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20 pages, 6437 KiB

Open AccessArticle

Genome-Wide Analysis, Identification, and Transcriptional Profile of the Response to Abiotic Stress of the Purple Acid Phosphatases (PAP) Gene Family in Apple

by Hong-Chao Liu, Lei Rao, Jia-Hui Meng, Wen-Teng Zuo and Ting-Ting Sun

Int. J. Mol. Sci. 2025, 26(3), 1011; https://doi.org/10.3390/ijms26031011 - 24 Jan 2025

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Abstract

Purple acid phosphatases (PAPs) play a significant role in plant phosphorus nutrition and can not only release phosphorus from the soil but also regulate the distribution of phosphorus in plants throughout their entire growth and development process. Moreover, members of the PAP protein [...] Read more.

Purple acid phosphatases (PAPs) play a significant role in plant phosphorus nutrition and can not only release phosphorus from the soil but also regulate the distribution of phosphorus in plants throughout their entire growth and development process. Moreover, members of the PAP protein family exert a more extensive influence on plant mineral homeostasis, developmental processes, and stress responses. Three clusters of purple acid phosphatases, including 31 putative genes, were identified in apples (Malus domestica) by searching the Genome Database for Rosaceae. The structure, chromosomal distribution and location, phylogeny, motifs, and cis-acting elements in the gene promoter regions of the MdPAP gene family are reviewed. These genes exhibit different expression patterns in different tissues. For example, almost all MdPAP genes are strongly expressed in the roots, except for MdPAP10, MdPAP12, and MdPAP27. Similarily, all MdPAPs were expressed in the leaves while the transcript levels of MdPAP7, MdPAP10, MdPAP15, MdPAP21, MdPAP24, MdPAP26, MdPAP29, and MdPAP30 were highest in apple flowers. Overall, the expression of the 31 genes significantly changed in either the roots or leaves following the application of phosphorus and/or drought stress. These results indicate that MdPAP family members play a role in plant adaptation to adverse environments. This work explores the adaptative responses to phosphorus and/or drought conditions in apple and establishes a foundation for an enhanced comprehension of the evolution of PAP families and the exploration of the genes of interest. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

15 pages, 3529 KiB

Open AccessArticle

Malus xiaojinensis MxbHLH30 Confers Iron Homeostasis Under Iron Deficiency in Arabidopsis

by Yu Xu, Yingnan Li, Zhuo Chen, Xinze Chen, Xingguo Li, Wenhui Li, Longfeng Li, Qiqi Li, Zihan Geng, Saiyu Shi, Lihua Zhang and Deguo Han

Int. J. Mol. Sci. 2025, 26(1), 368; https://doi.org/10.3390/ijms26010368 - 3 Jan 2025

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Abstract

Iron stress adversely impacts plants’ growth and development. Transcription factors (TFs) receive stress signals and modulate plant tolerance by influencing the expression of related functional genes. In the present study, we investigated the role of an apple bHLH transcription factor MxbHLH30 in the [...] Read more.

Iron stress adversely impacts plants’ growth and development. Transcription factors (TFs) receive stress signals and modulate plant tolerance by influencing the expression of related functional genes. In the present study, we investigated the role of an apple bHLH transcription factor MxbHLH30 in the tolerance to iron stresses. The expression of MxbHLH30 was induced significantly by low-iron and high-iron treatments and MxbHLH30-overexpressed Arabidopsis plants displayed iron-stress-tolerant phenotypes. A determination of physiological and biochemical indexes associated with abiotic stress responses showed that overexpression of MxbHLH30 increased the activities of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in Arabidopsis plants treated with iron stress, and decreased the contents of H₂O₂ and malondialdehyde (MDA), which contribute to reduce cell membrane lipid peroxidation. Meanwhile, the accumulation of proline in transgenic plant cells increased, regulating cell osmotic pressure. Furthermore, quantitative expression analysis indicated that overexpression of MxbHLH30 improved the expression levels of positive functional genes’ responses to iron stress, improving plant resistance. Interestingly, MxbHLH30 may have the ability to balance the homeostasis of iron and other metal ions for the iron homeostasis of Arabidopsis cell under low-iron environments. This research demonstrates that MxbHLH30 is a key regulator of cell iron homeostasis in Arabidopsis plants under iron deficiency, providing new knowledge for plant resistance regulation. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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13 pages, 4227 KiB

Open AccessArticle

StUBC13, a Ubiquitin-Conjugating Enzyme, Positively Regulates Salt and Osmotic Stresses in Potato

by Xue Fu, Xun Tang, Ning Zhang and Huaijun Si

Int. J. Mol. Sci. 2024, 25(23), 13197; https://doi.org/10.3390/ijms252313197 - 8 Dec 2024

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Abstract

Protein ubiquitination is an important regulatory mechanism for biological growth and development against environmental influences, and can affect several biological processes, including the growth, development, and stress responses of plants. However, the function of potato-related ubiquitin-conjugating enzymes in abiotic stress tolerance is poorly [...] Read more.

Protein ubiquitination is an important regulatory mechanism for biological growth and development against environmental influences, and can affect several biological processes, including the growth, development, and stress responses of plants. However, the function of potato-related ubiquitin-conjugating enzymes in abiotic stress tolerance is poorly understood. In this study, a StUBC13 with a UBC conserved structural domain was identified in potato and its function was investigated under osmotic stress and salt stress conditions. The observation of plant phenotypes under stress conditions revealed that overexpressed plants grew better than wild-type plants. In line with the above results, the determination of stress-related physiological indices revealed that the overexpression transgenic plants had better stress tolerance and stronger adaptation to environmental stress, and the transgenic plants were found to tolerate better drought and salt stress by decreasing their malondialdehyde (MDA) content and increasing their superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) contents under stress conditions. Based on these results, StUBC13 has an important regulatory role in the response of plants to abiotic stresses (osmotic stress and salt stress), and overexpression of this gene can improve the tolerance of potatoes to osmotic and salt stresses. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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18 pages, 9282 KiB

Open AccessArticle

Overexpression of the Potato StPYL20 Gene Enhances Drought Resistance and Root Development in Transgenic Plants

by Panfeng Yao, Junmei Cui, Chunli Zhang, Jia Wei, Xinglong Su, Chao Sun, Zhenzhen Bi, Zhen Liu, Jiangping Bai and Yuhui Liu

Int. J. Mol. Sci. 2024, 25(23), 12748; https://doi.org/10.3390/ijms252312748 - 27 Nov 2024

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Abstract

Drought is a primary limiting factor for potato growth. PYR/PYL/RCAR (referred to hereafter as PYL) proteins, as receptors for abscisic acid (ABA), play a crucial role in the plant response to drought stress. However, the underlying mechanisms of this control remain largely elusive [...] Read more.

Drought is a primary limiting factor for potato growth. PYR/PYL/RCAR (referred to hereafter as PYL) proteins, as receptors for abscisic acid (ABA), play a crucial role in the plant response to drought stress. However, the underlying mechanisms of this control remain largely elusive in potatoes. In this study, a potato StPYL20 gene was identified through genome-wide investigation and transcriptome analysis under drought stress. Molecular feature analysis revealed that the StPYL20 gene exhibits the highest expression level in tubers, and is significantly up-regulated under ABA and drought stress conditions. The StPYL20 protein harbors a conserved domain exclusive to the PYL family. Further functional analysis showed that both transient and stable expressions of StPYL20 in tobacco enhanced the drought resistance of transgenic plants, resulting in increased plant height, leaf number, and fresh weight, and an improved root system. Compared to wild-type plants under drought conditions, transgenic tobacco with the StPYL20 gene exhibited lower levels of malondialdehyde (MDA), higher proline (Pro) accumulation, and increased antioxidant enzyme activity. Moreover, overexpression of the StPYL20 gene heightened the sensitivity of transgenic plants to ABA. Furthermore, StPYL20 up-regulated the expression of stress response and development-related genes in transgenic plants under drought stress. In conclusion, our findings indicated that StPYL20 enhances drought resistance and root development in transgenic plants, and plays a positive regulatory role in the potato’s response to drought stress. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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15 pages, 8589 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Alfalfa (Medicago sativa L.) U-Box Gene Family in Response to Abiotic Stresses

by Shuaixian Li, Xiuhua Chen, Meiyan Guo, Xiaoyue Zhu, Wangqi Huang, Changhong Guo and Yongjun Shu

Int. J. Mol. Sci. 2024, 25(22), 12324; https://doi.org/10.3390/ijms252212324 - 17 Nov 2024

Viewed by 838

Abstract

E3 ubiquitin ligases known as plant U-box (PUB) proteins regulate a variety of aspects of plant growth, development, and stress response. However, the functions and characteristics of the PUB gene family in alfalfa remain unclear. This work involved a genome-wide examination of the [...] Read more.

E3 ubiquitin ligases known as plant U-box (PUB) proteins regulate a variety of aspects of plant growth, development, and stress response. However, the functions and characteristics of the PUB gene family in alfalfa remain unclear. This work involved a genome-wide examination of the alfalfa U-box E3 ubiquitin ligase gene. In total, 210 members were identified and divided into five categories according to their homology with the members of the U-box gene family in Arabidopsis thaliana. The phylogenetic analysis, conserved motifs, chromosomal localization, promoters, and regulatory networks of this gene were investigated. Chromosomal localization and covariance analyses indicated that the MsPUB genes expanded MsPUB gene family members through gene duplication events during evolution. MsPUB genes may be involved in the light response, phytohormone response, growth, and development of several biological activities, according to cis-acting element analysis of promoters. In addition, transcriptome analysis and expression analysis by qRT-PCR indicated that most MsPUB genes were significantly upregulated under cold stress, drought stress, and salt stress treatments. Among them, MsPUBS106 and MsPUBS185 were significantly and positively correlated with cold resistance in alfalfa. MsPUBS110, MsPUBS067, MsPUBS111 and MsPUB155 were comprehensively involved in drought stress, low temperature, and salt stress resistance. All things considered, these discoveries offer fresh perspectives on the composition, development, and roles of the PUB gene family in alfalfa. They also provide theoretical guidance for further investigations into the mechanisms regulating the development, evolution, and stress tolerance of MsPUB. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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29 pages, 6797 KiB

Open AccessArticle

Integrating Physiology, Transcriptome, and Metabolome Analyses Reveals the Drought Response in Two Quinoa Cultivars with Contrasting Drought Tolerance

by Yang Wang, Yang Wu, Qinghan Bao, Huimin Shi and Yongping Zhang

Int. J. Mol. Sci. 2024, 25(22), 12188; https://doi.org/10.3390/ijms252212188 - 13 Nov 2024

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Abstract

Quinoa (Chenopodium quinoa Willd.) is an annual broadleaf plant belonging to the Amaranthaceae family. It is a nutritious food crop and is considered to be drought-tolerant, but drought is still one of the most important abiotic stress factors limiting its yield. Quinoa [...] Read more.

Quinoa (Chenopodium quinoa Willd.) is an annual broadleaf plant belonging to the Amaranthaceae family. It is a nutritious food crop and is considered to be drought-tolerant, but drought is still one of the most important abiotic stress factors limiting its yield. Quinoa responses to drought are related to drought intensity and genotype. This study used two different drought-responsive quinoa cultivars, LL1 (drought-tolerant) and ZK1 (drought-sensitive), to reveal the important mechanisms of drought response in quinoa by combining physiological, transcriptomic, and metabolomic analyses. The physiological analysis indicated that Chla/Chlb might be important for drought tolerance in quinoa. A total of 1756 and 764 differentially expressed genes (DEGs) were identified in LL1 and ZK1, respectively. GO (Gene Ontology) enrichment analysis identified 52 common GO terms, but response to abscisic acid (GO:0009737) and response to osmotic stress (GO:0006970) were only enriched in LL1. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that glycerophospholipid metabolism (ko00564) and cysteine and methionine metabolism (ko00270) ranked at the top of the list in both cultivars. A total of 1844 metabolites were identified by metabolomic analysis. “Lipids and lipid-like” molecules had the highest proportions. The DEMs in LL1 and ZK1 were mainly categorized 6 and 4 Human Metabolome Database (HMDB) superclasses, respectively. KEGG analysis revealed that the ‘α-linolenic acid metabolism’ was enriched in both LL1 and ZK1. Joint KEGG analysis also revealed that the ‘α-linolenic acid metabolism’ pathway was enriched by both the DEGs and DEMs of LL1. There were 17 DEGs and 8 DEMs enriched in this pathway, and methyl jasmonate (MeJA) may play an important role in the drought response of quinoa. This study will provide information for the identification of drought resistance in quinoa, research on the molecular mechanism of drought resistance, and genetic breeding for drought resistance in quinoa. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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19 pages, 7637 KiB

Open AccessArticle

Genome-Wide Identification of Basic Helix–Loop–Helix (bHLH) Family in Peanut: Potential Regulatory Roles in Iron Homeostasis

by Gangrong Shi, Zheng Zhang and Jinxiu Li

Int. J. Mol. Sci. 2024, 25(22), 12057; https://doi.org/10.3390/ijms252212057 - 9 Nov 2024

Viewed by 897

Abstract

The basic helix–loop–helix (bHLH) superfamily is the second-largest transcription factor family that participates in a wide range of biological processes in plants, including iron homeostasis. Although the family has been studied in several plant species, a comprehensive investigation is still needed for peanut [...] Read more.

The basic helix–loop–helix (bHLH) superfamily is the second-largest transcription factor family that participates in a wide range of biological processes in plants, including iron homeostasis. Although the family has been studied in several plant species, a comprehensive investigation is still needed for peanut (Arachis hypogaea). Here, a genome-wide analysis identified 373 AhbHLH genes in peanut, which were divided into 14 groups or subfamilies according to phylogenetic analysis. Clustered members generally share similar gene/protein structures, supporting the evolutionary relationships among AhbHLH proteins. Most AhbHLHs experienced whole-genome or segmental duplication. The majority of AhbHLH proteins had a typical bHLH domain, while several phylogenetic groups, including Group VI, X, XIII, and XIV, had the HLH domain. The expression of several AhbHLH genes, including AhbHLH001.3, AhbHLH029.1/.2, AhbHLH047.1/.2, AhbHLH115.1/.2, AhbHLH097.1/.2, AhbHLH109.4, and AhbHLH135.1, was induced by Fe deficiency for both cultivars, or at least in Silihong, suggesting an important role in the Fe deficiency response in peanut. Nine genes (AhbHLH001.3, AhbHLH029.1/.2, AhbHLH047.1/.2, AhbHLH097.1/.2, and AhbHLH115.1/.2) were specifically induced by Fe deficiency in Silihong, and their expression was higher in Silihong than that in Fenghua 1. These genes might be responsible for higher tolerance to Fe deficiency in Silihong. Our findings provide comprehensive information for further elucidating the regulatory mechanism of Fe homeostasis in peanut. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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21 pages, 8465 KiB

Open AccessArticle

Integrated Analysis of Transcriptome and Metabolome Provides Insights into Flavonoid Biosynthesis of Blueberry Leaves in Response to Drought Stress

by Xinghua Feng, Sining Bai, Lianxia Zhou, Yan Song, Sijin Jia, Qingxun Guo and Chunyu Zhang

Int. J. Mol. Sci. 2024, 25(20), 11135; https://doi.org/10.3390/ijms252011135 - 17 Oct 2024

Cited by 2 | Viewed by 1186

Abstract

Blueberries (Vaccinium spp.) are extremely sensitive to drought stress. Flavonoids are crucial secondary metabolites that possess the ability to withstand drought stress. Therefore, improving the drought resistance of blueberries by increasing the flavonoid content is crucial for the development of the blueberry [...] Read more.

Blueberries (Vaccinium spp.) are extremely sensitive to drought stress. Flavonoids are crucial secondary metabolites that possess the ability to withstand drought stress. Therefore, improving the drought resistance of blueberries by increasing the flavonoid content is crucial for the development of the blueberry industry. To explore the underlying molecular mechanism of blueberry in adaptation to drought stress, we performed an integrated analysis of the metabolome and transcriptome of blueberry leaves under drought stress. We found that the most enriched drought-responsive genes are mainly involved in flavonoid biosynthesis and plant hormone signal transduction pathways based on transcriptome data and the main drought-responsive metabolites come from the flavonoid class based on metabolome data. The UDP-glucose flavonoid 3-O-glucosyl transferase (UFGT), flavonol synthase (FLS), and anthocyanidin reductase (ANR-2) genes may be the key genes for the accumulation of anthocyanins, flavonols, and flavans in response to drought stress in blueberry leaves, respectively. Delphinidin 3-glucoside and delphinidin-3-O-glucoside chloride may be the most important drought-responsive flavonoid metabolites. VcMYB1, VcMYBPA1, MYBPA1.2, and MYBPA2.1 might be responsible for drought-induced flavonoid biosynthesis and VcMYB14, MYB14, MYB102, and MYB108 may be responsible for blueberry leaf drought tolerance. ABA responsive elements binding factor (ABF) genes, MYB genes, bHLH genes, and flavonoid biosynthetic genes might form a regulatory network to regulate drought-induced accumulation of flavonoid metabolites in blueberry leaves. Our study provides a useful reference for breeding drought-resistant blueberry varieties. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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26 pages, 7667 KiB

Open AccessArticle

An Enhanced Interaction of Graft and Exogenous SA on Photosynthesis, Phytohormone, and Transcriptome Analysis in Tomato under Salinity Stress

by Chen Miao, Yongxue Zhang, Jiawei Cui, Hongmei Zhang, Hong Wang, Haijun Jin, Panling Lu, Lizhong He, Qiang Zhou, Jizhu Yu and Xiaotao Ding

Int. J. Mol. Sci. 2024, 25(19), 10799; https://doi.org/10.3390/ijms251910799 - 8 Oct 2024

Cited by 1 | Viewed by 900

Abstract

Salt stress can adversely affect global agricultural productivity, necessitating innovative strategies to mitigate its adverse effects on plant growth and yield. This study investigated the effects of exogenous salicylic acid (SA), grafting (G), and their combined application (GSA) on various parameters in tomato [...] Read more.

Salt stress can adversely affect global agricultural productivity, necessitating innovative strategies to mitigate its adverse effects on plant growth and yield. This study investigated the effects of exogenous salicylic acid (SA), grafting (G), and their combined application (GSA) on various parameters in tomato plants subjected to salt stress. The analysis focused on growth characteristics, photosynthesis, osmotic stress substances, antioxidant enzyme activity, plant hormones, ion content, and transcriptome profiles. Salt stress severely inhibits the growth of tomato seedlings. However, SA, G, and GSA improved the plant height by 22.5%, 26.5%, and 40.2%; the stem diameter by 11.0%, 26.0%, and 23.7%; the shoot fresh weight by 76.3%, 113.2%, and 247.4%; the root fresh weight by 150.9%, 238.6%, and 286.0%; the shoot dry weight by 53.5%, 65.1%, and 162.8%; the root dry weight by 150.0%, 150.0%, and 166.7%, and photosynthesis by 4.0%, 16.3%, and 32.7%, with GSA presenting the most pronounced positive effect. Regarding the osmotic stress substances, the proline content increased significantly by more than 259.2% in all treatments, with the highest levels in GSA. Under salt stress, the tomato seedlings accumulated high Na⁺ levels; the SA, G, and GSA treatments enhanced the K⁺ and Ca²⁺ absorption while reducing the Na⁺ and Al³⁺ levels, thereby alleviating the ion toxicity. The transcriptome analysis indicated that SA, G, and GSA influenced tomato growth under salt stress by regulating specific signaling pathways, including the phytohormone and MAPK pathways, which were characterized by increased endogenous SA and decreased ABA content. The combined application of grafting and exogenous SA could be a promising strategy for enhancing plant tolerance to salt stress, offering potential solutions for sustainable agriculture in saline environments. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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14 pages, 3336 KiB

Open AccessArticle

Integration Linkage Mapping and Comparative Transcriptome Analysis to Dissect the Genetic Basis of Rice Salt Tolerance Associated with the Germination Stage

by Leiyue Geng, Tuo Zou, Wei Zhang, Shuo Wang, Yutao Yao, Zhenyu Zheng, Qi Du and Longzhi Han

Int. J. Mol. Sci. 2024, 25(19), 10376; https://doi.org/10.3390/ijms251910376 - 26 Sep 2024

Viewed by 861

Abstract

Soil salinity poses a serious threat to rice production. The salt tolerance of rice at the germination stage is one of the major determinants of stable stand establishment, which is very important for direct seeding in saline soil. The complexity and polygenic nature [...] Read more.

Soil salinity poses a serious threat to rice production. The salt tolerance of rice at the germination stage is one of the major determinants of stable stand establishment, which is very important for direct seeding in saline soil. The complexity and polygenic nature of salt tolerance have limited the efficiency of discovering and cloning key genes in rice. In this study, an RIL population with an ultra-high-density genetic map was employed to investigate the salt-tolerant genetic basis in rice, and a total of 20 QTLs were detected, including a major and stable QTL (qRCL3-1). Subsequently, salt-specific DEGs from a comparative transcriptome analysis were overlaid onto annotated genes located on a stable QTL interval, and eight putative candidate genes were further identified. Finally, from the sequence alignment and variant analysis, OsCam1-1 was confirmed to be the most promising candidate gene for regulating salinity tolerance in rice. This study provides important information for elucidating the genetic and molecular basis of rice salt tolerance at the germination stage, and the genes detected here will be useful for improvements in rice salt tolerance. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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15 pages, 2624 KiB

Open AccessArticle

Wheat Transcription Factor TaMYB60 Modulates Cuticular Wax Biosynthesis by Activating TaFATB and TaCER1 Expression

by Xiaoyu Wang, Wanzhen Chen, Pengfei Zhi and Cheng Chang

Int. J. Mol. Sci. 2024, 25(19), 10335; https://doi.org/10.3390/ijms251910335 - 26 Sep 2024

Cited by 2 | Viewed by 901

Abstract

Cuticular wax mixtures cover the epidermis of land plants and shield plant tissues from abiotic and biotic stresses. Although cuticular wax-associated traits are employed to improve the production of bread wheat, regulatory mechanisms underlying wheat cuticular wax biosynthesis remain poorly understood. In this [...] Read more.

Cuticular wax mixtures cover the epidermis of land plants and shield plant tissues from abiotic and biotic stresses. Although cuticular wax-associated traits are employed to improve the production of bread wheat, regulatory mechanisms underlying wheat cuticular wax biosynthesis remain poorly understood. In this research, partially redundant transcription factors TaMYB60-1 and TaMYB60-2 were identified as positive regulators of wheat cuticular wax biosynthesis. Knock-down of wheat TaMYB60-1 and TaMYB60-2 genes by virus-induced gene silencing resulted in attenuated wax accumulation and enhanced cuticle permeability. The roles of wheat fatty acyl-ACP thioesterase genes TaFATB1 and TaFATB2 in cuticular wax biosynthesis were characterized. Silencing wheat TaFATB1 and TaFATB2 genes led to reduced wax accumulation and increased cuticle permeability, suggesting that TaFATB1 and TaFATB2 genes positively contribute to wheat cuticular wax biosynthesis. Importantly, transcription factors TaMYB60-1 and TaMYB60-2 exhibit transcriptional activation ability and could stimulate the expression of wax biosynthesis genes TaFATB1, TaFATB2, and ECERIFERUM 1 (TaCER1). These findings support that transcription factor TaMYB60 positively regulates wheat cuticular wax biosynthesis probably by activating transcription of TaFATB1, TaFATB2, and TaCER1 genes. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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17 pages, 8112 KiB

Open AccessArticle

Silicon Nanomaterials Enhance Seedling Growth and Plant Adaptation to Acidic Soil by Promoting Photosynthesis and Antioxidant Activity in Mustard (Brassica campestris L.)

by Md. Kamrul Hasan, Jannat Shopan, Israt Jahan and Tonima Islam Suravi

Int. J. Mol. Sci. 2024, 25(19), 10318; https://doi.org/10.3390/ijms251910318 - 25 Sep 2024

Viewed by 1571

Abstract

Soil acidity is a divesting factor that restricts crop growth and productivity. Conversely, silicon nanomaterials (Si-NMs) have been praised as a blessing of modern agricultural intensification by overcoming the ecological barrier. Here, we performed a sequential study from seed germination to the yield [...] Read more.

Soil acidity is a divesting factor that restricts crop growth and productivity. Conversely, silicon nanomaterials (Si-NMs) have been praised as a blessing of modern agricultural intensification by overcoming the ecological barrier. Here, we performed a sequential study from seed germination to the yield performance of mustard (Brassica campestris) crops under acid-stressed conditions. The results showed that Si-NMs significantly improved seed germination and seedling growth under acid stress situations. These might be associated with increased antioxidant activity and the preserve ratio of GSH/GSSG and AsA/DHA, which is restricted by soil acidity. Moreover, Si-NMs in field regimes significantly diminished the acid-stress-induced growth inhibitions, as evidenced by increased net photosynthesis and biomass accumulations. Again, Si-NMs triggered all the critical metrics of crop productivity, including the seed oil content. Additionally, Si-NMs, upon dolomite supplementation, further triggered all the metrics of yields related to farming resilience. Therefore, the present study highlighted the crucial roles of Si-NMs in sustainable agricultural expansion and cropping intensification, especially in areas affected by soil acidity. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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17 pages, 5639 KiB

Open AccessArticle

Comprehensive, Genome-Wide Identification and Expression Analyses of Phenylalanine Ammonia-Lyase Family under Abiotic Stresses in Brassica oleracea

by Umer Karamat, Juxian Guo, Shizheng Jiang, Imran Khan, Mengting Lu, Mei Fu and Guihua Li

Int. J. Mol. Sci. 2024, 25(19), 10276; https://doi.org/10.3390/ijms251910276 - 24 Sep 2024

Viewed by 968

Abstract

Phenylalanine ammonia-lyase (PAL) acts as the rate-limiting enzyme for anthocyanin biosynthesis through the phenylpropanoid pathway, a crucial component of plant secondary metabolism. The PAL gene family plays a crucial role in plants’ defense and stress responses, but its in silico identification and expression [...] Read more.

Phenylalanine ammonia-lyase (PAL) acts as the rate-limiting enzyme for anthocyanin biosynthesis through the phenylpropanoid pathway, a crucial component of plant secondary metabolism. The PAL gene family plays a crucial role in plants’ defense and stress responses, but its in silico identification and expression analyses in Brassica oleracea under different abiotic stresses remain unexplored. In this study, nine BolPAL, seven BrPAL, four AtPAL, and seventeen BnPAL genes were obtained from the genomes of B. oleracea, Brassica rapa, Arabidopsis thaliana, and Brassica napus, respectively. Segmental duplication and purifying selection are the causes of the BolPAL gene’s amplification and evolution. The BolPAL genes with comparable intron–exon architectures and motifs were grouped together in the same clade. Three categories comprised the cis-regulatory elements: abiotic stressors, phytohormones, and light. According to the results of the qRT-PCR experiments, the majority of the BolPAL genes were expressed highly under MeJA, a low temperature, and a high temperature, and they were downregulated under ABA. Under white light (100 µmol m⁻² s⁻¹) with 50, 100, or 150 µmol m⁻² s⁻¹ far-red (FR), only a small number of the PAL genes were expressed at 50 and 100 µmol m⁻² s⁻¹ FR, while the majority of the PAL genes were slightly elevated at 150 µmol m⁻² s⁻¹ FR. This work offers a theoretical foundation for molecular breeding research to investigate the role of BolPAL genes and their role in anthocyanin biosynthesis. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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19 pages, 15258 KiB

Open AccessArticle

Integrated miRNA and mRNA Transcriptome Analysis Reveals Regulatory Mechanisms in the Response of Winter Brassica rapa to Drought Stress

by Li Ma, Yanxia Xu, Xiaolei Tao, Abbas Muhammad Fahim, Xianliang Zhang, Chunyang Han, Gang Yang, Wangtian Wang, Yuanyuan Pu, Lijun Liu, Tingting Fan, Junyan Wu and Wancang Sun

Int. J. Mol. Sci. 2024, 25(18), 10098; https://doi.org/10.3390/ijms251810098 - 20 Sep 2024

Viewed by 990

Abstract

Drought is a major abiotic stress factor that reduces agricultural productivity. Understanding the molecular regulatory network of drought response in winter rape is of great significance for molecular Brassica rapa. In order to comprehensively analyze the network expression of DEGs and DEMIs [...] Read more.

Drought is a major abiotic stress factor that reduces agricultural productivity. Understanding the molecular regulatory network of drought response in winter rape is of great significance for molecular Brassica rapa. In order to comprehensively analyze the network expression of DEGs and DEMIs in winter rape under drought stress, in this study we used Longyou 7 as the experimental material to identify DEGs and DEMIs related to drought stress by transcriptome and miRNA sequencing. A total of 14–15 key differential mRNA genes related to drought stress and biological stress were screened out under different treatments in the three groups. and 32 differential miRNAs were identified through targeted regulatory relationships, and the mRNA expression of 20 target genes was negatively regulated by the targeting regulatory relationship. It is mainly enriched in starch and sucrose metabolism, carbon metabolism and other pathways. Among them, gra-MIR8731-p3_2ss13GA18GA regulated the expression of multiple mRNAs in the three treatments. miRNA is mainly involved in the drought resistance of Chinese cabbage winter rape by regulating the expression of target genes, such as starch and sucrose metabolism, amino acid biosynthesis, and carbon metabolism. These miRNAs and their target genes play an indispensable role in winter rapeseed drought stress tolerance regulation. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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23 pages, 5144 KiB

Open AccessArticle

FaTEDT1L of Octoploid Cultivated Strawberry Functions as a Transcriptional Activator and Enhances Abiotic Stress Tolerance in Transgenic Arabidopsis

by Ching-Ying Chu, Lee-Fong Lin, Shang-Chih Lai, Jui-Hung Yang and Ming-Lun Chou

Int. J. Mol. Sci. 2024, 25(18), 10091; https://doi.org/10.3390/ijms251810091 - 19 Sep 2024

Viewed by 908

Abstract

Plants may encounter abiotic stresses, such as drought, flooding, salinity, and extreme temperatures, thereby negatively affecting their growth, development, and reproduction. In order to enhance their tolerance to such stresses, plants have developed intricate signaling networks that regulate stress-responsive gene expression. For example, [...] Read more.

Plants may encounter abiotic stresses, such as drought, flooding, salinity, and extreme temperatures, thereby negatively affecting their growth, development, and reproduction. In order to enhance their tolerance to such stresses, plants have developed intricate signaling networks that regulate stress-responsive gene expression. For example, Arabidopsis Enhanced Drought Tolerance1/HOMEODOMAIN GLABROUS 11 (AtEDT1/HDG11), one of the transcription factor genes from the group IV of homeodomain-leucine zipper (HD-ZIP) gene family, has been shown to increase drought tolerance in various transgenic plants. However, the underlying molecular mechanisms of enhanced stress tolerance remain unclear. In this study, we identified a homologous gene related to AtEDT1/HDG11, named FaTEDT1L, from the transcriptome sequencing database of cultivated strawberry. Phylogenetic analysis revealed the close relationship of FaTEDT1L with AtEDT1/HDG11, which is one of the group IV members of the HD-ZIP gene family. Yeast one-hybrid analysis showed that FaTEDT1L functions as a transcriptional activator. Transgenic Arabidopsis plants overexpressing FaTEDT1L under the control of the cauliflower mosaic virus (CaMV) 35S promoter exhibited significantly enhanced tolerance to osmotic stress (both drought and salinity) when compared to the wild-type (WT) plants. Under osmotic stress, the average root length was 3.63 ± 0.83 cm, 4.20 ± 1.03 cm, and 4.60 ± 1.14 cm for WT, 35S::FaTEDT1L T₂ #3, and 35S:: FaTEDT1L T₂ #5, respectively. Substantially increased root length in 35S::FaTEDT1L T₂ #3 and 35S::FaTEDT1L T₂ #5 was noted when compared to the WT. In addition, the average water loss rates were 64%, 57.1%, and 55.6% for WT, 35S::FaTEDT1L T2 #3, and 35S::FaTEDT1L T₂ #5, respectively, after drought treatment, indicating a significant decrease in water loss rate of 35S:: FaTEDT1L T₂ #3 and 35S::FaTEDT1L T₂ #5 is a critical factor in enhancing plant drought resistance. These findings thus highlight the crucial role of FaTEDT1L in mitigating drought and salt stresses and regulating plant osmotic stress tolerance. Altogether, FaTEDT1L shows its potential usage as a candidate gene for strawberry breeding in improving crop resilience and increasing agricultural productivity under adverse environmental conditions. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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19 pages, 9897 KiB

Open AccessArticle

Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity

by Jinguo Zhang, Dezhuang Meng, Jianfeng Li, Yaling Bao, Peng Yu, Guohui Dou, Jinmeng Guo, Chenghang Tang, Jiaqi Lv, Xinchen Wang, Xingmeng Wang, Fengcai Wu and Yingyao Shi

Int. J. Mol. Sci. 2024, 25(18), 9815; https://doi.org/10.3390/ijms25189815 - 11 Sep 2024

Cited by 1 | Viewed by 933

Abstract

Based on the genome information of rice (Nipponbare), this study screened and identified six raffinose synthase (RS) genes and analyzed their physical and chemical properties, phylogenetic relationship, conserved domains, promoter cis-acting elements, and the function and genetic diversity of the gene-CDS-haplotype (gcHap). The [...] Read more.

Based on the genome information of rice (Nipponbare), this study screened and identified six raffinose synthase (RS) genes and analyzed their physical and chemical properties, phylogenetic relationship, conserved domains, promoter cis-acting elements, and the function and genetic diversity of the gene-CDS-haplotype (gcHap). The results showed that these genes play key roles in abiotic stress response, such as OsRS5, whose expression in leaves changed significantly under high salt, drought, ABA, and MeJA treatments. In addition, the OsRS genes showed significant genetic variations in different rice populations. The main gcHaps of most OsRS loci had significant effects on key agronomic traits, and the frequency of these alleles varied significantly among different rice populations and subspecies. These findings provide direction for studying the RS gene family in other crops. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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Review

Jump to: Research

24 pages, 1436 KiB

Open AccessReview

Impact of High-Temperature Stress on Maize Seed Setting: Cellular and Molecular Insights of Thermotolerance

by Zhaoyi Fan, Haoqi Song, Mengyuan Qi, Mengqing Wang, Yunfeng Bai, Yuhui Sun and Haidong Yu

Int. J. Mol. Sci. 2025, 26(3), 1283; https://doi.org/10.3390/ijms26031283 - 2 Feb 2025

Viewed by 217

Abstract

Global warming poses a significant threat to crop production and food security, with maize (Zay mays L.) particularly vulnerable to high-temperature stress (HTS). This review explores the detrimental impacts of elevated temperatures on maize development across various growth stages, analyzed within the [...] Read more.

Global warming poses a significant threat to crop production and food security, with maize (Zay mays L.) particularly vulnerable to high-temperature stress (HTS). This review explores the detrimental impacts of elevated temperatures on maize development across various growth stages, analyzed within the source–sink framework, with a particular focus on seed setting and yield reduction. It provides a broad analysis of maize cellular and molecular responses to HTS, highlighting the key roles of plant hormone abscisic acid (ABA) signaling, calcium signaling, chloroplast, and the DNA damage repair (DDR) system in maize. HTS disrupts ABA signaling pathways, impairing stomatal regulation and reducing water-use efficiency, while calcium signaling orchestrates stress responses by activating heat shock proteins and other protective mechanisms. Chloroplasts, as central to photosynthesis, are particularly sensitive to HTS, often exhibiting photosystem II damage and chlorophyll degradation. Recent studies also highlight the significance of the DDR system, with genes like ZmRAD51C playing crucial roles in maintaining genomic stability during reproductive organ development. DNA damage under HTS conditions emerges as a key factor contributing to reduced seed set, although the precise molecular mechanisms remain to be fully elucidated. Furthermore, the review examines cutting-edge genetic improvement strategies, aimed at developing thermotolerant maize cultivars. These recent research advances underscore the need for further investigation into the molecular basis of thermotolerance and open the door for future advancements in breeding thermotolerant crops. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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32 pages, 2762 KiB

Open AccessReview

Molecular Communication of Microbial Plant Biostimulants in the Rhizosphere Under Abiotic Stress Conditions

by Sajid Ali, Muhammad Saeed Akhtar, Muhammad Siraj and Wajid Zaman

Int. J. Mol. Sci. 2024, 25(22), 12424; https://doi.org/10.3390/ijms252212424 - 19 Nov 2024

Viewed by 1747

Abstract

Microbial plant biostimulants offer a promising, sustainable solution for enhancing plant growth and resilience, particularly under abiotic stress conditions such as drought, salinity, extreme temperatures, and heavy metal toxicity. These biostimulants, including plant growth-promoting rhizobacteria, mycorrhizal fungi, and nitrogen-fixing bacteria, enhance plant tolerance [...] Read more.

Microbial plant biostimulants offer a promising, sustainable solution for enhancing plant growth and resilience, particularly under abiotic stress conditions such as drought, salinity, extreme temperatures, and heavy metal toxicity. These biostimulants, including plant growth-promoting rhizobacteria, mycorrhizal fungi, and nitrogen-fixing bacteria, enhance plant tolerance through mechanisms such as phytohormone production, nutrient solubilization, osmotic adjustment, and antioxidant enzyme activation. Advances in genomics, metagenomics, transcriptomics, and proteomics have significantly expanded our understanding of plant–microbe molecular communication in the rhizosphere, revealing mechanisms underlying these interactions that promote stress resilience. However, challenges such as inconsistent field performance, knowledge gaps in stress-related molecular signaling, and regulatory hurdles continue to limit broader biostimulant adoption. Despite these challenges, microbial biostimulants hold significant potential for advancing agricultural sustainability, particularly amid climate change-induced stresses. Future studies and innovation, including Clustered Regularly Interspaced Short Palindromic Repeats and other molecular editing tools, should optimize biostimulant formulations and their application for diverse agro-ecological systems. This review aims to underscore current advances, challenges, and future directions in the field, advocating for a multidisciplinary approach to fully harness the potential of biostimulants in modern agriculture. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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25 pages, 5224 KiB

Open AccessReview

Insights into the Epigenetic Basis of Plant Salt Tolerance

by Dongyu Zhang, Duoqian Zhang, Yaobin Zhang, Guanlin Li, Dehao Sun, Bo Zhou and Jingrui Li

Int. J. Mol. Sci. 2024, 25(21), 11698; https://doi.org/10.3390/ijms252111698 - 31 Oct 2024

Cited by 1 | Viewed by 1851

Abstract

The increasing salinity of agricultural lands highlights the urgent need to improve salt tolerance in crops, a critical factor for ensuring food security. Epigenetic mechanisms are pivotal in plant adaptation to salt stress. This review elucidates the complex roles of DNA methylation, histone [...] Read more.

The increasing salinity of agricultural lands highlights the urgent need to improve salt tolerance in crops, a critical factor for ensuring food security. Epigenetic mechanisms are pivotal in plant adaptation to salt stress. This review elucidates the complex roles of DNA methylation, histone modifications, histone variants, and non-coding RNAs in the fine-tuning of gene expression in response to salt stress. It emphasizes how heritable changes, which do not alter the DNA sequence but significantly impact plant phenotype, contribute to this adaptation. DNA methylation is notably prevalent under high-salinity conditions and is associated with changes in gene expression that enhance plant resilience to salt. Modifications in histones, including both methylation and acetylation, are directly linked to the regulation of salt-tolerance genes. The presence of histone variants, such as H2A.Z, is altered under salt stress, promoting plant adaptation to high-salinity environments. Additionally, non-coding RNAs, such as miRNAs and lncRNAs, contribute to the intricate gene regulatory network under salt stress. This review also underscores the importance of understanding these epigenetic changes in developing plant stress memory and enhancing stress tolerance. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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26 pages, 853 KiB

Open AccessReview

Molecular Mechanisms Underlying Freezing Tolerance in Plants: Implications for Cryopreservation

by Magdalena Białoskórska, Anna Rucińska and Maja Boczkowska

Int. J. Mol. Sci. 2024, 25(18), 10110; https://doi.org/10.3390/ijms251810110 - 20 Sep 2024

Cited by 1 | Viewed by 2167

Abstract

Cryopreservation is a crucial technique for the long-term ex situ conservation of plant genetic resources, particularly in the context of global biodiversity decline. This process entails freezing biological material at ultra-low temperatures using liquid nitrogen, which effectively halts metabolic activities and preserves plant [...] Read more.

Cryopreservation is a crucial technique for the long-term ex situ conservation of plant genetic resources, particularly in the context of global biodiversity decline. This process entails freezing biological material at ultra-low temperatures using liquid nitrogen, which effectively halts metabolic activities and preserves plant tissues over extended periods. Over the past seven decades, a plethora of techniques for cryopreserving plant materials have been developed. These include slow freezing, vitrification, encapsulation dehydration, encapsulation–vitrification, droplet vitrification, cryo-plates, and cryo-mesh techniques. A key challenge in the advancement of cryopreservation lies in our ability to understand the molecular processes underlying plant freezing tolerance. These mechanisms include cold acclimatization, the activation of cold-responsive genes through pathways such as the ICE–CBF–COR cascade, and the protective roles of transcription factors, non-coding RNAs, and epigenetic modifications. Furthermore, specialized proteins, such as antifreeze proteins (AFPs) and late embryogenesis abundant (LEA) proteins, play crucial roles in protecting plant cells during freezing and thawing. Despite its potential, cryopreservation faces significant challenges, particularly in standardizing protocols for a wide range of plant species, especially those from tropical and subtropical regions. This review highlights the importance of ongoing research and the integration of omics technologies to improve cryopreservation techniques, ensuring their effectiveness across diverse plant species and contributing to global efforts regarding biodiversity conservation. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 2nd Edition)

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