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20 pages, 2176 KB

Open AccessArticle

Comprehensive Assessment of Drought Tolerance in Native Melon Germplasms from Xinjiang at the Germination Stage

by Yafei Li, Qingqing Wang, Junzhuo Yang, Shan Su, Tiantian Yang, Huilin Wang, Zuyun Dai, Zhongzhou Yang, Feishi Luan, Shi Liu, Chong Du and Chaonan Wang

Plants 2026, 15(15), 2249; https://doi.org/10.3390/plants15152249 - 23 Jul 2026

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Abstract

Drought and water deficit have severely restricted melon (Cucumis melo L.) production in Xinjiang, and large-scale systematic evaluations of drought tolerance at the germination stage are still extremely limited. Physiological and biochemical indicators related to the germination stage, including osmotic adjustment substances [...] Read more.

Drought and water deficit have severely restricted melon (Cucumis melo L.) production in Xinjiang, and large-scale systematic evaluations of drought tolerance at the germination stage are still extremely limited. Physiological and biochemical indicators related to the germination stage, including osmotic adjustment substances and antioxidant enzyme activities, have not yet been incorporated into prediction models for the rapid identification of germplasm drought resistance. To address these research gaps, this study selected 60 accessions of local melon germplasm resources in Xinjiang and used polyethylene glycol (PEG) solutions at four different concentrations (0%, 10%, 20% and 30%) to simulate drought stress conditions. Drought tolerance was evaluated to develop a method for the rapid screening of drought-tolerant germplasms. The findings demonstrated that PEG stress significantly suppressed seed germination and had both stimulatory and inhibitory effects on radicle growth. With the increase in PEG concentration, germination indices consistently exhibited a downward trend. Under 10% PEG treatment, the variation among different germplasms was relatively small, while 30% PEG completely inhibited seed germination. Notably, 20% PEG fell within the semi-lethal concentration range for all tested germplasms and yielded the maximum coefficient of variation for germination rate, which could maximally differentiate the drought resistance differences among germplasms. Therefore, 20% PEG was determined to be the optimal screening concentration. Under 20% polyethylene glycol (PEG) stress, the degree of membrane lipid peroxidation (malondialdehyde, MDA), contents of osmotic regulators (proline, Pro; soluble protein, SP), and activities of antioxidant enzymes (superoxide dismutase, SOD; peroxidase, POD; catalase, CAT; ascorbate peroxidase, APX) in the radicles of melon germplasms were universally elevated. However, the variation ranges and trends of biochemical indices among different germplasms exhibited significant differences. The proline content of melon accessions with strong drought resistance increased, the malondialdehyde (a product of membrane damage) was low, and the enzyme activities increased significantly. The proline content of non-drought-tolerant melon accessions increased less, malondialdehyde accumulated in large amounts, and the activity of some protective enzymes decreased. Correlation analysis demonstrated that Pro exerted a synergistic effect in conjunction with antioxidant enzymes (SOD, CAT) to mitigate drought stress. Cluster analysis classified the germplasm into 14 high-tolerance types, 10 medium-tolerance types, and 9 low-tolerance types. Based on extreme germination phenotypes, 27 germplasms were identified as drought-sensitive types. A prediction model for drought tolerance was established via stepwise regression: D = −0.309 + 0.053 × Pro (proline content) + 0.319 × RL (radicle length) + 0.469 × MDA (malondialdehyde) + 0.137 × SOD (superoxide dismutase), with four core indicators (RL, MDA, Pro, SOD) identified. These findings provide a scientific basis and technical support for drought tolerance breeding, parental selection, and large-scale, precise, and rapid drought tolerance screening of melon germplasms in the arid regions of Xinjiang. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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15 pages, 4009 KB

Open AccessArticle

From Weed Evolution to Crop Design: A Computational Blueprint for a Novel, Synergistic Herbicide-Resistant Allele in Wheat

by Yuexing Wang, Qinge Chen, Zhangpeng Shi, Tian Mi, Yujiu Wu, Na Niu and Lingjian Ma

Plants 2026, 15(13), 2023; https://doi.org/10.3390/plants15132023 - 30 Jun 2026

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Abstract

The escalating crisis of herbicide-resistant weeds threatens global wheat production. While key mutations are well-documented in weeds, the principles governing their interactions in wheat remain largely unknown. Here, we first developed a novel wheat germplasm carrying the acetolactate synthase (TaALS) Ser-627-Asn [...] Read more.

The escalating crisis of herbicide-resistant weeds threatens global wheat production. While key mutations are well-documented in weeds, the principles governing their interactions in wheat remain largely unknown. Here, we first developed a novel wheat germplasm carrying the acetolactate synthase (TaALS) Ser-627-Asn (S627N) mutation via ethyl methanesulfonate (EMS) mutagenesis. We then employed a computational design strategy to explore its synergy with the prevalent Trp-548-Leu (W548L) mutation—a combination not yet reported in nature. Integrated molecular dynamics (MD) simulations and free energy landscape analysis revealed that the in silico W548L/S627N double mutant triggers synergistic global destabilization of the herbicide–enzyme complex. Binding affinity progressively weakened from wild-type (−25.54 ± 2.05 kcal/mol) to the double mutant (−18.13 ± 2.76 kcal/mol), driven by a polarity inversion at the Arg-347 anchor. Comparative transcriptomic profiling of the S627N germplasm confirmed the absence of deleterious metabolic feedback in the branched-chain amino acid biosynthesis pathway. This work exemplifies a paradigm shift from mimicking natural variation to predictive crop design via multiplex gene editing. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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14 pages, 12594 KB

Open AccessArticle

The Effects of Different Organic Amendment Strategies on Soil Properties and Microbial Communities in Maize Monocropping

by Ming Fang, Jianan Sun, Xinyue Li, Jiaming Zhang, Chuyi Wang, Shuxuan Qi, Yixin Guan, Qiang Lyu, Gang Yang, Man Ao, Yubo Zhu and Bo Li

Plants 2026, 15(12), 1805; https://doi.org/10.3390/plants15121805 - 11 Jun 2026

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Abstract

The black soil layer has undergone substantial degradation in Northeast China, and it is crucial to adopt reasonable tillage measures to prevent black soil degradation. Organic amendment strategies provide an effective solution for mitigating nutrient loss in black soil; meanwhile, there is still [...] Read more.

The black soil layer has undergone substantial degradation in Northeast China, and it is crucial to adopt reasonable tillage measures to prevent black soil degradation. Organic amendment strategies provide an effective solution for mitigating nutrient loss in black soil; meanwhile, there is still a lack of systematic investigation into their impact on soil microbial communities. Thus, we carried out a five-year field experiment from 2020 to 2025 in Jilin Province. Four organic amendment strategies were set up: conventional tillage (CT); straw returning (SR); straw returning + inorganic fertilizer (SRI); and straw returning + inorganic fertilizer + organic fertilizer (SRIO). Furthermore, we investigated the effects of organic materials on soil properties and microbial communities during the maize seedling stage. The results showed that SR significantly increased the relative abundance of Bradyrhizobium, Tausonia and Coprinopsis, while SRI led to a 140.3% increase in Nocardioides. In SRIO treatment, Gaiella and Fusarium were significantly enriched by 103.9% and 142.5%, respectively. Moreover, SR treatment significantly decreased the fungal Shannon and Simpson index by 18.8% and 4.2%, respectively. Organic matter, alkali nitrogen, and available potassium were the primary environmental factors shaping both bacterial and fungal community structures. Additionally, the co-occurrence network suggested that straw returning promoted more diverse interactions among soil bacterial and fungal communities. Our study highlights the potential of organic amendment strategies in enhancing black soil nutrients, as well as their important role in maintaining soil microbial function and stability. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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19 pages, 11113 KB

Open AccessArticle

Alternative Splicing of SCL30a Generates Distinct Isoforms to Modulate ABA Signaling in Arabidopsis

by Tiantian Wu, Ping Lin, Ying Li, Yuan Tian, Mohammad Saidur Rhaman, Fuyuan Zhu, Yinggao Liu and Yanjie Xie

Plants 2026, 15(11), 1735; https://doi.org/10.3390/plants15111735 - 3 Jun 2026

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Abstract

Alternative splicing (AS) coupled with nonsense-mediated decay (NMD) is an important post-transcriptional mechanism that regulates the expression of many genes, including serine/arginine-rich (SR) proteins across eukaryotes. In plants, SR proteins participate in diverse developmental processes and stress responses, particularly in abscisic acid (ABA) [...] Read more.

Alternative splicing (AS) coupled with nonsense-mediated decay (NMD) is an important post-transcriptional mechanism that regulates the expression of many genes, including serine/arginine-rich (SR) proteins across eukaryotes. In plants, SR proteins participate in diverse developmental processes and stress responses, particularly in abscisic acid (ABA) signaling. However, the functional differences among individual splice isoforms of SR proteins remain poorly understood. Here, we investigated SCL30a, a plant-specific SR protein in Arabidopsis thaliana. By integrating third-generation long-read transcriptome sequencing, NMD stability assays, and subcellular localization analyses, we identified five alternatively spliced SCL30a transcripts. Among them, SCL30a.2 and SCL30a.3 contain premature termination codons (PTCs), display nucleocytoplasmic localization, and are rapidly degraded through the NMD pathway. In contrast, the other three isoforms, SCL30a.1, SCL30a.4, and SCL30a.5, retain an intact RS domain and localize exclusively to the nucleus. Functional analyses showed that SCL30a acts as a positive regulator of ABA signaling. Loss-of-function mutants of SCL30a displayed reduced ABA sensitivity in both root growth and seed germination assays, whereas complementation or overexpression of three stable isoforms of SCL30a (SCL30a.1, SCL30a.4, and SCL30a.5) enhanced ABA responsiveness. Transcriptome analysis further showed that the expression of a subset of ABA-related genes, particularly SnRK2.6, was significantly altered in ABA-treated scl30a mutants and SCL30a.1-OE lines compared with WT plants. In addition, genetic evidence showed that overexpression of SnRK2.6 rescued the ABA-insensitive phenotype of the scl30a mutant. Together, these findings suggest that SnRK2.6 may function as a candidate downstream component associated with SCL30a-mediated ABA responses. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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19 pages, 3728 KB

Open AccessArticle

Paraburkholderia Mediates Salt Stress Alleviation in Cucumber Seedlings

by Xinyu Jia, Bin Tian, Jingwen Li, Shanyu Li, Mengxin Chen, Sai Wang, Yonghui Zhao, Lin Hao and Wei Fu

Plants 2026, 15(7), 1104; https://doi.org/10.3390/plants15071104 - 3 Apr 2026

Viewed by 600

Abstract

To elucidate the cooperative regulatory mechanisms underlying Paraburkholderia sp. GD17-mediated salt tolerance in cucumber plants. Hydroponically grown cucumber plants were inoculated with GD17 and subsequently subjected to NaCl treatment. Physiological, biochemical parameters, as well as gene expression profiles, were comprehensively analyzed. GD17 inoculation [...] Read more.

To elucidate the cooperative regulatory mechanisms underlying Paraburkholderia sp. GD17-mediated salt tolerance in cucumber plants. Hydroponically grown cucumber plants were inoculated with GD17 and subsequently subjected to NaCl treatment. Physiological, biochemical parameters, as well as gene expression profiles, were comprehensively analyzed. GD17 inoculation significantly improved plant growth, developmental performance, and salinity tolerance. Under salt stress, GD17-inoculated plants exhibited higher leaf nutrient contents compared to non-inoculated controls, particularly an elevated K⁺/Na⁺ ratio, which was closely associated with the upregulated expression of Na⁺ extrusion-related genes. A substantial increase in proline content and the corresponding biosynthesis-related gene expression indicated that enhanced osmoprotectant synthesis played a critical role in GD17-conferred salt tolerance. Phytohormone levels and their signaling-related gene expression were also significantly upregulated in GD17-inoculated plants under salt stress. Moreover, transcription factor gene expression was markedly increased in GD17-treated plants following salt exposure. GD17 inoculation alleviated salt-induced photosynthetic inhibition, as demonstrated by improved photosynthetic efficiency and reduced suppression of photosynthesis-related gene expression. Transcriptional profiling further revealed that starch degradation, photorespiration, and the pentose phosphate pathway were crucial for GD17-mediated salt tolerance. Reduced oxidative damage, driven by enhanced antioxidative activity, further contributed to the observed protective mechanisms. This study demonstrates that the application of Paraburkholderia sp. GD17 concurrently enhances cucumber growth and salinity tolerance, effectively resolving the trade-off between growth and defense. Multi-level analyses provided comprehensive mechanistic insights into these synergistic effects. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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27 pages, 3055 KB

Open AccessArticle

Integrative Genome-Wide Association and Transcriptome Analyses Identify Candidate Genes for Salt Tolerance During Cotton Germination

by Yin Wang, Yilei Long, Shen Jin, Yinan Yang, Shixiao Fang, Xiutong Wu, Teng Liu and Xiantao Ai

Plants 2026, 15(6), 937; https://doi.org/10.3390/plants15060937 - 19 Mar 2026

Viewed by 821

Abstract

Genome-wide association analysis and transcriptomics were used to investigate salt tolerance traits during germination in 300 Gossypium hirsutum L. germplasm accessions, with the objective of identifying genes and molecular markers associated with salt tolerance. Under 200 mmol L⁻¹ NaCl stress, six traits [...] Read more.

Genome-wide association analysis and transcriptomics were used to investigate salt tolerance traits during germination in 300 Gossypium hirsutum L. germplasm accessions, with the objective of identifying genes and molecular markers associated with salt tolerance. Under 200 mmol L⁻¹ NaCl stress, six traits were evaluated, germination rate, root length, shoot length, root fresh weight, shoot fresh weight, and total fresh weight, as well as their respective salt tolerance indices. A total of 1277 significantly associated single-nucleotide polymorphism (SNP) markers were identified and mapped to 94 quantitative trait loci (QTLs). Of these, 49 QTLs were detected by three or more analytical models, and three QTLs were prioritized for further investigation. Subsequent analysis of these QTLs identified 73 candidate genes potentially involved in cotton salt tolerance. Integration of transcriptomic data revealed that three candidate genes were among the differentially expressed genes (DEGs). Examination of their RNA-seq expression profiles demonstrated significant differences in fragments per kilobase of transcript per million mapped reads (FPKM) values across sampling time points. These three candidate genes are therefore predicted to be associated with salt tolerance during cotton germination. The results provide new insights into the molecular regulatory mechanisms of salt stress tolerance in cotton and offer valuable genetic resources and molecular markers for the genetic improvement of salt tolerance. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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26 pages, 14801 KB

Open AccessArticle

FLA1, Enhancing GA₃ Contents in Flag Leaf Lamina Joint, Increases Flag Leaf Angle to Improve Outcross Rate and Hybrid Rice Seed Production

by Zhiyao Dong, Dalu Li, Xiaoxiao Hu, Xuanchi Liu, Nuoya Fei, Guocan Wu, Erbao Liu, Xiaojing Dang, Siyuan Zeng, Yuzhu Chen and Delin Hong

Plants 2026, 15(3), 446; https://doi.org/10.3390/plants15030446 - 31 Jan 2026

Viewed by 1278

Abstract

Flag leaf angle (FLA) in rice (Oryza sativa L.) is one of the important traits affecting F₁ seed production by mechanization. Here, we report the map-based cloning and functional characterization of the FLA1 (FLAG-LEAF-ANGLE 1) gene, which resides at [...] Read more.

Flag leaf angle (FLA) in rice (Oryza sativa L.) is one of the important traits affecting F₁ seed production by mechanization. Here, we report the map-based cloning and functional characterization of the FLA1 (FLAG-LEAF-ANGLE 1) gene, which resides at a major-effect quantitative trait locus (QTL). Through cell morphological observations and exogenous hormone treatment assays, we demonstrate that gibberellin (GA) modulates rice FLA by altering both the number of cell layers and cell length. Combining genetic and molecular biological analyses with genetic complementation and gene overexpression assays, we elucidated and validated the biological function of FLA1. In addition, we found that FLA1 is constitutively expressed and encodes a protein localized to both the cell membrane and nucleus. Via RT-qPCR assays, we further demonstrated that the FLA1^fla-R allele from the rice accession fla-R enhances GA biosynthesis by upregulating the expression of CLA1 and GA20ox2. Furthermore, yeast two-hybrid assays revealed that auxin-repressed protein 1 (ARP1) interacts with FLA1, suggesting a potential role of this interaction in the modulation of rice FLA. Collectively, our results demonstrate that optimizing rice FLA via molecular manipulation of FLA1 can resolve the problem of flag leaf shearing during F₁ hybrid rice seed production without compromising F₁ hybrid seed yield, thereby facilitating mechanized F₁ hybrid rice seed production. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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10 pages, 2301 KB

Open AccessCommunication

GhNRPB3 Negatively Regulates Drought and Salt Tolerance in Cotton

by Yi Wang, Jiacong Zeng, Yuehua Yu and Zhiyong Ni

Plants 2025, 14(16), 2575; https://doi.org/10.3390/plants14162575 - 19 Aug 2025

Viewed by 1046

Abstract

RNA polymerase II (Pol II) has been shown to participate in various biological processes in plants, but its function in response to abiotic stress in cotton remains unclear. This study aimed to elucidate the role of the third-largest subunit of Pol II (NRPB3) [...] Read more.

RNA polymerase II (Pol II) has been shown to participate in various biological processes in plants, but its function in response to abiotic stress in cotton remains unclear. This study aimed to elucidate the role of the third-largest subunit of Pol II (NRPB3) in the response of cotton to drought and salt stress through molecular biology and physiological methods. Real-time fluorescence quantitative PCR was used to analyze the expression pattern of GhNRPB3 in roots, stems, leaves, and cotyledons and to detect changes in its expression under drought, NaCl, and ABA treatments. Using virus-induced gene silencing (VIGS) technology, GhNRPB3-silenced plants were obtained, and their physiological indicators under drought and salt stress, as well as the expression levels of the drought stress-related genes GhRD22 and GhRD26, were measured. This study revealed that GhNRPB3 is widely expressed in roots, stems, leaves, and cotyledons and that its expression is significantly induced by drought, NaCl, and ABA treatments. Compared to wild-type plants, the drought resistance, survival rate, and peroxidase activity of the GhNRPB3-silenced plants significantly increased, whereas the malondialdehyde content significantly decreased. Moreover, the expression levels of the drought-responsive genes GhRD22 and GhRD26 significantly increased. The salt tolerance of the GhNRPB3-silenced plants also increased, as reflected by decreased leaf wilting and significant increases in root growth parameters (including root length, root area, and root volume). These results indicate that GhNRPB3 plays a crucial role in mediating the adaptation of cotton to drought and salt stress by regulating the expression of stress-related genes. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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16 pages, 7336 KB

Open AccessArticle

Identification of Quality-Related Genomic Regions and Candidate Genes in Silage Maize by Combining GWAS and Meta-Analysis

by Yantian Lu, Yongfu Ding, Can Xu, Shubin Chen, Chunlan Xia, Li Zhang, Zhiqing Sang and Zhanqin Zhang

Plants 2025, 14(15), 2250; https://doi.org/10.3390/plants14152250 - 22 Jul 2025

Cited by 1 | Viewed by 2125

Abstract

Enhancing quality traits is a primary objective in silage maize breeding programs. The use of genome-wide association studies (GWAS) for quality traits, in combination with the integration of genetic resources, presents an opportunity to identify crucial genomic regions and candidate genes influencing silage [...] Read more.

Enhancing quality traits is a primary objective in silage maize breeding programs. The use of genome-wide association studies (GWAS) for quality traits, in combination with the integration of genetic resources, presents an opportunity to identify crucial genomic regions and candidate genes influencing silage maize quality. In this study, a GWAS was conducted on 580 inbred lines of silage maize, and a meta-analysis was performed on 477 quantitative trait loci (QTLs) from 34 studies. The analysis identified 27 significant single nucleotide polymorphisms (SNPs) and 87 consensus QTLs (cQTLs), with 7 cQTLs associated with multiple quality traits. By integrating the SNPs identified through association mapping, one SNP was found to overlap with the cQTL interval related to crude protein, neutral detergent fiber, and starch content. Furthermore, enrichment analysis predicted 300 and 5669 candidate genes through GWAS and meta-analysis, respectively, highlighting pathways such as cellular metabolism, the biosynthesis of secondary metabolites, ribosome function, carbon metabolism, protein processing in the endoplasmic reticulum, and amino acid biosynthesis. The examination of 13 candidate genes from three co-located regions revealed Zm00001d050977 as a cytochrome P450 family gene, while the other 2 genes primarily encode proteins involved in stress responses and other biological pathways. In conclusion, this research presents a methodology combining GWAS and meta-analysis to identify genomic regions and potential genes influencing quality traits in silage maize. These findings serve as a foundation for the identification of significant QTLs and candidate genes crucial for improving silage maize quality. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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11 pages, 1440 KB

Open AccessCommunication

GAG Protein of Arabidopsis thaliana LTR Retrotransposon Forms Retrosome-like Cytoplasmic Granules and Activates Stress Response Genes

by Alexander Polkhovskiy, Roman Komakhin and Ilya Kirov

Plants 2025, 14(13), 1894; https://doi.org/10.3390/plants14131894 - 20 Jun 2025

Cited by 1 | Viewed by 2024

Abstract

LTR retrotransposons are widespread genomic elements that significantly impact genome structure and function. In Arabidopsis thaliana, the EVD LTR retrotransposon encodes a GAG protein essential for retrotransposon particle assembly. Here, we present a comprehensive analysis of the structural features, intracellular localization, and [...] Read more.

LTR retrotransposons are widespread genomic elements that significantly impact genome structure and function. In Arabidopsis thaliana, the EVD LTR retrotransposon encodes a GAG protein essential for retrotransposon particle assembly. Here, we present a comprehensive analysis of the structural features, intracellular localization, and transcriptomic effects of the EVD GAG (evdGAG) protein. Using AlphaFold3, we identified canonical capsid (CA-NTD and CA-CTD) and nucleocapsid (NC) domains, with predicted disordered regions likely facilitating oligomerization. Transient expression of GFP-tagged evdGAG in protoplasts of A. thaliana and distant plant species (Nicotiana benthamiana and Helianthus annuus) revealed the formation of multiple large cytoplasmic aggregates resembling retrosomes, often localized near the nucleus. Stable overexpression of evdGAG in wild-type and ddm1 mutant backgrounds induced significant transcriptomic changes, including up-regulation of stress response and defense-related genes and downregulation of photosynthesis and chloroplast-associated pathways. Importantly, genes linked to stress granule formation were also up-regulated, suggesting a role for evdGAG in modulating cellular stress responses. Our findings provide novel insights into the cellular and molecular properties of plant retrotransposon GAG proteins and their influence on host gene expression. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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14 pages, 1708 KB

Open AccessArticle

Comprehensive Evaluation of 202 Cotton Varieties (Lines) and Their Physiological Drought Resistance Response During Seedling Stage

by Jiazila Baha, Wenhong Liu, Xiaoman Ma, Yage Li, Xiaohong Zhao, Xue Zhai, Xinchuan Cao and Weifeng Guo

Plants 2025, 14(12), 1770; https://doi.org/10.3390/plants14121770 - 10 Jun 2025

Cited by 4 | Viewed by 1447

Abstract

To identify seedling traits closely associated with drought resistance and to screen for drought-tolerant germplasm, 202 cotton varieties (lines) were evaluated under controlled indoor conditions using a nutrient soil cultivation method. Seedling-stage traits measured included plant height, cotyledon node diameter, true leaf number, [...] Read more.

To identify seedling traits closely associated with drought resistance and to screen for drought-tolerant germplasm, 202 cotton varieties (lines) were evaluated under controlled indoor conditions using a nutrient soil cultivation method. Seedling-stage traits measured included plant height, cotyledon node diameter, true leaf number, chlorophyll content, and fresh and dry biomass of both shoots and roots. Drought resistance was assessed using drought resistance coefficients for each trait, followed by descriptive statistics, principal component analysis (PCA), partial correlation analysis, and comprehensive evaluation via the entropy weight method. PCA and partial correlation analysis revealed that plant height, cotyledon node diameter, aboveground fresh weight, and underground fresh weight were strongly associated with drought resistance at the seedling stage. The comprehensive drought resistance index (D-value) classified the 202 cotton lines into four categories: highly drought-resistant, moderately drought-resistant, drought-sensitive, and highly drought-sensitive. Physiological assays indicated that malondialdehyde (MDA) content in drought-resistant lines first increased and then declined with prolonged drought stress, while it continued to increase in sensitive lines. In contrast, proline (Pro) content and superoxide dismutase (SOD) activity increased steadily in drought-resistant lines but showed negligible changes in sensitive lines. These four morphological traits and three physiological indicators represent reliable criteria for evaluating drought resistance in cotton seedlings. Four highly drought-resistant and thirteen moderately drought-resistant lines were identified, providing valuable germplasm for genetic improvement of drought tolerance in cotton. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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19 pages, 5427 KB

Open AccessArticle

Screening and Identification of Drought-Tolerant Genes in Tomato (Solanum lycopersicum L.) Based on RNA-Seq Analysis

by Yue Ma, Yushan Li, Fan Wang, Quan Qing, Chengzhu Deng, Hao Wang and Yu Song

Plants 2025, 14(10), 1471; https://doi.org/10.3390/plants14101471 - 14 May 2025

Cited by 4 | Viewed by 2824

Abstract

Drought is one of the major abiotic stresses that inhibits plant growth and development. Therefore, it is critical to explore drought resistance genes in crops to obtain high-quality breeding materials. In this study, the drought-sensitive tomato line “FQ118” and the resistant line “FQ119” [...] Read more.

Drought is one of the major abiotic stresses that inhibits plant growth and development. Therefore, it is critical to explore drought resistance genes in crops to obtain high-quality breeding materials. In this study, the drought-sensitive tomato line “FQ118” and the resistant line “FQ119” were treated with PEG-6000 and, at 0 h (CK), 6 h, 24 h, 36 h and 48 h, the plants were evaluated for growth and physiological indicators, and leaf tissues were collected for RNA-seq. The growth indicators (growth trend, dry and fresh weights above- and below-ground, etc.) and the antioxidant enzyme system reflect that “FQ119” has stronger drought tolerance. Through RNA-seq analysis, a total of 68,316 transcripts (37,908 genes) were obtained. The largest number of significant differentially expressed genes (DEGs) in the comparison of “FQ118” and “FQ119” was observed at 6 h and 48 h. KEGG analysis demonstrated the significant enrichment of certain pathways associated with drought stress, such as glycerolipid metabolism and galactose metabolism. Co-expression analysis revealed that 7 hub DEGs, including genes encoding a photosystem reaction center subunit protein, chlorophyll a-b binding protein, glyceraldehyde-3-phosphate dehydrogenase A (GAPDH), and others, were coenriched in both comparisons. In addition, three hub genes specific to the comparison during the 6-h processing stage, encoding oxygen-evolving enhancer protein 1, receptor-like serine/threonine-protein kinase and calcium-transporting ATPase, were identified. The above hub genes were related to plant resistance to drought stress, and RT‒qPCR verified that the overall magnitudes of the differences in expression between the two lines gradually increased over time. Virus-induced gene silencing (VIGS) experiments have demonstrated that GAPDH plays a relevant role in the drought resistance pathway. In addition, the differences in expression of 7 DEGs encoding transcription factors, including Dofs, WRKYs, MYBs, and MYCs, also tended to increase with increasing duration of drought treatment, as determined via qPCR. In summary, this study identified several valuable genes related to plant drought resistance by screening genes with differential transcription under drought stress. This in-depth gene mining may provide valuable references and resources for future breeding for drought resistance in tomato. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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Review

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32 pages, 4171 KB

Open AccessReview

Flavonoids in Plant Salt Stress Responses: Biosynthesis, Regulation, Functions, and Signaling Networks

by Muhammad Tanveer Akhtar, Maryam Noor, Xinyi Lin, Zhaogeng Lu and Biao Jin

Plants 2026, 15(1), 171; https://doi.org/10.3390/plants15010171 - 5 Jan 2026

Cited by 26 | Viewed by 3921

Abstract

Soil salinity is a major constraint on global crop production, disrupting photosynthesis, ion homeostasis, and growth. Beyond the roles of classic osmoprotectants and antioxidant enzymes, flavonoids have emerged as versatile mediators of salt stress tolerance at the interface of redox control, hormone signaling, [...] Read more.

Soil salinity is a major constraint on global crop production, disrupting photosynthesis, ion homeostasis, and growth. Beyond the roles of classic osmoprotectants and antioxidant enzymes, flavonoids have emerged as versatile mediators of salt stress tolerance at the interface of redox control, hormone signaling, and developmental plasticity. This review summarizes current evidence on how salinity remodels flavonoid biosynthesis, regulation, and function from cellular to whole-plant scales. We first outline the phenylpropanoid–flavonoid pathway, with emphasis on transcriptional control by MYB, bHLH, and NAC factors and their integration with ABA, JA, and auxin signaling. We then discussed how post-synthetic modifications such as glycosylation and methylation adjust flavonoid stability, compartmentation, and activity under salt stress. Functional sections highlight roles of flavonoids in ROS scavenging, Na⁺/K⁺ homeostasis, membrane integrity, and the modulation of ABA/MAPK/Ca²⁺ cascades and noncoding RNA networks. Spatial aspects, including root–shoot communication and rhizosphere microbiota recruitment, are also considered. Based on this synthesis, we propose a flavonoid-centered stress network (FCSN), in which specific flavonoids function as key nodes that connect metabolic flux with hormonal crosstalk and stress signaling pathways. We argue that reconceptualizing flavonoids as central stress network regulators, rather than generic antioxidants, provides a basis for metabolic engineering, bio-stimulant design, and breeding strategies aimed at improving crop performance on saline soils. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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