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Abiotic Stress in Plant: Molecular Genetics and Genomics

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 25 July 2026 | Viewed by 6149

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Dr. Weicong Qi

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Guest Editor

Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
Interests: omics; molecular marker; plant stress tolerance; herbicide; crop germplasm; GMO; genome editing
Special Issues, Collections and Topics in MDPI journals

Dr. Hongyan Wang

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Guest Editor

Laboratory of Plant Epigenetics and Evolution, School of Life Sciences, Liaoning University, Shenyang 110036, China
Interests: abiotic stress; epigentics; DNA methylation; transposon

Special Issue Information

Dear Colleagues,

We are excited to invite submissions for a Special Issue of the MDPI journal Genes, which is focused on “Abiotic Stress in Plant: Molecular Genetics and Genomics”. This collection aims to explore the latest advancements in understanding how plants respond to abiotic stresses such as drought, salinity, temperature extremes, and nutrient deficiencies at the molecular and genomic levels.

We welcome original research articles, reviews, and short communications that delve into (but are not limited to) the following areas:

The identification and functional analysis of stress-responsive genes and regulatory networks.
Genomic and transcriptomic approaches to unravel the complex mechanisms of stress tolerance.
The role of epigenetics and non-coding RNAs in plant stress responses.
Advances in breeding strategies and biotechnological interventions to enhance stress resilience.
Case studies on model and non-model plants that provide new insights into stress adaptation.

This Special Issue seeks to bring together cutting-edge research that will contribute to the development of crops with improved stress tolerance, ultimately supporting global food security and sustainable agriculture.

Dr. Weicong Qi
Dr. Hongyan Wang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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. Genes is an international peer-reviewed open access monthly 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 2600 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
molecular genetics
genomics
plant stress response
epigenetics
crop improvement
sustainable agriculture

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Published Papers (7 papers)

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Research

31 pages, 4910 KB

Open AccessArticle

Multi-Omics Reveals Light-Quality-Dependent Phytohormone and Transcription Factor Networks Regulating Flavonoid Biosynthesis in Ludisia discolor

by Mingyue Qiu, Yuman Shi, Tiankai Shen, Kunxiu Cai, Luan Li, Xiaoyue Qiu, Tao Zheng and Ying Chen

Genes 2026, 17(4), 445; https://doi.org/10.3390/genes17040445 - 13 Apr 2026

Viewed by 466

Abstract

Background/Objectives: Ludisia discolor, an endangered medicinal orchid, is a vital source of bioactive flavonoids which requires in vitro tissue culture for propagation and metabolite production. While light quality influences metabolic processes, the mechanisms connecting light conditions, phytohormone signaling, and flavonoid biosynthesis remain unclear. This study investigates how specific light qualities trigger secondary metabolism to improve tissue culture and conservation strategies. Methods: L. discolor was cultivated under strictly regulated LED environments (blue, red, yellow, and green). An integrated multi-omics approach, combining transcriptomic sequencing and targeted metabolomic profiling, was employed to analyze leaves, correlating plant hormone changes with flavonoid metabolite levels. Results: LED light qualities significantly altered flavonoid and phytohormone profiles, yielding 80 unique flavonoids. Blue and red light effectively promoted flavonoid accumulation, whereas yellow light suppressed it. Transcriptomics, validated by qRT-PCR, revealed distinct expression patterns in key structural genes (e.g., 4CL, PAL, CYP73A, FLS, CCoAOMT, C12RT1). Ten transcription factors (including MYB93, bZIP36, bHLH4, and bZIP44) with hormone-responsive cis-elements were co-expressed with 16 structural genes. Notably, blue light induced reactive oxygen species (ROS) signaling, activating phytohormone production (IAA, GA, ABA). These hormones subsequently stimulated transcription factors, increasing the biosynthesis of compounds like neohesperidin and hesperetin. Conclusions: We propose a novel regulatory model where light-induced ROS and phytohormone cascades activate specific transcription factors, enhancing structural gene expression in the flavonoid pathway. These findings elucidate the molecular mechanisms of light-driven secondary metabolism, providing valuable insights for the sustainable agriculture and ex situ conservation of endangered medicinal orchids. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)

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19 pages, 4836 KB

Open AccessArticle

Comprehensive Characterization of BrSULTRs Family and Their Expression Profiles Under Salt and Low-Temperature Stresses

by Shangjia Liu, Bingxue Han, Zekun Hu, Xiaojia Yin, Xiaoyan Wang and Fengchao Cui

Genes 2026, 17(4), 394; https://doi.org/10.3390/genes17040394 - 30 Mar 2026

Viewed by 436

Abstract

Background: Sulfate transporters (SULTRs) are integral membrane proteins responsible for sulfate uptake, translocation, and plant adaptation to abiotic stresses. However, knowledge regarding the SULTR gene family in the economically important crop, Brassica rapa (Chinese cabbage), limited. The aim of this study is to conduct a genome-wide identification and functional characterization of BrSULTR genes and to explore their potential functions under abiotic stress. Methods: We identified 19 BrSULTR genes in the B. rapa genome by performing homology searches with Arabidopsis thaliana SULTR sequences as queries. Subsequent bioinformatics analysis included phylogenetic classification, chromosomal localization, gene structure, conserved motif dissection, cis-regulatory element prediction, and protein–protein interaction (PPI) network analysis. Tissue-specific expression profiles of BrSULTRs were assessed using publicly available transcriptome data. Furthermore, their expression dynamics under salt (150 mM NaCl) and low-temperature (4 °C) stress were investigated by integrating transcriptomic, proteomic, and qRT-PCR data. Results: The 19 identified BrSULTR members were phylogenetically categorized into four subfamilies and were mapped unevenly across seven chromosomes. Promoter analysis identified an array of cis-regulatory elements associated with development, hormone response, and stress response. Expression profiles revealed distinct tissue-specific patterns in roots, stems, leaves, flowers, and siliques. Under salt stress, BrSULTR13 was significantly upregulated, while BrSULTR9 and BrSULTR11 were significantly suppressed under low-temperature stress. PPI network projection indicated that the Arabidopsis homologs of BrSULTR5 may physically interact with stress-regulating enzymes such as APS and APR. Conclusions: Our work presents a comprehensive genomic and functional overview of the BrSULTR gene family in B. rapa. The results underscore the potential functions of BrSULTRs, highlighting their involvement in sulfate transport and abiotic stress responses. These insights establish valuable insights and a foundation for further research aiming at improving stress tolerance in B. rapa through the manipulation of sulfur metabolism pathways. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)

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25 pages, 16634 KB

Open AccessArticle

Genome-Wide Evolution and Stress-Responsive Regulation of 2-Oxoglutarate-Dependent Dioxygenases in Gossypium

by Mingjv Zhu, Peiyu Li, Yuanlong Wu, Abudukeyoumu Abudurezike, Sijia Liang, Chuanyin Zhu, Yi Zhou, Lin Xu, Zhibo Li, Shihe Jiang, Xinhui Nie and Shuangxia Jin

Genes 2026, 17(2), 180; https://doi.org/10.3390/genes17020180 - 31 Jan 2026

Viewed by 696

Abstract

Purpose: Gibberellins (GAs) are key phytohormones that regulate plant growth, development, and responses to environmental stress, and their metabolism is mediated by 2-oxoglutarate-dependent dioxygenases (2OGDs). Cotton (Gossypium spp.) is a polyploid crop with a complex genome; however, the evolutionary characteristics and stress-responsive regulation of GA-related 2OGDs remain poorly understood. This study aimed to systematically investigate the evolution, expression patterns, and stress-associated regulation of the cotton 2OGD multigene family, with particular emphasis on GA-related members. Methods: 2OGD genes were identified genome-wide in four Gossypium species and Arabidopsis thaliana. Phylogenetic relationships, gene structures, conserved motifs, cis-acting regulatory elements, and synteny were analyzed. Transcriptomic data from multiple tissues and developmental stages, together with time-course RNA-seq under salt stress, were examined. Transcriptome–metabolome association analysis, endogenous GA quantification, and predicted protein–protein interaction analysis were conducted. Results: A total of 583 2OGD genes were identified and classified into three major classes, including a Class C group comprising GA2ox, GA3ox, and GA20ox genes. Polyploidization-associated duplication contributed to the expansion of the 2OGD family, and most duplicated gene pairs exhibited signatures of purifying selection. GA-related 2OGDs displayed conserved motif compositions with variation in cis-acting elements. Promoter analysis identified abundant hormone-responsive, stress-responsive, and growth-related cis-elements, suggesting complex regulatory control of GA-related 2OGDs in cotton. Under salt stress, GhGA2OX1 and GhGA20OX2 were upregulated, whereas GhGA3OX1 was downregulated, accompanied by reduced endogenous GA levels. Conclusions: GA-related 2OGDs in cotton are transcriptionally responsive to salt stress and are associated with changes in GA metabolism, providing a basis for future functional studies. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)

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22 pages, 3472 KB

Open AccessArticle

Exploring the Genetic Foundations of Salt Tolerance in Common Vetch (Vicia sativa L.) via Genome-Wide Association Analysis

by Hui Jin, Jumei Zhang, Yordan Dimtrov, Xue Yang, Ruonan Du, Yu-e Wu, Danna Chang, Rui Zhang and Haibin Zhao

Genes 2026, 17(1), 32; https://doi.org/10.3390/genes17010032 - 30 Dec 2025

Viewed by 626

Abstract

Background/Objectives: Common vetch (Vicia sativa L.) is a globally cultivated leguminous crop, valued for its high nutritional content and role in sustainable agriculture. Methods: To identify loci or genes significantly associated with salt tolerance, we conducted a genome-wide association study (GWAS) using 172 common vetch accessions primarily from diverse geographic regions. Single-nucleotide polymorphisms (SNPs) were obtained through re-sequencing, and five salt tolerance-related traits, including the germination rate (GR), germination potential (GP), germination index (GI), shoot length (SL), and root length (RL), were evaluated under salt stress conditions. We have identified 20 loci significantly associated with salt tolerance-related traits, and explaining 9.7–21.8% of the phenotypic variation. Notably, 13 loci exhibited pleiotropic effects on multiple traits; include qST1.1 (associated with SL, GR, GI), qST1.3 (RL, SL, GP), qST2.5 (SL, GR, GI, GP), and qST2.7 (SL, RL, GP, GI), and should be prioritized in future breeding programs. All 20 loci are novel compared to previous reports. Furthermore, we identified 7 candidate genes encoding key regulatory proteins, including a zinc finger MYM-type protein, ubiquitin-like domain-containing protein, transcription factor bHLH, ethylene-responsive transcription factor, auxin-responsive protein, and serine/threonine-protein kinase, as potential regulators of salt tolerance. Conclusions: This study advances our understanding of the genetic basis of salt tolerance in common vetch and provides valuable loci, molecular tools, and elite accessions. HZMC1352, GLF303, GLF301, HZMC1387, GLF306, GLF368, GLF342, HZMC1384, HZMC1355, GLF307, HZMC1366 are used for improving salt tolerance in breeding programs. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)

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14 pages, 3048 KB

Open AccessArticle

Genome-Wide Characterization of SlABCG Genes in Tomato Reveals Their Role in Saline–Alkali Tolerance

by Ying Li, Wentao Guo, Hongliang Ji, Weilin Cao, Gaoqing Li, Ruirui Xu and Liming Gan

Genes 2026, 17(1), 19; https://doi.org/10.3390/genes17010019 - 26 Dec 2025

Viewed by 600

Abstract

Background: The ATP-binding cassette (ABC) G subfamily, a key member of the ABC protein family, mediates plant stress responses by transporting metabolites across membranes, but its mechanism of action in tomato (Solanum lycopersicum L.) remains poorly understood. Methods: We systematically analyzed the evolutionary relationships, structural characteristics, stress-responsive expression patterns, and functional roles in response to saline-alkali stress of the SlABCG gene family in tomato, using a combination of approaches including phylogenetic analysis (MEGA), gene structure and motif analysis (GSDS, MEME), cis-acting element prediction, homology analysis, transcriptome analysis, protein-protein interaction prediction, and qRT-PCR validation. Results: We identified a total of 41 SlABCG genes from the tomato genome. These genes, together with 43 ABCG genes from Arabidopsis thaliana, were clustered into five distinct clades. There are 35 collinear gene pairs between the SlABCG gene family in tomato and the ABCG gene family in Arabidopsis, while 39 collinear gene pairs exist among ABCG genes within the tomato genome itself.The promoter regions of SlABCG genes contain cis-acting elements associated with responses to salicylic acid, low temperature, and gibberellin stresses. Transcriptome sequencing revealed that six SlABCG genes responded to saline-alkali stress. Gene regulatory network prediction revealed that multiple genes related to saline-alkali stress were regulated. Expression profile analysis of the 25 upregulated genes revealed that all of them were significantly upregulated during the saline-alkali stress treatment. Conclusions: In summary, our results provide deep insights into the characteristics of the SlABCG subfamily, facilitate the design of effective analysis strategies, and offer data support for exploring the roles of ABCG transporters under different stress conditions. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)

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14 pages, 14356 KB

Open AccessArticle

Characterization of LTR Retrotransposon Reverse Transcriptase in Tamarix chinensis L. and Activity Analysis Under Salt and Alkali Stresses

by Long Wang, Bo Li, Yuqian Wang, Shiji Wang, Meichun Zhang, Mengyao Li, Tong Zheng and Hongyan Wang

Genes 2025, 16(11), 1262; https://doi.org/10.3390/genes16111262 - 26 Oct 2025

Viewed by 954

Abstract

Transposable elements (TEs) are major components of plant genomes and play crucial roles in adaptive genome evolution and stress tolerance. Under abiotic stress, activated TEs can generate abundant genetic variation and regulate the expression of stress-responsive genes. As a pioneer species in desert and saline–alkali environments, Tamarix chinensis L. has been little studied with respect to the abundance and evolutionary relationships of its LTR retrotransposons, particularly their activation patterns under salt and alkali stresses. This study aimed to investigate the characteristics of the reverse transcriptase (RT) domain of LTR retrotransposons in T. chinensis and to determine their patterns of activation in response to salt and alkali stresses. A total of 629 Ty1-copia and 607 Ty3-gypsy RT nucleotide sequences, which displayed high AT/GC ratios and evidence of stop codon insertions, were identified in T. chinensis by amplicon sequencing. Among these, 211 Ty1-copia and 117 Ty3-gypsy RT sequences with potential transpositional activity each contained distinct domains, suggesting a high degree of conservation. Phylogenetic analysis revealed that the RT sequences of T. chinensis are closely related to those of mangrove, wild potato, and Ipomoea, and may have undergone horizontal transfer. Expression analysis showed that 634 and 181 RT sequences were activated under salt and alkali stresses, respectively, with the majority belonging to salt-induced Ty1-copia families. Compared with the control group, under salt and alkali stresses, the cTy1-copia elements (Ty1-copia with amplificated from cDNA of T. chinensis, the same below) with dominant abundance were mainly concentrated in the Angela subfamily, while the cTy3-gypsy elements induced by alkali stress were primarily distributed in the Tekay and Reina subfamilies. Furthermore, four cTy1-copia and five cTy3-gypsy were identified as candidate key LTR retrotransposons responsive to salt and alkali stresses. Overall, this study provides new insights into the epigenetic mechanisms underlying the adaptation of T. chinensis to saline and alkali stresses and offers a theoretical basis for its potential applications in saline–alkali land reclamation. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)

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17 pages, 5483 KB

Open AccessArticle

Genome-Wide Analysis of HIPP Gene Family in Maize Reveals Its Role in the Cadmium Stress Response

by Chunyan Gao, Zhirui Zhang, Yuxuan Zhu, Jiaxin Tian, Kaili Yu, Jinbo Hou, Dan Luo, Jian Cai and Youcheng Zhu

Genes 2025, 16(7), 770; https://doi.org/10.3390/genes16070770 - 30 Jun 2025

Cited by 5 | Viewed by 1787

Abstract

Background: Phytoremediation is an efficient approach for remediating heavy metal-contaminated soils. Heavy metal-associated isoprenylated plant proteins (HIPPs)—crucial for metal ion homeostasis—are unique to vascular plants, featuring a heavy metal-associated (HMA) domain and an isoprenylated CaaX motif. However, ZmHIPP genes have not been systematically or functionally characterized in maize. Methods: This study characterizes ZmHIPP at the genome-wide level, including phylogenetic classification, motif/gene structure, chromosome location, gene duplication events, promoter elements, and tissue expression patterns. Cadmium (Cd) responses were evaluated by specific ZmHIPP expression and Cd accumulation in shoots and roots under Cd treatment. Results: A total of 66 ZmHIPPs were distributed unevenly across ten chromosomes, classified into five phylogenetic groups phylogenetically. Gene collinearity revealed 26 pairs of segmental duplications in ZmHIPPs. Numerous synteny genes were detected in rice and sorghum, but none in Arabidopsis, suggesting high conservation of HIPP genes in crop evolution. Transcriptomic analysis revealed tissue-specific expression patterns of ZmHIPP members in maize. Cis-acting element analysis linked several binding elements to abscisic acid, MeJA response, and MYB and MYC transcription factors. Under Cd stress, 53 out of 66 ZmHIPP genes were significantly induced, exhibiting three expression patterns. Cd exposure confirmed that the expression of ZmHIPP11, ZmHIPP30, and ZmHIPP48 was generally higher in shoots than roots, while ZmHIPP02 and ZmHIPP57 exhibited the opposite. Cd accumulation was higher in roots than shoots, peaking at 72 h (96 mg/kg) in shoots and exceeding 1000 mg/kg in roots after 120 h. Conclusions: This study not only provides fundamental genetic and molecular insights into HIPP function in maize but also identifies specific ZmHIPP genes as promising genetic resources for breeding Cd-tolerant maize, aiding in phytoremediation of Cd-contaminated soils. Full article

(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)

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