the regulatory circuitry involving m6A effectors such as OsMTA, OsFIP37, and YTH domain proteins and their integration with known drought-signaling pathways including ABA and reactive oxygen species (ROS) cascades. We also highlight emerging high-resolution technologies such as m6A-seq, direct RNA sequencing, and nanopore-based detection that facilitate epitranscriptomic profiling in rice. Finally, we propose future directions for translating epitranscriptomic knowledge into crop improvement, including CRISPR/Cas-based modulation of RNA modification machinery to enhance drought tolerance. Full article
(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)
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18 pages, 2801 KB  
Review
Understanding the Brassinosteroid-Dependent Environmental Adaption in Brassicaceae Plants
by Zhenni Lu, Changrui Ma, Yuzhen Xie, Yuqing Zeng, Jiashi Peng, Dinggang Zhou and Jinfeng Wu
Plants 2025, 14(10), 1554; https://doi.org/10.3390/plants14101554 - 21 May 2025
Viewed by 818
Abstract
Plant adaptation to various stresses depends on transmitting the external stress signals into internal signals. Brassinosteroids (BRs) play pivotal roles in connecting the external and internal signals in Brassicaceae plants, particularly under abiotic stresses such as drought, cold, heat and salinity. They modulate [...] Read more.
Plant adaptation to various stresses depends on transmitting the external stress signals into internal signals. Brassinosteroids (BRs) play pivotal roles in connecting the external and internal signals in Brassicaceae plants, particularly under abiotic stresses such as drought, cold, heat and salinity. They modulate plant growth and stress responses through receptor kinase-mediated signaling pathways, which integrate with redox homeostasis, antioxidant systems and crosstalk with other phytohormones, including auxin, abscisic acid, ethylene, cytokinins, gibberellines, jasmonates and salicylic acid. BR-dependent pathways are critical for balancing stress resilience and productivity in Brassicaceae plants. In this review, we introduce BR metabolism, signaling transduction and discuss their functions in regulating growth and development processes under adverse environment in Brassicaceae plants. We also emphasize recent advances in the crosstalk among BR and other phytohormones in stresses response. Understanding the mechanisms of BR-dependent pathways offers new approaches for enhancing the adaptation under adverse conditions in Brassicaceae crops. Full article
(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)
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20 pages, 2582 KB  
Review
Recent Advances in Transcriptome Analysis Within the Realm of Low Arsenic Rice Breeding
by Guanrong Huang, Guoping Yu, Huijuan Li, Haipeng Yu, Zengying Huang, Lu Tang, Pengfei Yang, Zhengzheng Zhong, Guocheng Hu, Peng Zhang and Hanhua Tong
Plants 2025, 14(4), 606; https://doi.org/10.3390/plants14040606 - 17 Feb 2025
Viewed by 1227
Abstract
Arsenic (As), a toxic element, is widely distributed in soil and irrigation water. Rice (Oryza sativa L.), the staple food in Southern China, exhibits a greater propensity for As uptake compared to other crops. Arsenic pollution in paddy fields not only impairs [...] Read more.
Arsenic (As), a toxic element, is widely distributed in soil and irrigation water. Rice (Oryza sativa L.), the staple food in Southern China, exhibits a greater propensity for As uptake compared to other crops. Arsenic pollution in paddy fields not only impairs rice growth but also poses a serious threat to food security and human health. Nevertheless, the molecular mechanism underlying the response to As toxicity has not been completely revealed until now. Transcriptome analysis represents a powerful tool for revealing the mechanisms conferring phenotype formation and is widely employed in crop breeding. Consequently, this review focuses on the recent advances in transcriptome analysis within the realm of low As breeding in rice. It particularly highlights the applications of transcriptome analysis in identifying genes responsive to As toxicity, revealing gene interaction regulatory modules and analyzing secondary metabolite biosynthesis pathways. Furthermore, the molecular mechanisms underlying rice As tolerance are updated, and the recent outcomes in low As breeding are summarized. Finally, the challenges associated with applying transcriptome analysis to low-As breeding are deliberated upon, and future research directions are envisioned, with the aim of providing references to expedite high-yield and low-arsenic breeding in rice. Full article
(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)
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