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Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 October 2025) | Viewed by 10831

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Prof. Dr. Liezhao Liu

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College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Interests: rapeseed; stress response; agronomic traits; gene function
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Dear Colleagues,

Dear Colleagues, As climate change advances, this places a great amount of pressure on crop production. Climate change induces more frequent drought stress, high temperature, water logging, salinity, etc. With the population increasing and demand becoming greater with the development of society, it is necessary to maintain crop production sustainably, even with increasing productivity. There are different measures to alleviate environmental stresses, and the main one is to breed cultivars with the abiotic stress tolerance gene.

Our Special Issue “Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes” will address a selection of recent research topics and current review articles in the field of abiotic stress-related gene identification, cloning, function validation, etc. Abiotic stresses include drought, high temperature, water logging, salinity, and so on.

Prof. Dr. Liezhao Liu
Guest Editor

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Keywords

plant
abiotic stress
gene
identification
function

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Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes: 2nd Edition in International Journal of Molecular Sciences

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Research

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18 pages, 6544 KB

Open AccessArticle

In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd.

by Jean Carlo Paredes Malca, Michell Maheba Fuentes Apaza, María Rosario Elsa Valderrama-Valencia, Roxana Bardales Álvarez, Eloy Condori Mamani and Sandro Jhonatan Condori-Pacsi

Int. J. Mol. Sci. 2025, 26(23), 11657; https://doi.org/10.3390/ijms262311657 - 1 Dec 2025

Viewed by 1167

Abstract

Quinoa (Chenopodium quinoa Willd.), an Andean crop with exceptional nutritional value, thrives in ecosystems exposed to intense ultraviolet-B (UV-B) radiation; yet the molecular mechanisms underlying its photoreception remain largely unknown. The UV Resistance locus 8 (UVR8) protein, a member of the Regulator of Chromosome Condensation 1 (RCC1) family, is the primary UV-B photoreceptor in plants. Here, we report the first in silico characterization of the RCC1 gene family in C. quinoa, aimed at identifying and structurally analyzing UVR8 homologs. Genomic analysis uncovered 40 CqRCC1 genes, exhibiting extensive structural diversity. Phylogenetic reconstruction identified two proteins, CqRCC1_20 and CqRCC1_23, as the closest homologs of AtUVR8 from Arabidopsis thaliana. Homology modeling revealed that CqRCC1_20 maintains the canonical seven-bladed β-propeller architecture of UVR8, whereas CqRCC1_23 carries a deletion leading to a six-bladed structure. Both isoforms retain the critical tryptophan residues (W233, W285, W337) and the C-terminal Valine-Proline (VP) motif required for photoperception and Constitutive Photomorphogenic 1 (COP1) interaction. Notably, the CqRCC1_23 model predicts fewer hydrogen bonds at the dimer interface and structural alterations at key regulatory interaction sites. Collectively, these results indicate that quinoa harbors functionally conserved UVR8 isoforms with structural divergence, such as CqRCC1_23, which may influence photoreceptor stability and enable a sustained UV-B response, potentially conferring an adaptive advantage in high-radiation environments. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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17 pages, 7821 KB

Open AccessArticle

Systematic Analysis of Fertility Conversion via WGCNA Implicates a Compensatory Regulatory Network in a Reverse Thermosensitive Genic Male Sterility Line of Eggplant (Solanum melongena L.)

by Bing Li, Yongpeng Li, Peng Tian, Jingjing Zhang, Wei Liu, Xiurui Gao and Yanrong Wu

Int. J. Mol. Sci. 2025, 26(22), 10873; https://doi.org/10.3390/ijms262210873 - 9 Nov 2025

Viewed by 682

Abstract

Thermosensitive genic male sterility (TGMS) lines are vital for two-line hybrid breeding. However, the molecular mechanism in the reverse TGMS line 05ms in eggplant remains unclear. Weighted gene co-expression network analysis (WGCNA) of RNA-seq data revealed modules correlated with fertility conversion enriched in carbohydrate metabolism, lipid metabolism, and mRNA surveillance pathways. Hub genes within these modules were predominantly associated with sugar-related processes, fatty acid metabolism, and nucleotide processing. BSA-seq defined candidate genomic intervals. Integrated analysis of BSA-seq intervals and transcriptomic data identified a candidate gene, SmHTH, with consistently lower expression in 05ms compared to S63. Its homologs exhibited temperature-induced expression, possibly compensating for SmHTH deficiency under high temperatures to restore fertility. The homologs co-expressed with three transcription factors are likely intricately linked to this response. We propose a compensatory model demonstrating that low SmHTH expression at low temperatures disrupts key metabolic pathways, causing male sterility. Conversely, elevated expression of homologous genes and transcription factors (TFs) at higher temperatures compensates for the loss of SmHTH function, thereby restoring fertility. The findings of this research not only deepen the theoretical understanding of plant male sterility mechanisms but also provide valuable resources for developing stress-resilient vegetable varieties through modern breeding techniques. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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33 pages, 7500 KB

Open AccessArticle

In Silico Characterisation and Determination of Gene Expression Levels of the CPK Family Under Saline Stress Conditions in Chenopodium quinoa Willd

by Luz Lima-Huanca, Andrea Alvarez-Vasquez, María Valderrama-Valencia and Sandro Condori-Pacsi

Int. J. Mol. Sci. 2025, 26(21), 10658; https://doi.org/10.3390/ijms262110658 - 1 Nov 2025

Viewed by 1039

Abstract

Quinoa (Chenopodium quinoa Willd.) is a highly nutritious crop known for its tolerance to salt stress; however, the molecular mechanisms underlying this trait remain poorly understood. This study aims to perform the in silico characterisation of calcium-dependent protein kinase (CPK) gene family sequences and to evaluate their expression profiles under salt stress conditions. Using bioinformatics tools, CPK family gene sequences were identified and in silico-characterised, including conserved domains, cis-regulatory motifs, and physicochemical properties. Experimentally, two contrasting accessions were compared: a salt-tolerant one (UNSA_VP033) and a salt-sensitive one (UNSA_VP021). Salt tolerance indices were determined during germination, gene expression levels were quantified by RT-qPCR, and antioxidant enzyme activities, along with malondialdehyde (MDA) content, were evaluated under different NaCl concentrations. Sixteen sequences with characteristic CPK family domains were identified. Promoter analysis revealed cis-elements associated with hormonal and stress responses. Physicochemical parameters predicted proteins of 50–60 kDa with variable isoelectric points. Experimentally, UNSA_VP033 showed the significant overexpression of CqCPK12, CqCPK17, CqCPK20, and CqCPK32, correlated with the higher antioxidant activity of superoxide dismutase (SOD) and peroxidase (POD), and lower MDA levels at 200 mM NaCl. In contrast, the sensitive accession exhibited significant reductions in gene expression and antioxidant activity. In conclusion CPK genes play a key role in the salt stress response in quinoa, particularly CqCPK12, CqCPK17, CqCPK20, and CqCPK32 in the tolerant accession. These findings may contribute to the development of more salt-tolerant varieties, thereby enhancing agricultural sustainability in saline soils. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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14 pages, 6295 KB

Open AccessArticle

Anther Transcriptome Analysis of Two Heat Tolerance-Differentiated Indica Rice Restorer Lines Reveals the Importance of Non-Structural Carbohydrates and ATP in the Regulation of Heat Tolerance

by Jieqiang Zhou, Yingfeng Wang, Jiangfeng Li, Zijian Song, Yunhua Xiao, Huabing Deng, Xiong Liu, Qiuhong Chen, Wenbang Tang and Guilian Zhang

Int. J. Mol. Sci. 2025, 26(7), 3161; https://doi.org/10.3390/ijms26073161 - 29 Mar 2025

Viewed by 1110

Abstract

Screening and breeding more resistant heat stress restorer lines represent an effective approach to addressing the decline in hybrid rice seed production caused by heat stress (HS). However, the molecular mechanisms affecting the differences in the heat resistance of anthers under HS remain unclear. This study compared the gene expression patterns of two hybrid rice restorer lines with differing heat resistances under HS and discusses the mechanisms of the heat response in rice. Under heat stress, 247 DEGs were co-expressed across varieties and were involved in biological processes such as protein processing and carbon metabolism, with heat shock proteins being the most ubiquitous. Interestingly, a substantial enrichment of genes related to non-structural carbohydrates and ATP was observed among the unique DEGs in R996 and R4628. Simultaneously, the contents of non-structural carbohydrates and ATP levels in the young spikes of R996 were significantly higher than those in R4628. This suggests that starch, soluble sugars and ATP play significant roles in heat tolerance during the flowering stage of rice. Overall, this study provides novel insights into the molecular mechanisms underlying heat stress resistance in indica rice restorer lines and informs future strategies for the genetic improvement of heat tolerance in these varieties. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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15 pages, 3308 KB

Open AccessArticle

Identification and Expression Analysis of the Soybean Serine Acetyltransferase (SAT) Gene Family Under Salt Stress

by Caiyun Fan, Hui Zou, Miao Zhang, Yu Jiang, Baohui Liu, Zhihui Sun and Bohong Su

Int. J. Mol. Sci. 2025, 26(5), 1882; https://doi.org/10.3390/ijms26051882 - 22 Feb 2025

Cited by 3 | Viewed by 1478

Abstract

Serine acetyltransferase (SAT) is a critical enzyme in the sulfur-assimilation pathway of cysteine, playing an essential role in numerous physiological functions in plants, particularly in their response to environmental stresses. However, the structural characteristics of the soybean SAT gene family remain poorly understood. Members of the soybean SAT gene family were identified using the Hidden Markov Model approach. Bioinformatics tools, such as ExPASy, PlantCARE, MEME, and TBtools-II, were employed to examine the physicochemical properties, cis-regulatory elements, conserved motifs, gene structures, and chromosomal positions of the GmSAT genes. RT-qPCR was conducted to evaluate the expression profiles of GmSAT genes under NaCl-induced stress, identifying genes likely involved in the salt-stress response. A total of ten GmSAT genes were identified in the soybean genome and grouped into three subfamilies. Genes within each subfamily shared notable structural similarities and conserved motifs. Analysis of cis-regulatory elements revealed that the promoters of these genes contain several elements linked to plant growth and stress-related responses. Expression patterns of GmSAT genes varied across different soybean tissues, with GmSAT10 showing higher expression in roots, while GmSAT1 and GmSAT2 had lower expression in the same tissue. Following NaCl treatment, expression levels of seven GmSAT genes were significantly increased in the roots, indicating their potential involvement in the plant’s adaptation to salt stress. GmSAT genes appear to play crucial roles in soybean’s response to salt stress, offering insights that could aid in the development of salt-tolerant soybean varieties. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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24 pages, 3197 KB

Open AccessArticle

Integrated Physiological, Transcriptomic and Metabolomic Analyses of the Response of Rice to Aniline Toxicity

by Jingjing Wang, Ruixin Wang, Lei Liu, Wenrui Zhang, Zhonghuan Yin, Rui Guo, Dan Wang and Changhong Guo

Int. J. Mol. Sci. 2025, 26(2), 582; https://doi.org/10.3390/ijms26020582 - 11 Jan 2025

Cited by 3 | Viewed by 1811

Abstract

The accumulation of aniline in the natural environment poses a potential threat to crops, and thus, investigating the effects of aniline on plants holds practical implications for agricultural engineering and its affiliated industries. This study combined physiological, transcriptomic, and metabolomic methods to investigate the growth status and molecular-level response mechanisms of rice under stress from varying concentrations of aniline. At a concentration of 1 mg/L, aniline exhibited a slight growth-promoting effect on rice. However, higher concentrations of aniline significantly inhibited rice growth and even caused notable damage to the rice seedlings. Physiological data indicated that under aniline stress, the membrane of rice underwent oxidative damage. Furthermore, when the concentration of aniline was excessively high, the cells suffered severe damage, resulting in the inhibition of antioxidant enzyme synthesis and activity. Transcriptomic and metabolomic analyses indicated that the phenylpropanoid biosynthesis pathway became quite active under aniline stress, with alterations in various enzymes and metabolites related to lignin synthesis. In addition to the phenylpropanoid biosynthesis pathway, amino acid metabolism, lipid metabolism, and purine metabolism were also critical pathways related to rice’s response to aniline stress. Significant changes occurred in the expression levels of multiple genes (e.g., PRX, C4H, GST, and ilvH, among others) associated with functions such as antioxidant activity, membrane remodeling, signal transduction, and nitrogen supply. Similarly, notable alterations were observed in the accumulation of various metabolites (for instance, glutamic acid, phosphatidic acid, phosphatidylglycerol, and asparagine, etc.) related to these functions. Our research findings have unveiled the potential of compounds such as phenylpropanoids and amino acids in assisting rice to cope with aniline stress. A more in-depth and detailed exploration of the specific mechanisms by which these substances function in the process of plant resistance to aniline stress (for instance, utilizing carbon-14 isotope tracing to monitor the metabolic pathway of aniline within plants) will facilitate the cultivation of plant varieties that are resistant to aniline. This will undoubtedly benefit activities such as ensuring food production and quality in aniline-contaminated environments, as well as utilizing plants for the remediation of aniline-polluted environments. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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13 pages, 3947 KB

Open AccessArticle

Promoter of Vegetable Pea PsPIP2-4 Responds to Abiotic Stresses in Transgenic Tobacco

by Zhijuan Feng, Na Liu, Yuanpeng Bu, Guwen Zhang, Bin Wang and Yaming Gong

Int. J. Mol. Sci. 2024, 25(24), 13574; https://doi.org/10.3390/ijms252413574 - 18 Dec 2024

Cited by 1 | Viewed by 1430

Abstract

Plasma membrane intrinsic proteins (PIPs), one sub-family of aquaporins (AQPs), are responsible for plant abiotic stress responses. However, little information is currently available about the stress responsiveness of the PIP promoter in vegetable pea. In the present study, one novel promoter of PsPIP2-4 which shared high similarity to the PIP2-type AQPs from other plants, was isolated. Quantitative real-time PCR (qRT-PCR) assays suggested that PsPIP2-4 was predominantly expressed in leaves and abundantly induced by abiotic stress treatments (polyethylene glycol (PEG) 6000, NaCl, and methyl jasmonate (MeJA)). Further, the promoter activity of PsPIP2-4 was verified in transgenic tobacco plants. Beta-glucuronidase (GUS) staining driven by the PsPIP2-4 promoter confirmed that it was mainly detected in the leaves of transgenic seedlings, especially in the guard cells. Exposure of transgenic seedlings to various environmental stimuli proved that the promoter activity of PsPIP2-4 was abundantly strengthened by osmotic, salt, and MeJA stresses. This research provides one stress-inducible promoter enabling targeted gene expression under abiotic stresses and demonstrates its usefulness in the genetic improvement of plant stress resistance. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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Review

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26 pages, 4366 KB

Open AccessReview

The Central Role of GSNOR: Decoding Nitric Oxide Signaling for Crop Stress Tolerance

by Ashim Kumar Das, Da-Sol Lee, Geum-Jin Lee, Ye-Song Kim, Sajeel Hussain, Moon-Sub Lee, Byung-Wook Yun and Bong-Gyu Mun

Int. J. Mol. Sci. 2025, 26(23), 11486; https://doi.org/10.3390/ijms262311486 - 27 Nov 2025

Cited by 1 | Viewed by 1038

Abstract

S-nitrosoglutathione (GSNO) reductase (GSNOR) is a major and conserved enzyme in prokaryotes and eukaryotes. It reduces a stable nitric oxide (NO) reservoir, GSNO, to balance the organisms’ redox status through S-nitrosylation. Over the last few decades, much of our understanding of GSNOR’s roles in plant biology has been updated. Here, therefore, we review the current knowledge of GSNOR in plant physiology and signaling under abiotic and biotic stresses. We observe that the role of GSNOR in plant abiotic stress is widely studied in both model and crop plants, whereas studies on its role in biotic stress have mainly focused on model plants. Under abiotic stresses, GSNOR plays a pleiotropic role in terms of plant tolerance and sensitivity. The presence or absence of GSNOR activity modulates the endogenous NO pool that balances plant reactive nitrogen species (RNS) and reactive oxygen species (ROS) under stress conditions. Moreover, GSNOR regulates hormonal levels, like ethylene, abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA), in response to abiotic and biotic stress conditions. Although GSNOR is important in plant physiology, its regulation of the redox switch is directly influenced by the extent of S-nitrosylation, where S-nitrosylated proteins generally enhance plant tolerance to abiotic stress but simultaneously suppress plant immunity. We further highlight a new perspective on NO-based nanotechnology in agriculture, focusing on GSNO encapsulated in nanocarriers. This technology improves NO stability and opens new avenues by allowing an evaluation of GSNOR’s role for sustainable crop production. Intriguingly, we discuss knowledge gaps, which are crucial to understanding the role of GSNOR in plant stress tolerance. Overall, this review accumulates a comprehensive understanding of the GSNOR enzyme in crop biology, which could aid in harnessing its function to address the impacts of climate change. Full article

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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