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Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition
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Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Response to Abiotic Stress and Climate Change".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 11586

Special Issue Editor

Prof. Dr. Zhaoshi Xu

E-Mail Website
Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China
Interests: drought; salt; heat; fusarium crown rot (FCR); regulation network; wheat; soybean
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due in part to climate change and increasing water scarcity, drought, heat, and salt, dry-hot winds pose a substantial threat to agriculture worldwide, especially to the productivity of field crops. The time of onset, duration and intensity of drought stress can affect crop production to different degrees, and drought during the reproductive period can directly lead to losses of over 50% in average yield. Therefore, improving the abiotic stress tolerance of crops is of great importance.

With the advance in high-throughput sequencing technologies and release of crop reference genomes, the isolation of multiple genes and analysis of gene regulation networks has rapidly expanded in recent years. Genome information is laying the foundation for precision genome editing, ushering in a new era of soybean molecular breeding. This Special Issue will highlight abiotic stress responses, genomic research, gene–abiotic stress interactions, gene regulation mechanisms, and stress signal transduction.

Prof. Dr. Zhaoshi Xu
Guest Editor

Manuscript Submission Information

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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 response
  • gene function
  • gene regulation
  • stress signal transduction
  • stress tolerance
  • tolerant mechanism
  • genomic research
  • gene editing
  • yield

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Related Special Issue

Published Papers (10 papers)

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Research

14 pages, 2077 KiB  
Article
Winter Wheat Vernalization Alleles and Freezing Tolerance at the Seedling and Jointing Stages
by Fangfang Liu, Wenxin Cao, Qiqi Zhang, Yao Li, Heng Zhou and Yingxiu Wan
Plants 2025, 14(9), 1350; https://doi.org/10.3390/plants14091350 - 30 Apr 2025
Viewed by 339
Abstract
This study explores the relationship between allelic variation of the vernalization genes (VRN) and the freezing tolerance at the seedling and jointing stages of winter wheat growth. It provides a basis for molecular marker development for freezing tolerance breeding of winter [...] Read more.
This study explores the relationship between allelic variation of the vernalization genes (VRN) and the freezing tolerance at the seedling and jointing stages of winter wheat growth. It provides a basis for molecular marker development for freezing tolerance breeding of winter wheat. A total of 435 wheat accessions were used to identify and evaluate the freezing tolerance at the seedling stage using field tests, while 192 wheat accessions were used to evaluate the freezing tolerance at the jointing stage in climate chamber tests. The VRN genes of the wheat accessions were detected using allele-specific markers of the VRN-A1, VRN-B1, VRN-D1 and VRN-B3 loci, and the relationship between VRN genotype and freezing tolerance at the two developmental stages was tested. There were significant differences in freezing tolerance between the wheat accessions. Assessing the freezing tolerance of 52 wheat accessions at both the seedling and jointing stages revealed no significant correlation between tolerance at these two stages. The genotypic analysis found that Vrn-D1 was the most frequent dominant allele in winter wheat, while no accession contained the dominant alleles Vrn-A1 and Vrn-B3. Notably, freezing tolerance showed stage-specific genetic regulation; seedling-stage freezing tolerance strongly correlated with vernalization gene allelic combinations (p < 0.05), whereas jointing-stage freezing tolerance exhibited no such association. The presence of all recessive alleles vrn-A1, vrn-B1, vrn-D1 and vrn-B3 was required for strong seedling-stage freezing tolerance. The VRN-D1 marker was effective for screening freezing tolerance materials under the premise that vrn-A1 and vrn-B1 alleles are recessive at winter wheat seedling stage. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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18 pages, 30114 KiB  
Article
Genome-Wide Identification of ATL Gene Family in Wheat and Their Expression Analysis in Response to Salt Stress
by Xuqing Li, Shuotong Liu and Pei Yu
Plants 2025, 14(9), 1306; https://doi.org/10.3390/plants14091306 - 25 Apr 2025
Viewed by 451
Abstract
Wheat (Triticum aestivum) is one of the most important cereal crops globally, with significant economic value. The Arabidopsis Tóxicos en Levadura (ATL) gene family, which comprises members of ubiquitin ligase enzymes (E3s), functions in substrate protein tagging during ubiquitin-mediated [...] Read more.
Wheat (Triticum aestivum) is one of the most important cereal crops globally, with significant economic value. The Arabidopsis Tóxicos en Levadura (ATL) gene family, which comprises members of ubiquitin ligase enzymes (E3s), functions in substrate protein tagging during ubiquitin-mediated protein modification. Recent studies have demonstrated its involvement in stress responses. However, the ATL gene family in wheat remains poorly characterized. This study aimed to identify the members of the ATL gene family in wheat and investigate their roles under salt stress. We identified 334 TaATL genes in the wheat genome, all of which contain either RING-H2, RING U-box, or RAD18 superfamily domains, exhibiting a remarkably low proportion of intron-containing genes. The Ka/Ks (non-synonymous to synonymous substitution rate) analysis and cis-acting element analysis of the TaATL gene family indicate that its sequences are highly conserved and functionally constrained, suggesting that it may participate in abiotic stress responses through the ABA, MeJA, and MYB signaling pathways. Both RNA-seq analysis and RT-qPCR data demonstrated that the expression levels of the TaATL gene family were significantly upregulated under stress conditions, indicating their crucial roles in stress responses. This study demonstrates that the targeted regulation of stress-responsive signaling pathways mediated by superior TaATL gene family members can effectively enhance wheat salt tolerance, thereby providing a viable strategy for the development of high-yielding cultivars adapted to saline agricultural ecosystems. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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19 pages, 10380 KiB  
Article
Identification and Characterization of SQUAMOSA Promoter Binding Protein-like Transcription Factor Family Members in Zanthoxylum bungeanum and Their Expression Profiles in Response to Abiotic Stresses
by Shengshu Wang, Weiming Hu, Xueli Zhang, Yulin Liu and Fen Liu
Plants 2025, 14(4), 520; https://doi.org/10.3390/plants14040520 - 8 Feb 2025
Viewed by 596
Abstract
Plant-specific transcription factors known as SQUAMOSA promoter binding protein-like (SPL) genes are essential for development, growth, and abiotic stress responses. While the SPL gene family has been extensively studied in various plant species, a systematic characterization in Zanthoxylum bungeanum (Zb [...] Read more.
Plant-specific transcription factors known as SQUAMOSA promoter binding protein-like (SPL) genes are essential for development, growth, and abiotic stress responses. While the SPL gene family has been extensively studied in various plant species, a systematic characterization in Zanthoxylum bungeanum (Zb) is lacking. This study used transcriptomic and bioinformatics data to conduct a thorough genomic identification and expression investigation of the ZbSPL gene family. Eight subfamilies including 73 ZbSPL members were identified, most of which are predicted to be localized in the nucleus. Ka/Ks ratio analysis indicates that most ZbSPL genes have undergone purifying selection. According to evolutionary research, segmental duplication is a major factor in the amplification of the ZbSPL gene family. Gene structures, conserved motifs, and domains were found to be highly conserved among paralogs. Cis-element research revealed that ZbSPLs may be implicated in hormone and abiotic stress responses. Codon usage pattern analysis showed that the ZbSPL gene family was more inclined to A/T base endings; the higher the A/T content, the stronger the preference of the codons; and the use pattern was mainly affected by natural selection. Additionally, 36 ZbSPLs were found to be potential targets of miR156. RNA-seq demonstrated that SPL genes in Zb are differentially expressed in response to distinct abiotic stressors. Two ZbSPL genes (ZbSPL10 and ZbSPL17) were implicated in the response to salt stress, while four ZbSPL genes (ZbSPL06, ZbSPL43, ZbSPL60, and ZbSPL61) showed response to drought stress, based on a qRT-PCR investigation of the ZbSPL genes under various abiotic stress conditions. This study will help us gain a deeper understanding of the functions of ZbSPLs and lay a genetic foundation for future breeding of high-quality, highly abiotic resistant varieties of Z. bungeanum. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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15 pages, 4295 KiB  
Article
Long-Term Salinity-Responsive Transcriptome in Advanced Breeding Lines of Tomato
by Monther T. Sadder, Ahmad Abdelrahim Mohamed Ali, Abdullah A. Alsadon and Mahmoud A. Wahb-Allah
Plants 2025, 14(1), 100; https://doi.org/10.3390/plants14010100 - 1 Jan 2025
Viewed by 1029
Abstract
Soil salinity and the scarcity of freshwater resources are two of the most common environmental constraints that negatively affect plant growth and productivity worldwide. The tomato (Solanum lycopersicum Mill.) plant is moderately sensitive to salinity. The identification of salinity-responsive genes in tomato [...] Read more.
Soil salinity and the scarcity of freshwater resources are two of the most common environmental constraints that negatively affect plant growth and productivity worldwide. The tomato (Solanum lycopersicum Mill.) plant is moderately sensitive to salinity. The identification of salinity-responsive genes in tomato that control long-term salt tolerance could provide important guidelines for its breeding programs and genetic engineering. In this study, a holistic approach of RNA sequencing combined with measurements of physiological and agronomic traits were applied in two advanced tomato breeding lines (susceptible L46 and tolerant L56) under long-term salinity stress (9.6 dS m−1). Genotype L56 showed the up-regulation of known and novel differentially expressed genes (DEGs) that aid in the salinity tolerance, which was supported by a high salt tolerance index (81%). Genotype L46 showed both similar and different gene families of DEGs. For example, 22 paralogs of CBL-interacting kinase genes were more up-regulated in L56 than in L45. In addition, L56 deployed more SALT OVERLY SENSITIVE paralogs than L45. However, both genotypes showed the up-regulation of ROS-detoxifying enzymes and ROS-scavenging proteins under salinity stress. Therefore, L56 was more effective in conveying the stress message downstream along all available regulatory pathways. The salt-tolerant genotype L56 is genetically robust, as it shows an enhanced expression of a complete network of salt-responsive genes in response to saline conditions. In contrast, the salt-susceptible genotype L46 shows some potential genetic background. Both genotypes have great potential in future breeding programs. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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14 pages, 2971 KiB  
Article
Identification of ZmSNAC06, a Maize NAC Family Transcription Factor with Multiple Transcripts Conferring Drought Tolerance in Arabidopsis
by Fei Wang, Yong Chen, Ruisi Yang, Ping Luo, Houwen Wang, Runze Zhang, Wenzhe Li, Ke Yang, Xinlong Xu, Zhuanfang Hao and Xinhai Li
Plants 2025, 14(1), 12; https://doi.org/10.3390/plants14010012 - 24 Dec 2024
Cited by 1 | Viewed by 730
Abstract
Drought is one of the most serious environmental stresses affecting crop production. NAC transcription factors play a crucial role in responding to various abiotic stresses in plants. Here, we identified a maize NAC transcription factor, ZmSNAC06, between drought-tolerant and drought-sensitive inbred lines [...] Read more.
Drought is one of the most serious environmental stresses affecting crop production. NAC transcription factors play a crucial role in responding to various abiotic stresses in plants. Here, we identified a maize NAC transcription factor, ZmSNAC06, between drought-tolerant and drought-sensitive inbred lines through RNA-seq analysis and characterized its function in Arabidopsis. ZmSNAC06 had five transcripts, of which ZmSNAC06-T02 had a typical NAC domain, while ZmSNAC06-P02 was localized in the nucleus of maize protoplasts and had transactivation activity in yeasts. The expression of ZmSNAC06 in maize was induced by drought. The overexpression of ZmSNAC06-T02 in Arabidopsis resulted in hypersensitivity to abscisic acid (ABA) at the germination stage, and overexpression lines exhibited higher survival rates and higher antioxidant enzyme activities compared with the wild-type under drought stress. These results suggest that ZmSNAC06 acts as a positive regulator in drought tolerance and may be used to improve drought tolerance in crops. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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17 pages, 3100 KiB  
Article
Genome-Wide Identification of the GPAT Family in Medicago sativa L. and Expression Profiling Under Abiotic Stress
by Jianzhi Ma, Mingyang Du, Huiyan Xiong and Ruijun Duan
Plants 2024, 13(23), 3392; https://doi.org/10.3390/plants13233392 - 3 Dec 2024
Viewed by 1182
Abstract
Glycerol-3-phosphate acyltransferase (GPAT), as a rate-limiting enzyme engaged in lipid synthesis pathways, exerts an important role in plant growth and development as well as environmental adaptation throughout diverse growth stages. Alfalfa (Medicago sativa L.) is one of the most significant leguminous forages [...] Read more.
Glycerol-3-phosphate acyltransferase (GPAT), as a rate-limiting enzyme engaged in lipid synthesis pathways, exerts an important role in plant growth and development as well as environmental adaptation throughout diverse growth stages. Alfalfa (Medicago sativa L.) is one of the most significant leguminous forages globally; however, its growth process is frequently exposed to environmental stress, giving rise to issues such as impeded growth and decreased yield. At present, the comprehension of the GPAT genes in alfalfa and their reactions to abiotic stresses is conspicuously deficient. This study identified 15 GPATs from the genome of “Zhongmu No. 1” alfalfa, which were phylogenetically categorized into three major groups (Groups I ~ III). Furthermore, Group III is further subdivided into three distinct subgroups. MsGPATs belonging to the same subfamily exhibited similar protein conserved motifs and gene structural characteristics, in which groups with simple conserved motifs had more complex gene structures. A multitude of regulatory cis-elements pertinent to hormones and responses to environmental stress were detected in their promoter regions. In addition, a spatial–temporal expression analysis showed that MsGPATs have significant tissue specificity. Furthermore, the transcriptomic analysis of ABA treatment and the qRT-PCR results under drought, salt, and cold stress demonstrated that the majority of MsGPATs respond to abiotic stress with pronounced timely characteristics. It was also ascertained that these GPAT genes might assume a crucial role in salt and drought stress. This research can further constitute a fundamental basis for the exploration of the alfalfa GPAT family, the screening of key GPATs, and the investigation of their functionalities. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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22 pages, 5921 KiB  
Article
Genome-Wide Identification of PR10 Family Members in Durum Wheat: Expression Profile and In Vitro Analyses of TdPR10.1 in Response to Various Stress Conditions
by Emna Khanfir, Ikram Zribi, Hanen Dhouib, Mouna Ghorbel, Karama Hamdi, Olfa Jrad, Inès Yacoubi and Faiçal Brini
Plants 2024, 13(22), 3128; https://doi.org/10.3390/plants13223128 - 7 Nov 2024
Viewed by 1340
Abstract
The functional characterization of PR10 proteins has been extensively studied in many plant species. However, little is known about the role of TdPR10 in the response of durum wheat (Triticum durum Desf.) to stress. In this study, we identified members of the [...] Read more.
The functional characterization of PR10 proteins has been extensively studied in many plant species. However, little is known about the role of TdPR10 in the response of durum wheat (Triticum durum Desf.) to stress. In this study, we identified members of the T. durum PR10 family, which are divided into three major subfamilies based on phylogenetic analyses. The analysis revealed that tandem duplication was the primary driver of the expansion of the T. durum PR10 gene family. Additionally, gene structure and motif analyses showed that PR10 family genes were relatively conserved during evolution. We also identified several cis-regulatory elements in the TdPR10 promoter regions related not only to abiotic and biotic stress but also to phytohormonal responses. In response to abiotic stresses and phytohormones, several TdPR10 genes were highly expressed in the leaves and roots of durum wheat. Moreover, TdPR10.1 family members improve RNase activity, increase LDH protective activity under abiotic stress conditions, and ensure resistance to fungi in vitro. Collectively, these findings provide a basis for further functional studies of TdPR10 genes, which could be leveraged to enhance stress tolerance in durum wheat. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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14 pages, 6553 KiB  
Article
GmTRAB1, a Basic Leucine Zipper Transcription Factor, Positively Regulates Drought Tolerance in Soybean (Glycine max. L)
by Hui Li, Qiu-Yu Zhang, Ping Xu, Xiao-Hua Wang, Sheng-Jie Dai, Zhen-Ning Liu, Meng Xu, Xue Cao and Xiao-Yu Cui
Plants 2024, 13(21), 3104; https://doi.org/10.3390/plants13213104 - 4 Nov 2024
Cited by 3 | Viewed by 1276
Abstract
The basic leucine zipper (bZIP) transcription factors play crucial roles in plant resistance to environmental challenges, but the biological functions of soybean bZIP members are still unclear. In this study, a drought-related soybean bZIP gene, GmTRAB1, was analyzed. The transcript of GmTRAB1 [...] Read more.
The basic leucine zipper (bZIP) transcription factors play crucial roles in plant resistance to environmental challenges, but the biological functions of soybean bZIP members are still unclear. In this study, a drought-related soybean bZIP gene, GmTRAB1, was analyzed. The transcript of GmTRAB1 was upregulated under drought, ABA, and oxidative stresses. Overexpression of GmTRAB1 improved the osmotic stress tolerance of transgenic Arabidopsis and soybean hairy roots associated with increased proline content and activity of antioxidant enzymes and reduced accumulations of malonaldehyde and reactive oxide species. However, RNA interference silencing of GmTRAB1 in the soybean hairy roots improved drought sensitivity. Furthermore, GmTRAB1 increased the sensitivity of transgenic plants to ABA and participated in modulating ABA-regulated stomatal closure upon drought stress. In addition, GmTRAB1 stimulated the transcript accumulation of drought-, ABA-, and antioxidant-related genes to respond to drought. Collectively, this research will contribute to understanding the molecular mechanisms of bZIP transcription factors in soybean’s resistance to drought. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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20 pages, 3338 KiB  
Article
Enhancing Coleoptile Length of Rice Seeds under Submergence through NAL11 Knockout
by Zhe Zhao, Yuelan Xie, Mengqing Tian, Jinzhao Liu, Chun Chen, Jiyong Zhou, Tao Guo and Wuming Xiao
Plants 2024, 13(18), 2593; https://doi.org/10.3390/plants13182593 - 17 Sep 2024
Cited by 1 | Viewed by 1572
Abstract
Submergence stress challenges direct seeding in rice cultivation. In this study, we identified a heat shock protein, NAL11, with a DnaJ domain, which can regulate the length of rice coleoptiles under flooded conditions. Through bioinformatics analyses, we identified cis-regulatory elements in [...] Read more.
Submergence stress challenges direct seeding in rice cultivation. In this study, we identified a heat shock protein, NAL11, with a DnaJ domain, which can regulate the length of rice coleoptiles under flooded conditions. Through bioinformatics analyses, we identified cis-regulatory elements in its promoter, making it responsive to abiotic stresses, such as hypoxia or anoxia. Expression of NAL11 was higher in the basal regions of shoots and coleoptiles during flooding. NAL11 knockout triggered the rapid accumulation of abscisic acid (ABA) and reduction of Gibberellin (GA), stimulating rice coleoptile elongation and contributes to flooding stress management. In addition, NAL11 mutants were found to be more sensitive to ABA treatments. Such knockout lines exhibited enhanced cell elongation for coleoptile extension. Quantitative RT-PCR analysis revealed that NAL11 mediated the gluconeogenic pathway, essential for the energy needed in cell expansion. Furthermore, NAL11 mutants reduced the accumulation of reactive oxygen species (ROS) and malondialdehyde under submerged stress, attributed to an improved antioxidant enzyme system compared to the wild-type. In conclusion, our findings underscore the pivotal role of NAL11 knockout in enhancing the tolerance of rice to submergence stress by elucidating its mechanisms. This insight offers a new strategy for improving resilience against flooding in rice cultivation. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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20 pages, 4756 KiB  
Article
The Physiological and Molecular Mechanisms of Exogenous Melatonin Promote the Seed Germination of Maize (Zea mays L.) under Salt Stress
by Jiajie Wang, Di Yan, Rui Liu, Ting Wang, Yijia Lian, Zhenzong Lu, Yue Hong, Ye Wang and Runzhi Li
Plants 2024, 13(15), 2142; https://doi.org/10.3390/plants13152142 - 2 Aug 2024
Cited by 10 | Viewed by 2355
Abstract
Salt stress caused by high concentrations of Na+ and Cl- in soil is one of the most important abiotic stresses in agricultural production, which seriously affects grain yield. The alleviation of salt stress through the application of exogenous substances is important [...] Read more.
Salt stress caused by high concentrations of Na+ and Cl- in soil is one of the most important abiotic stresses in agricultural production, which seriously affects grain yield. The alleviation of salt stress through the application of exogenous substances is important for grain production. Melatonin (MT, N-acetyl-5-methoxytryptamine) is an indole-like small molecule that can effectively alleviate the damage caused by adversity stress on crops. Current studies have mainly focused on the effects of MT on the physiology and biochemistry of crops at the seedling stage, with fewer studies on the gene regulatory mechanisms of crops at the germination stage. The aim of this study was to explain the mechanism of MT-induced salt tolerance at physiological, biochemical, and molecular levels and to provide a theoretical basis for the resolution of MT-mediated regulatory mechanisms of plant adaptation to salt stress. In this study, we investigated the germination, physiology, and transcript levels of maize seeds, analyzed the relevant differentially expressed genes (DEGs), and examined salt tolerance-related pathways. The results showed that MT could increase the seed germination rate by 14.28–19.04%, improve seed antioxidant enzyme activities (average increase of 11.61%), and reduce reactive oxygen species accumulation and membrane oxidative damage. In addition, MT was involved in regulating the changes of endogenous hormones during the germination of maize seeds under salt stress. Transcriptome results showed that MT affected the activity of antioxidant enzymes, response to stress, and seed germination-related genes in maize seeds under salt stress and regulated the expression of genes related to starch and sucrose metabolism and phytohormone signal transduction pathways. Taken together, the results indicate that exogenous MT can affect the expression of stress response-related genes in salt-stressed maize seeds, enhance the antioxidant capacity of the seeds, reduce the damage induced by salt stress, and thus promote the germination of maize seeds under salt stress. The results provide a theoretical basis for the MT-mediated regulatory mechanism of plant adaptation to salt stress and screen potential candidate genes for molecular breeding of salt-tolerant maize. Full article
(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—2nd Edition)
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