International Journal of Molecular Sciences

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17 pages, 21053 KiB

Open AccessArticle

Overexpression of StCDPK13 in Potato Enhances Tolerance to Drought Stress

by Zhenzhen Bi, Simon Dontoro Dekomah, Yihao Wang, Zhuanfang Pu, Xiangdong Wang, Richard Dormatey, Chao Sun, Yuhui Liu, Zhen Liu, Jiangping Bai and Panfeng Yao

Int. J. Mol. Sci. 2024, 25(23), 12620; https://doi.org/10.3390/ijms252312620 - 24 Nov 2024

Viewed by 402

Abstract

Calcium-dependent protein kinases (CDPKs), which are activated by transient changes in the Ca²⁺ concentration in plants, are important for various biological processes, such as growth, development, defense against biotic and abiotic stresses, and others. Mannitol is commonly used as an osmotic regulatory [...] Read more.

Calcium-dependent protein kinases (CDPKs), which are activated by transient changes in the Ca²⁺ concentration in plants, are important for various biological processes, such as growth, development, defense against biotic and abiotic stresses, and others. Mannitol is commonly used as an osmotic regulatory substance in culture medium or nutrient solutions to create water-deficit conditions. Here, we cloned the potato (Solanum tuberosum L.) StCDPK13 gene and generated stable transgenic StCDPK13-overexpression potato plants. To investigate the potential functions of StCDPK13 in response to drought stress, overexpression-transgenic (OE1, OE2, and OE7) and wild-type (WT) potato seedlings were cultured on MS solid media without or with mannitol, representing the control or drought stress, for 20 days; the elevated mannitol concentrations (150 and 200 mM) were the drought stress conditions. The StCDPK13 gene was consistently expressed in different tissues and was induced by drought stress in both OE and WT plants. The phenotypic traits and an analysis of physiological indicators revealed that the transgenic plants exhibited more tolerance to drought stress than the WT plants. The overexpression lines showed an increased plant height, number of leaves, dry shoot weight, root length, root number, root volume, number of root tips, fresh root weight, and dry root weight under drought stress. In addition, the activities of antioxidant enzymes (CAT, SOD, and POD) and the accumulation of proline and neutral sugars were significantly increased, whereas the levels of malondialdehyde (MDA) and reactive oxygen species (ROS), including hydrogen peroxide (H₂O₂) and O₂^•−, were significantly reduced in the OE lines compared to WT plants under drought stress. Moreover, the stomatal aperture of the leaves and the water loss rate in the leaves of the OE lines were significantly reduced under drought stress compared to the WT plants. In addition, the overexpression of StCDPK13 upregulated the expression levels of stress-related genes under drought stress. Collectively, these results indicate that the StCDPK13 gene plays a positive role in drought tolerance by reducing the stomatal aperture, promoting ROS scavenging, and alleviating oxidative damage under drought stress in potatoes. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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14 pages, 2472 KiB

Open AccessArticle

Surface Display of Multiple Metal-Binding Domains in Deinococcus radiodurans Alleviates Cadmium and Lead Toxicity in Rice

by Liangyan Wang, Yudong Wang, Shang Dai and Binqiang Wang

Int. J. Mol. Sci. 2024, 25(23), 12570; https://doi.org/10.3390/ijms252312570 - 22 Nov 2024

Viewed by 263

Abstract

Cadmium (Cd) and lead (Pb) are the primary hazardous heavy metals that accumulate in crops and pose substantial risks to public health via the food chain. Limiting the migration of these toxic metals from contaminated environments to rice is the most direct and [...] Read more.

Cadmium (Cd) and lead (Pb) are the primary hazardous heavy metals that accumulate in crops and pose substantial risks to public health via the food chain. Limiting the migration of these toxic metals from contaminated environments to rice is the most direct and crucial remediation approach. Bioremediation with microorganisms has been extensively utilized for managing heavy metal contamination in the natural environment, and the interplay between microbes and crops is important to alleviate heavy metal stress. Here, we express Lpp-OmpA fused with two metal-binding domains (PbBD and MTT5) in the outer membrane of Deinococcus radiodurans to enhance both Cd and Pb adsorption. Our results showed that the recombinant strain LOPM, which displayed an increased tolerance to both Cd and Pb stress, exhibited a 4.9-fold higher Cd adsorption and 3.2-fold higher Pb adsorption compared to wild-type strain R1. After LOPM cells colonized the rice root, Cd content reduced to 47.0% in root and 43.4% in shoot; Pb content reduced to 55.4% in root and 26.9% in shoot, as compared to the plant’s exposure to Cd and Pb. In addition, cells of LOPM strain colonized on rice roots alleviate Cd- and Pb-induced oxidative stress by reducing ROS levels and enhancing antioxidant enzyme activities in rice. This study supplies a promising application of genetic-engineering extremophile bacteria in reducing heavy metal accumulation and toxicity in rice. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

16 pages, 7655 KiB

Open AccessArticle

Genome-Wide Identification of Freezing-Responsive Genes in a Rapeseed Line NTS57 Tolerant to Low-Temperature

by Guodong Zhao, Jiaping Wei, Junmei Cui, Shichang Li, Guoqiang Zheng and Zigang Liu

Int. J. Mol. Sci. 2024, 25(23), 12491; https://doi.org/10.3390/ijms252312491 - 21 Nov 2024

Viewed by 257

Abstract

Winter rapeseed is a high-oil crop that exhibits significant sensitivity to low temperatures, leading to a substantial reduction in production. Hence, it is of great significance to elucidate the genomic genetic mechanism of strong freezing-resistant winter rapeseed to improve their freezing-resistant traits. In [...] Read more.

Winter rapeseed is a high-oil crop that exhibits significant sensitivity to low temperatures, leading to a substantial reduction in production. Hence, it is of great significance to elucidate the genomic genetic mechanism of strong freezing-resistant winter rapeseed to improve their freezing-resistant traits. In this study, global transcriptome expression profiles of the freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained for the years 2015, 2016, and 2017 by RNA sequencing (RNA-seq). Most differentially expressed genes (DEGs) were involved in the plant hormone signal transduction, alpha-linolenic acid metabolism, protein processing, glutathione metabolism, and plant-pathogen interaction pathways. Antioxidant enzyme activities and lipid peroxidation levels were significantly positively and negatively correlated with overwintering rate (OWR), respectively. After freezing treatment, the formation of freezing resistance of NS was attributed to the increase in antioxidant enzyme activities and content of osmotic regulation substances, as well as the decrease in lipid peroxidation level. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and phenotypic verification indicated that heat stress transcription factor A2 (HSFA2) and 17.6 kDa class II heat shock protein (HSP17.6) participated in the response to freezing stress. This study will further refine the regulatory network of plants against freezing stress and help to screen candidate genes for improving plant freezing resistance. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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16 pages, 7140 KiB

Open AccessArticle

Genome-Wide and Transcriptome Analysis of Autophagy-Related ATG Gene Family and Their Response to Low-Nitrogen Stress in Sugar Beet

by Rongli Jia, Ruxin Zhou, Yue Chang, Lei Wei, Liuxi Yi, Binjie Ma and Shude Shi

Int. J. Mol. Sci. 2024, 25(22), 11932; https://doi.org/10.3390/ijms252211932 - 6 Nov 2024

Viewed by 422

Abstract

Sugar beet (Beta vulgaris L.) is a significant global crop for sugar production, with nitrogen playing a crucial role in its growth, development, and sugar yield. Autophagy facilitates nutrient reabsorption and recycling under nutrient stress by degrading intracellular components, thereby enhancing plant [...] Read more.

Sugar beet (Beta vulgaris L.) is a significant global crop for sugar production, with nitrogen playing a crucial role in its growth, development, and sugar yield. Autophagy facilitates nutrient reabsorption and recycling under nutrient stress by degrading intracellular components, thereby enhancing plant nitrogen use efficiency. However, research on the autophagy response to low-nitrogen stress in sugar beet remains limited. In this study, 29 members of the ATG gene family were identified, with genes within the same subfamily displaying similar gene structures and conserved domains. These ATG genes in sugar beet contain various hormone and stress-response elements. Transcriptome data and qRT-PCR analysis further revealed that the expression levels of ATG4, ATG8b, ATG18a, TOR, NBR1, ATI, ATG8a, ATG12, and VTI12a were significantly upregulated under low-nitrogen stress, with most genes showing high expression levels across different tissues. These ATG genes are thus likely involved in regulating autophagy in response to low-nitrogen conditions. The observed increase in autophagosome numbers further supports the induction of autophagy by low-nitrogen stress. These nine genes can be considered key candidates for further research on nitrogen-sensitive autophagy in the sugar beet ATG gene family. This study provides a comprehensive analysis of the structure and biological functions of ATG genes in sugar beet, offering genetic resources for future efforts to improve sugar beet varieties through genetic engineering. Such efforts could focus on regulating autophagy to enhance nitrogen use efficiency and develop new germplasm. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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27 pages, 11777 KiB

Open AccessArticle

Transcriptional Profiling Analysis Providing Insights into the Harsh Environments Tolerance Mechanisms of Krascheninnikovia arborescens

by Hongyi Zhang, Yingnan Wang, Binjie Ma, Xiangqi Bu, Zhenhua Dang and Yingchun Wang

Int. J. Mol. Sci. 2024, 25(22), 11891; https://doi.org/10.3390/ijms252211891 - 5 Nov 2024

Viewed by 522

Abstract

Krascheninnikovia arborescens, an endemic shrub in China, thrives in desertification-prone environments due to its robust biomass, hairy leaves, and extensive root system. It is vital for ecological restoration and serves as a valuable forage plant. This study explored the molecular mechanisms underlying K. [...] Read more.

Krascheninnikovia arborescens, an endemic shrub in China, thrives in desertification-prone environments due to its robust biomass, hairy leaves, and extensive root system. It is vital for ecological restoration and serves as a valuable forage plant. This study explored the molecular mechanisms underlying K. arborescens’ adaptation to desert conditions, focusing on its physiological, biochemical, and transcriptomic responses to drought, salt, and alkali stresses. The results revealed that the three stresses have significant impacts on the photosynthetic, antioxidant, and ion balance systems of the plants, with the alkali stress inducing the most pronounced changes and differential gene expression. The clustering and functional enrichment analyses of differentially expressed genes (DEGs) highlighted the enrichment of the induced genes in pathways related to plant hormone signaling, phenylpropanoid biosynthesis, and transcription factors following stress treatments. In these pathways, the synthesis and signal transduction of abscisic acid (ABA) and ethylene, as well as the flavonoid and lignin synthesis pathways, and transcription factors such as MYB, AP2/ERF, bHLH, NAC, and WRKY responded actively to the stress and played pivotal roles. Through the WGCNA analysis, 10 key modules were identified, with the yellow module demonstrating a high correlation with the ABA and anthocyanin contents, while the turquoise module was enriched in the majority of genes related to hormone and phenylpropanoid pathways. The analysis of hub genes in these modules highlighted the significant roles of the bHLH and MYB transcription factors. These findings could offer new insights into the molecular mechanisms that enable the adaptation of K. arborescens to desert environments, enhancing our understanding of how other desert plants adapt to harsh conditions. These insights are crucial for exploring and utilizing high-quality forage plant germplasm resources and ecological development, with the identified candidate genes serving as valuable targets for further research on stress-resistant genes. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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19 pages, 15089 KiB

Open AccessArticle

Genome-Scale Identification of Wild Soybean Serine/Arginine-Rich Protein Family Genes and Their Responses to Abiotic Stresses

by Yanping Wang, Xiaomei Wang, Rui Zhang, Tong Chen, Jialei Xiao, Qiang Li, Xiaodong Ding and Xiaohuan Sun

Int. J. Mol. Sci. 2024, 25(20), 11175; https://doi.org/10.3390/ijms252011175 - 17 Oct 2024

Viewed by 638

Abstract

Serine/arginine-rich (SR) proteins mostly function as splicing factors for pre-mRNA splicing in spliceosomes and play critical roles in plant development and adaptation to environments. However, detailed study about SR proteins in legume plants is still lacking. In this report, we performed a genome-wide [...] Read more.

Serine/arginine-rich (SR) proteins mostly function as splicing factors for pre-mRNA splicing in spliceosomes and play critical roles in plant development and adaptation to environments. However, detailed study about SR proteins in legume plants is still lacking. In this report, we performed a genome-wide investigation of SR protein genes in wild soybean (Glycine soja) and identified a total of 31 GsSR genes from the wild soybean genome. The analyses of chromosome location and synteny show that the GsSRs are unevenly distributed on 15 chromosomes and are mainly under the purifying selection. The GsSR proteins can be phylogenetically classified into six sub-families and are conserved in evolution. Prediction of protein phosphorylation sites indicates that GsSR proteins are highly phosphorylated proteins. The protein–protein interaction network implies that there exist numerous interactions between GsSR proteins. We experimentally confirmed their physical interactions with the representative SR proteins of spliceosome-associated components such as U1-70K or U2AF35 by yeast two-hybrid assays. In addition, we identified various stress-/hormone-responsive cis-acting elements in the promoter regions of these GsSR genes and verified their expression patterns by RT-qPCR analyses. The results show most GsSR genes are highly expressed in root and stem tissues and are responsive to salt and alkali stresses. Splicing analysis showed that the splicing patterns of GsSRs were in a tissue- and stress-dependent manner. Overall, these results will help us to further investigate the biological functions of leguminous plant SR proteins and shed new light on uncovering the regulatory mechanisms of plant SR proteins in growth, development, and stress responses. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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17 pages, 4757 KiB

Open AccessArticle

Identification, Cloning, and Characterization of Two Acupuncture-Injury-Inducing Promoters in Rice

by Jianyu Wang, Zengfeng Ma, Dong Fu, Yan Wu, Zaihui Zhou, Changyan Li and Junhao Shen

Int. J. Mol. Sci. 2024, 25(19), 10564; https://doi.org/10.3390/ijms251910564 - 30 Sep 2024

Viewed by 658

Abstract

As an important global food crop, rice is damaged by a variety of piercing–sucking pests. Identifying a broad-spectrum promoter induced by the physical signal of sucking pests and applying it to transgenic breeding to mitigate the damage caused by different sucking pests will [...] Read more.

As an important global food crop, rice is damaged by a variety of piercing–sucking pests. Identifying a broad-spectrum promoter induced by the physical signal of sucking pests and applying it to transgenic breeding to mitigate the damage caused by different sucking pests will significantly improve the efficiency of our breeding. This study compared the transcriptome changes in two rice varieties under needle-wounding stress to investigate their differential responses to mechanical damage. The results showed that the insect-susceptible variety TN1 exhibited more differentially expressed genes (DEGs) and greater changes in expression levels after needle treatment, indicating a more active internal gene regulatory network. GO and KEGG enrichment analysis further revealed that TN1 not only exhibited changes in genes related to the extracellular environment, but also mobilized more genes associated with stress response and defense. By screening the differentially expressed genes, we identified two promoters (P1 and P2) with inducible expression characteristics in both the resistant and susceptible rice varieties. These promoters were able to effectively drive the expression of the insect resistance gene OsLecRK1* and enhance the resistance of transgenic plants against the brown planthopper. This study provides promoter resources for the development of insect-resistant transgenic crops. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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17 pages, 9711 KiB

Open AccessArticle

Exploring the Roles of the Swi2/Snf2 Gene Family in Maize Abiotic Stress Responses

by Jiarui Han, Qi Wang, Buxuan Qian, Qing Liu, Ziyu Wang, Yang Liu, Ziqi Chen, Weilin Wu, Chuang Zhang and Yuejia Yin

Int. J. Mol. Sci. 2024, 25(17), 9686; https://doi.org/10.3390/ijms25179686 - 7 Sep 2024

Viewed by 679

Abstract

The maize Snf2 gene family plays a crucial role in chromatin remodeling and response to environmental stresses. In this study, we identified and analyzed 35 members of the maize Snf2 gene family (ZmCHR1 to ZmCHR35) using the Ensembl Plants database. Each [...] Read more.

The maize Snf2 gene family plays a crucial role in chromatin remodeling and response to environmental stresses. In this study, we identified and analyzed 35 members of the maize Snf2 gene family (ZmCHR1 to ZmCHR35) using the Ensembl Plants database. Each protein contained conserved SNF2-N and Helicase-C domains. Phylogenetic analysis revealed six groups among the Snf2 proteins, with an uneven distribution across subfamilies. Physicochemical analysis indicated that the Snf2 proteins are hydrophilic, with varied amino acid lengths, isoelectric points, and molecular weights, and are predominantly localized in the nucleus. Chromosomal mapping showed that these genes are distributed across all ten maize chromosomes. Gene structure analysis revealed diverse exon–intron arrangements, while motif analysis identified 20 conserved motifs. Collinearity analysis highlighted gene duplication events, suggesting purifying selection. Cis-regulatory element analysis suggested involvement in abiotic and biotic stress responses. Expression analysis indicated tissue-specific expression patterns and differential expression under various stress conditions. Specifically, qRT-PCR validation under drought stress showed that certain Snf2 genes were upregulated at 12 h and downregulated at 24 h, revealing potential roles in drought tolerance. These findings provide a foundation for further exploration of the functional roles of the maize Snf2 gene family in development and stress responses. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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18 pages, 5588 KiB

Open AccessArticle

Pangenome Identification and Analysis of Terpene Synthase Gene Family Members in Gossypium

by Yueqin Song, Shengjie Han, Mengting Wang, Xueqi Ni, Xinzheng Huang and Yongjun Zhang

Int. J. Mol. Sci. 2024, 25(17), 9677; https://doi.org/10.3390/ijms25179677 - 6 Sep 2024

Viewed by 750

Abstract

Terpene synthases (TPSs), key gatekeepers in the biosynthesis of herbivore-induced terpenes, are pivotal in the diversity of terpene chemotypes across and within plant species. Here, we constructed a gene-based pangenome of the Gossypium genus by integrating the genomes of 17 diploid and 10 [...] Read more.

Terpene synthases (TPSs), key gatekeepers in the biosynthesis of herbivore-induced terpenes, are pivotal in the diversity of terpene chemotypes across and within plant species. Here, we constructed a gene-based pangenome of the Gossypium genus by integrating the genomes of 17 diploid and 10 tetraploid species. Within this pangenome, 208 TPS syntelog groups (SGs) were identified, comprising 2 core SGs (TPS5 and TPS42) present in all 27 analyzed genomes, 6 softcore SGs (TPS11, TPS12, TPS13, TPS35, TPS37, and TPS47) found in 25 to 26 genomes, 131 dispensable SGs identified in 2 to 24 genomes, and 69 private SGs exclusive to a single genome. The mutational load analysis of these identified TPS genes across 216 cotton accessions revealed a great number of splicing variants and complex splicing patterns. The nonsynonymous/synonymous Ka/Ks value for all 52 analyzed TPS SGs was less than one, indicating that these genes were subject to purifying selection. Of 208 TPS SGs encompassing 1795 genes, 362 genes derived from 102 SGs were identified as atypical and truncated. The structural analysis of TPS genes revealed that gene truncation is a major mechanism contributing to the formation of atypical genes. An integrated analysis of three RNA-seq datasets from cotton plants subjected to herbivore infestation highlighted nine upregulated TPSs, which included six previously characterized TPSs in G. hirsutum (AD1_TPS10, AD1_TPS12, AD1_TPS40, AD1_TPS42, AD1_TPS89, and AD1_TPS104), two private TPSs (AD1_TPS100 and AD2_TPS125), and one atypical TPS (AD2_TPS41). Also, a TPS-associated coexpression module of eight genes involved in the terpenoid biosynthesis pathway was identified in the transcriptomic data of herbivore-infested G. hirsutum. These findings will help us understand the contributions of TPS family members to interspecific terpene chemotypes within Gossypium and offer valuable resources for breeding insect-resistant cotton cultivars. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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11 pages, 2780 KiB

Open AccessArticle

Enhancement of Apple Stress Resistance via Proline Elevation by Sugar Substitutes

by Zi-Quan Feng, Tong Li, Xin-Yi Li, Long-Xin Luo, Zhi Li, Chun-Ling Liu, Shun-Feng Ge, Zhan-Ling Zhu, Yuan-Yuan Li, Han Jiang and Yuan-Mao Jiang

Int. J. Mol. Sci. 2024, 25(17), 9548; https://doi.org/10.3390/ijms25179548 - 2 Sep 2024

Viewed by 810

Abstract

Plants encounter numerous adversities during growth, necessitating the identification of common stress activators to bolster their resistance. However, the current understanding of these activators’ mechanisms remains limited. This study identified three anti-stress activators applicable to apple trees, all of which elevate plant proline [...] Read more.

Plants encounter numerous adversities during growth, necessitating the identification of common stress activators to bolster their resistance. However, the current understanding of these activators’ mechanisms remains limited. This study identified three anti-stress activators applicable to apple trees, all of which elevate plant proline content to enhance resistance against various adversities. The results showed that the application of these sugar substitutes increased apple proline content by two to three times compared to the untreated group. Even at a lower concentration, these activators triggered plant stress resistance without compromising apple fruit quality. Therefore, these three sugar substitutes can be exogenously sprayed on apple trees to augment proline content and fortify stress resistance. Given their effectiveness and low production cost, these activators possess significant application value. Since they have been widely used in the food industry, they hold potential for broader application in plants, fostering apple industry development. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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19 pages, 10086 KiB

Open AccessArticle

RcTRP5 Transcription Factor Mediates the Molecular Mechanism of Lignin Biosynthesis Regulation in R. chrysanthum against UV-B Stress

by Fushuai Gong, Wang Yu, Kun Cao, Hongwei Xu and Xiaofu Zhou

Int. J. Mol. Sci. 2024, 25(17), 9205; https://doi.org/10.3390/ijms25179205 - 24 Aug 2024

Viewed by 737

Abstract

UV-B stress destroys the photosynthetic system of Rhododendron chrysanthum Pall. (R. chrysanthum), as manifested by the decrease of photosynthetic efficiency and membrane fluidity, and also promotes the accumulation of lignin. The MYB (v-myb avian myeloblastosis viral oncogene homolog) family of transcription [...] Read more.

UV-B stress destroys the photosynthetic system of Rhododendron chrysanthum Pall. (R. chrysanthum), as manifested by the decrease of photosynthetic efficiency and membrane fluidity, and also promotes the accumulation of lignin. The MYB (v-myb avian myeloblastosis viral oncogene homolog) family of transcription factors can be involved in the response to UV-B stress through the regulation of lignin biosynthesis. This study indicated that both the donor and recipient sides of the R. chrysanthum were significantly damaged based on physiological index measurements made using OJIP curves under UV-B stress. The analysis of bioinformatics data revealed that the RcTRP5 transcription factor exhibits upregulation of acetylation at the K68 site, directly regulating the biosynthesis of lignin. Additionally, there was upregulation of the K43 site and downregulation of the K83 site of the CAD enzyme, as well as upregulation of the K391 site of the PAL enzyme. Based on these findings, we conjectured that the RcTRP5 transcription factor facilitates acetylation modification of both enzymes, thereby indirectly influencing the biosynthesis of lignin. This study demonstrated that lignin accumulation can alleviate the damage caused by UV-B stress to R. chrysanthum, which provides relevant ideas for improving lignin content in plants, and also provides a reference for the study of the metabolic regulation mechanism of other secondary substances. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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17 pages, 7124 KiB

Open AccessArticle

Gene Duplication and Functional Diversification of MADS-Box Genes in Malus × domestica following WGD: Implications for Fruit Type and Floral Organ Evolution

by Baoan Wang, Yao Xiao, Mengbo Yan, Wenqi Fan, Yuandi Zhu, Wei Li and Tianzhong Li

Int. J. Mol. Sci. 2024, 25(16), 8962; https://doi.org/10.3390/ijms25168962 - 17 Aug 2024

Viewed by 835

Abstract

The evolution of the MADS-box gene family is essential for the rapid differentiation of floral organs and fruit types in angiosperms. Two key processes drive the evolution of gene families: gene duplication and functional differentiation. Duplicated copies provide the material for variation, while [...] Read more.

The evolution of the MADS-box gene family is essential for the rapid differentiation of floral organs and fruit types in angiosperms. Two key processes drive the evolution of gene families: gene duplication and functional differentiation. Duplicated copies provide the material for variation, while advantageous mutations can confer new functions on gene copies. In this study, we selected the Rosaceae family, which includes a variety of fruit types and flower organs, as well as species that existed before and after whole-genome duplication (WGD). The results indicate that different fruit types are associated with different copies of MADS-box gene family duplications and WGD events. While most gene copies derived from WGD have been lost, MADS-box genes not only retain copies derived from WGD but also undergo further gene duplication. The sequences, protein structures, and expression patterns of these gene copies have undergone significant differentiation. This work provides a clear example of MADS-box genes in the context of gene duplication and functional differentiation, offering new insights into the evolution of fruit types and floral organs. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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16 pages, 3382 KiB

Open AccessArticle

Infestation of Rice Striped Stem Borer (Chilo suppressalis) Larvae Induces Emission of Volatile Organic Compounds in Rice and Repels Female Adult Oviposition

by Chen Shen, Shan Yu, Xinyang Tan, Guanghua Luo, Zhengping Yu, Jiafei Ju, Lei Yang, Yuxuan Huang, Shuai Li, Rui Ji, Chunqing Zhao and Jichao Fang

Int. J. Mol. Sci. 2024, 25(16), 8827; https://doi.org/10.3390/ijms25168827 - 13 Aug 2024

Viewed by 1009

Abstract

Plants regulate the biosynthesis and emission of metabolic compounds to manage herbivorous stresses. In this study, as a destructive pest, the pre-infestation of rice striped stem borer (SSB, Chilo suppressalis) larvae on rice (Oryza sativa) reduced the subsequent SSB female [...] Read more.

Plants regulate the biosynthesis and emission of metabolic compounds to manage herbivorous stresses. In this study, as a destructive pest, the pre-infestation of rice striped stem borer (SSB, Chilo suppressalis) larvae on rice (Oryza sativa) reduced the subsequent SSB female adult oviposition preference. Widely targeted volatilomics and transcriptome sequencing were used to identify released volatile metabolic profiles and differentially expressed genes in SSB-infested and uninfested rice plants. SSB infestation significantly altered the accumulation of 71 volatile organic compounds (VOCs), including 13 terpenoids. A total of 7897 significantly differentially expressed genes were identified, and genes involved in the terpenoid and phenylpropanoid metabolic pathways were highly enriched. Correlation analysis revealed that DEGs in terpenoid metabolism-related pathways were likely involved in the regulation of VOC biosynthesis in SSB-infested rice plants. Furthermore, two terpenoids, (−)-carvone and cedrol, were selected to analyse the behaviour of SSB and predators. Y-tube olfactometer tests demonstrated that both (−)-carvone and cedrol could repel SSB adults at higher concentrations; (−)-carvone could simultaneously attract the natural enemies of SSB, Cotesia chilonis and Trichogramma japonicum, and cedrol could only attract T. japonicum at lower concentrations. These findings provide a better understanding of the response of rice plants to SSB and contribute to the development of new strategies to control herbivorous pests. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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16 pages, 11940 KiB

Open AccessArticle

Overexpression of Potato PYL16 Gene in Tobacco Enhances the Transgenic Plant Tolerance to Drought Stress

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

Int. J. Mol. Sci. 2024, 25(16), 8644; https://doi.org/10.3390/ijms25168644 - 8 Aug 2024

Viewed by 806

Abstract

PYR/PYL/RCAR proteins are abscisic acid (ABA) receptors that play a crucial role in plant responses to abiotic stresses. However, there have been no research reports on potato PYL so far. In this study, a potato PYL gene named StPYL16 was identified based on [...] Read more.

PYR/PYL/RCAR proteins are abscisic acid (ABA) receptors that play a crucial role in plant responses to abiotic stresses. However, there have been no research reports on potato PYL so far. In this study, a potato PYL gene named StPYL16 was identified based on transcriptome data under drought stress. Molecular characteristics analysis revealed that the StPYL16 protein possesses an extremely conserved PYL family domain. The tissue expression results indicated that the StPYL16 is predominantly expressed at high levels in the underground parts, particularly in tubers. Abiotic stress response showed that StPYL16 has a significant response to drought treatment. Further research on the promoter showed that drought stress could enhance the activation activity of the StPYL16 promoter on the reporter gene. Then, transient and stable expression of StPYL16 in tobacco enhanced the drought resistance of transgenic plants, resulting in improved plant height, stem thickness, and root development. In addition, compared with wild-type plants, StPYL16 transgenic tobacco exhibited lower malondialdehyde (MDA) content, higher proline accumulation, and stronger superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. Meanwhile, StPYL16 also up-regulated the expression levels of stress-related genes (NtSOD, NtCAT, NtPOD, NtRD29A, NtLEA5, and NtP5CS) in transgenic plants under drought treatment. These findings indicated that the StPYL16 gene plays a positive regulatory role in potato responses to drought stress. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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17 pages, 4864 KiB

Open AccessArticle

Time-Course Analysis and Transcriptomic Identification of a Group III ERF CmTINY2 Involved in Waterlogging Tolerance in Chrysanthemums × morifolium Ramat.

by Xueting Gu, Xinyi Liu, Haodong Sha, Xuejie Du, Han Zhang, Yuexiao Miao, Weiliang Chen and Bizeng Mao

Int. J. Mol. Sci. 2024, 25(15), 8417; https://doi.org/10.3390/ijms25158417 - 1 Aug 2024

Viewed by 2374

Abstract

‘Hangju’ is a variety of Chrysanthemum × morifolium Ramat. with both edible and medicinal value, cultivated as a traditional Chinese medicine for four centuries. The cultivation of ‘Hangju’ is currently at risk due to waterlogging, yet there is a lack of comprehensive understanding [...] Read more.

‘Hangju’ is a variety of Chrysanthemum × morifolium Ramat. with both edible and medicinal value, cultivated as a traditional Chinese medicine for four centuries. The cultivation of ‘Hangju’ is currently at risk due to waterlogging, yet there is a lack of comprehensive understanding regarding its response to waterlogging stress. This study compared the waterlogging-tolerant ‘Hangju’ variety Enhanced Waterlogging Tolerance (EWT) with the waterlogging-sensitive variety CK (‘zaoxiaoyangju’). EWT exhibited a more developed aeration tissue structure and demonstrated rapid growth regarding the adventitious roots following waterlogging. The time-course transcriptome analysis indicated that EWT could swiftly adjust the expression of the genes involved in the energy metabolism signaling pathways to acclimate to the waterlogged environment. Through WGCNA analysis, we identified Integrase-Type DNA-Binding Protein (CmTINY2) as a key factor in regulating the waterlogging tolerance in EWT. CmTINY2, a transcription factor belonging to the ethylene-responsive factor (ERF) subfamily III, operated within the nucleus and activated downstream gene expression. Its role in enhancing the waterlogging tolerance might be linked to the control of the stomatal aperture via the Ethylene-Responsive Element (ERE) gene. In summary, our research elucidated that the waterlogging tolerance displayed by EWT is a result of a combination of the morphological structure and molecular regulatory mechanisms. Furthermore, the study of the functions of CmTINY2 from ERF subfamily III also broadened our knowledge of the role of the ERF genes in the waterlogging signaling pathways. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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19 pages, 8930 KiB

Open AccessArticle

Genome-Wide Characterization and Expression Profiling of the AP2/ERF Gene Family in Fragaria vesca L.

by Yangfan Wei, Yihan Kong, Huiwen Li, Anqi Yao, Jiaxin Han, Wenhao Zhang, Xingguo Li, Wenhui Li and Deguo Han

Int. J. Mol. Sci. 2024, 25(14), 7614; https://doi.org/10.3390/ijms25147614 - 11 Jul 2024

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Abstract

The wild strawberry (Fragaria vesca L.; F. vesca) represents a resilient and extensively studied model organism. While the AP2/ERF gene family plays a pivotal role in plant development, its exploration within F. vesca remains limited. In this study, we characterized the [...] Read more.

The wild strawberry (Fragaria vesca L.; F. vesca) represents a resilient and extensively studied model organism. While the AP2/ERF gene family plays a pivotal role in plant development, its exploration within F. vesca remains limited. In this study, we characterized the AP2/ERF gene family in wild strawberries using the recently released genomic data (F. vesca V6.0). We conducted an analysis of the gene family expansion pattern, we examined gene expression in stem segments and leaves under cold conditions, and we explored its functional attributes. Our investigation revealed that the FvAP2/ERF family comprises 86 genes distributed among four subfamilies: AP2 (17), RAV (6), ERF (62), and Soloist (1). Tandem and segmental duplications significantly contributed to the growth of this gene family. Furthermore, predictive analysis identified several cis-acting elements in the promoter region associated with meristematic tissue expression, hormone regulation, and resistance modulation. Transcriptomic analysis under cold stress unveiled diverse responses among multiple FvAP2/ERFs in stem segments and leaves. Real-time fluorescence quantitative reverse transcription PCR (RT-qPCR) results confirmed elevated expression levels of select genes following the cold treatment. Additionally, overexpression of FvERF23 in Arabidopsis enhanced cold tolerance, resulting in significantly increased fresh weight and root length compared to the wild-type control. These findings lay the foundation for further exploration into the functional roles of FvAP2/ERF genes. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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15 pages, 6971 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the High-Mobility Group B (HMGB) Gene Family in Plant Response to Abiotic Stress in Tomato

by Jinhui Zheng, Huimeng Tang, Jianquan Wang, Yue Liu, Lianjing Ge, Guobiao Liu, Qinghua Shi and Yan Zhang

Int. J. Mol. Sci. 2024, 25(11), 5850; https://doi.org/10.3390/ijms25115850 - 28 May 2024

Viewed by 979

Abstract

High-mobility group B (HMGB) proteins are a class of non-histone proteins associated with eukaryotic chromatin and are known to regulate a variety of biological processes in plants. However, the functions of HMGB genes in tomato (Solanum lycopersicum) remain largely unexplored. Here, [...] Read more.

High-mobility group B (HMGB) proteins are a class of non-histone proteins associated with eukaryotic chromatin and are known to regulate a variety of biological processes in plants. However, the functions of HMGB genes in tomato (Solanum lycopersicum) remain largely unexplored. Here, we identified 11 members of the HMGB family in tomato using BLAST. We employed genome-wide identification, gene structure analysis, domain conservation analysis, cis-acting element analysis, collinearity analysis, and qRT-PCR-based expression analysis to study these 11 genes. These genes were categorized into four groups based on their unique protein domain structures. Despite their structural diversity, all members contain the HMG-box domain, a characteristic feature of the HMG superfamily. Syntenic analysis suggested that tomato SlHMGBs have close evolutionary relationships with their homologs in other dicots. The promoter regions of SlHMGBs are enriched with numerous cis-elements related to plant growth and development, phytohormone responsiveness, and stress responsiveness. Furthermore, SlHMGB members exhibited distinct tissue-specific expression profiles, suggesting their potential roles in regulating various aspects of plant growth and development. Most SlHMGB genes respond to a variety of abiotic stresses, including salt, drought, heat, and cold. For instance, SlHMGB2 and SlHMGB4 showed positive responses to salt, drought, and cold stresses. SlHMGB1, SlHMGB3, and SlHMGB8 were involved in responses to two types of stress: SlHMGB1 responded to drought and heat, while SlHMGB3 and SlHMGB8 responded to salt and heat. SlHMGB6 and SlHMGB11 were solely regulated by drought and heat stress, respectively. Under various treatment conditions, the number of up-regulated genes significantly outnumbered the down-regulated genes, implying that the SlHMGB family may play a crucial role in mitigating abiotic stress in tomato. These findings lay a foundation for further dissecting the precise roles of SlHMGB genes. Full article

(This article belongs to the Special Issue Physiology and Molecular Biology of Plant Stress Tolerance)

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