Pub Date : 2026-02-03DOI: 10.1016/j.plaphy.2026.111105
Wenhui Lv , Manqiao Li , Yueyue Zhu , Kuixiu Li , Zihan Yang , Junliang Li , Fugang Wei , Shengchao Yang , Xuyan Liu , Guanze Liu
Panax notoginseng is highly susceptible to root rot during cultivation, severely affecting its production and quality. Phospholipases participate in plant immunity by producing free fatty acids and conjugated lipids that activate downstream signaling cascades. However, genome-wide identification of PnPL genes in P. notoginseng remains limited. A total of 72 PnPL genes were identified in P. notoginseng: 48 PnPLA genes, 9 PnPLC genes and 15 PnPLD genes. Transcriptome and qRT-PCR analyses between healthy and diseased plants (CK, RⅠ and RⅡ) revealed 13 differentially expressed genes from PnPL Gene Family, 11 of which belonged to the PnPLA genes superfamily. Notably, PnPLA1-8 exhibited sustained upregulation with worsening root rot. Further, RNA interference (RNAi) mediated silencing of PnPLA1-8 gene increased susceptibility to Fusarium oxysporum that the main pathogenic fungus in P. notoginseng, whereas overexpression of PnPLA1-8 gene in Nicotiana tabacum enhanced resistance to F. oxysporum. This study suggests that the PnPLA1-8 genes exhibit potential roles in resistance to F. oxysporum.
{"title":"Genome-wide identification of the phospholipase gene family in Panax notoginseng and functional analysis of PnPLA1-8 response to Fusarium oxysporum infection","authors":"Wenhui Lv , Manqiao Li , Yueyue Zhu , Kuixiu Li , Zihan Yang , Junliang Li , Fugang Wei , Shengchao Yang , Xuyan Liu , Guanze Liu","doi":"10.1016/j.plaphy.2026.111105","DOIUrl":"10.1016/j.plaphy.2026.111105","url":null,"abstract":"<div><div><em>Panax notoginseng</em> is highly susceptible to root rot during cultivation, severely affecting its production and quality. Phospholipases participate in plant immunity by producing free fatty acids and conjugated lipids that activate downstream signaling cascades. However, genome-wide identification of PnPL genes in <em>P. notoginseng</em> remains limited. A total of 72 PnPL genes were identified in <em>P. notoginseng</em>: 48 PnPLA genes, 9 PnPLC genes and 15 PnPLD genes. Transcriptome and qRT-PCR analyses between healthy and diseased plants (CK, RⅠ and RⅡ) revealed 13 differentially expressed genes from PnPL Gene Family, 11 of which belonged to the PnPLA genes superfamily. Notably, <em>PnPLA1-8</em> exhibited sustained upregulation with worsening root rot. Further, RNA interference (RNAi) mediated silencing of <em>PnPLA1-8</em> gene increased susceptibility to <em>Fusarium oxysporum</em> that the main pathogenic fungus in <em>P. notoginseng</em>, whereas overexpression of <em>PnPLA1-8</em> gene in <em>Nicotiana tabacum</em> enhanced resistance to <em>F. oxysporum</em>. This study suggests that the <em>PnPLA1-8</em> genes exhibit potential roles in resistance to <em>F. oxysporum</em>.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111105"},"PeriodicalIF":5.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146143355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-02DOI: 10.1016/j.plaphy.2026.111085
Ting Ou , Kun Jiang , Li Wang , Xiaojiao Liu , Keyao Zhang , Ju Wen , Wenlian Jiao , Jing Yu , Ruolin Zhao , Jie Xie
Rhizobacteria are crucial for plant adaptation to abiotic stresses; however, their contributions to waterlogging resilience of woody plants in fragile riparian zones remain poorly understood. Here, we investigated whether and how the rhizobacterium Klebsiella variicola HWS1, isolated from a riparian zone, improved waterlogging tolerance in mulberry. Our results demonstrated that HWS1 exhibited multiple plant-beneficial traits in vitro and harbored genomic signatures associated with plant growth promotion and stress adaptation. Co-cultivation with HWS1 significantly promoted mulberry growth and elevated antioxidant enzyme activities under waterlogging conditions. Transcriptomic profiling further revealed that stress primarily reprogrammed genes related to oxidoreductase activity, while HWS1 specifically enriched genes involved in hydrogen peroxide metabolism, implicating that alleviation of oxidative stress is a key mechanism for enhanced resilience. Interestingly, waterlogging triggered excessive accumulation of reactive oxygen species (ROS) in mulberry, whereas HWS1 displayed a robust capability to tolerate and detoxify hydrogen peroxide, thereby helping maintain host ROS homeostasis. Genetic analyses identified the bacterial ahpC and katG genes as essential for oxidative stress tolerance. In particular, deletion of katG significantly impaired its ability to scavenge plant-derived ROS and consequently compromised mulberry stress resistance. These findings reveal a mechanism in rhizobacteria-plant interaction whereby rhizobacterium coordinates the reprogramming of host ROS metabolic genes with its own antioxidant defenses to enhance plant resilience, highlighting ROS-detoxifying rhizobacteria as promising agents for mitigating waterlogging in riparian and agricultural ecosystems.
{"title":"Rhizobacterial coordination of reactive oxygen species homeostasis underpins mulberry resilience to waterlogging","authors":"Ting Ou , Kun Jiang , Li Wang , Xiaojiao Liu , Keyao Zhang , Ju Wen , Wenlian Jiao , Jing Yu , Ruolin Zhao , Jie Xie","doi":"10.1016/j.plaphy.2026.111085","DOIUrl":"10.1016/j.plaphy.2026.111085","url":null,"abstract":"<div><div>Rhizobacteria are crucial for plant adaptation to abiotic stresses; however, their contributions to waterlogging resilience of woody plants in fragile riparian zones remain poorly understood. Here, we investigated whether and how the rhizobacterium <em>Klebsiella variicola</em> HWS1, isolated from a riparian zone, improved waterlogging tolerance in mulberry. Our results demonstrated that HWS1 exhibited multiple plant-beneficial traits <em>in vitro</em> and harbored genomic signatures associated with plant growth promotion and stress adaptation. Co-cultivation with HWS1 significantly promoted mulberry growth and elevated antioxidant enzyme activities under waterlogging conditions. Transcriptomic profiling further revealed that stress primarily reprogrammed genes related to oxidoreductase activity, while HWS1 specifically enriched genes involved in hydrogen peroxide metabolism, implicating that alleviation of oxidative stress is a key mechanism for enhanced resilience. Interestingly, waterlogging triggered excessive accumulation of reactive oxygen species (ROS) in mulberry, whereas HWS1 displayed a robust capability to tolerate and detoxify hydrogen peroxide, thereby helping maintain host ROS homeostasis. Genetic analyses identified the bacterial <em>ahpC</em> and <em>katG</em> genes as essential for oxidative stress tolerance. In particular, deletion of <em>katG</em> significantly impaired its ability to scavenge plant-derived ROS and consequently compromised mulberry stress resistance. These findings reveal a mechanism in rhizobacteria-plant interaction whereby rhizobacterium coordinates the reprogramming of host ROS metabolic genes with its own antioxidant defenses to enhance plant resilience, highlighting ROS-detoxifying rhizobacteria as promising agents for mitigating waterlogging in riparian and agricultural ecosystems.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111085"},"PeriodicalIF":5.7,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-02DOI: 10.1016/j.plaphy.2026.111100
Abdelmonem Elshahat , Abebe Assefa Gobena , Samy A. Marey , Hai-Qiang Liu , Yin Luo , Essam Elatafi , Basma Elhendawy , Shariq Mahmood Alam , Rohoma Tahir , Mohamed A. Abdelsalam , Muhammad Ateeq , Yong-Zhong Liu
This study examined the effects of red, yellow, green, and blue 40–60% shade nets on carotenoid accumulation in the peel of 'Newhall' navel oranges over two seasons. The results indicated that the green 60% shade net significantly enhanced carotenoid accumulation, whereas the red 60% shade net reduced it compared with the control during both shaded seasons. HPLC analysis further revealed that the green 60% shade net significantly elevated the levels of essential carotenoids, including α-carotene, β-carotene, phytoene, violaxanthin, and lutein. In contrast, the red 60% shade net showed lower levels of these compounds than the open field. Both the green and red 60% shade nets effectively reduced temperature and light intensity while increasing relative humidity (RH). However, photosystem II (PSII) efficiency was superior under green 60% compared to red 60%, indicating optimal photosynthetic performance. The results suggest that variations in the color spectrum directly affect photochemical efficiency in citrus. Furthermore, green 60% increased carotenoid biosynthesis genes (CitPSY, CitLCYB1, and CitLCYBE) while downregulating degradation-related genes (CitCCD4 and CitNCED3), whereas red 60% exhibited the inverse effect. Moreover, the differential expression patterns were particularly evident in the second season, with CitPSY exhibiting maximal induction under green 60% and CitCCD4 reaching its peak under red 60% throughout all shading stages. These results underscore the potential of green 60% as an innovative, environmentally sustainable approach for citrus orchards, as it enhances the quality and coloration of citrus fruits by managing environmental and light conditions, thereby regulating the fundamental mechanisms of fruit color and quality.
{"title":"Green and red nets showed opposite influence on carotenoid accumulation in citrus by differential regulation of CitPSY and CitCCD4 gene expression","authors":"Abdelmonem Elshahat , Abebe Assefa Gobena , Samy A. Marey , Hai-Qiang Liu , Yin Luo , Essam Elatafi , Basma Elhendawy , Shariq Mahmood Alam , Rohoma Tahir , Mohamed A. Abdelsalam , Muhammad Ateeq , Yong-Zhong Liu","doi":"10.1016/j.plaphy.2026.111100","DOIUrl":"10.1016/j.plaphy.2026.111100","url":null,"abstract":"<div><div>This study examined the effects of red, yellow, green, and blue 40–60% shade nets on carotenoid accumulation in the peel of 'Newhall' navel oranges over two seasons. The results indicated that the green 60% shade net significantly enhanced carotenoid accumulation, whereas the red 60% shade net reduced it compared with the control during both shaded seasons. HPLC analysis further revealed that the green 60% shade net significantly elevated the levels of essential carotenoids, including α-carotene, β-carotene, phytoene, violaxanthin, and lutein. In contrast, the red 60% shade net showed lower levels of these compounds than the open field. Both the green and red 60% shade nets effectively reduced temperature and light intensity while increasing relative humidity (RH). However, photosystem II (PSII) efficiency was superior under green 60% compared to red 60%, indicating optimal photosynthetic performance. The results suggest that variations in the color spectrum directly affect photochemical efficiency in citrus. Furthermore, green 60% increased carotenoid biosynthesis genes (<em>CitPSY</em>, <em>CitLCYB1</em>, and <em>CitLCYBE</em>) while downregulating degradation-related genes (<em>CitCCD4</em> and <em>CitNCED3</em>), whereas red 60% exhibited the inverse effect. Moreover, the differential expression patterns were particularly evident in the second season, with <em>CitPSY</em> exhibiting maximal induction under green 60% and <em>CitCCD4</em> reaching its peak under red 60% throughout all shading stages. These results underscore the potential of green 60% as an innovative, environmentally sustainable approach for citrus orchards, as it enhances the quality and coloration of citrus fruits by managing environmental and light conditions, thereby regulating the fundamental mechanisms of fruit color and quality.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111100"},"PeriodicalIF":5.7,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1016/j.plaphy.2026.111094
Julia Zinsmeister , Naoto Sano , Imen Lounifi , Steven P.C. Groot , Dongli He , Mathilde Lagesse , Sandrine Balzergue , Stéphanie Huguet , Romain Huguet , Boris Collet , Gwendal Cueff , Gilles Clément , Loïc Rajjou , Marc Galland
In the context of global warming, the ability of seeds to withstand higher temperatures and humidity during dry storage is critical to maintain food production. Seed longevity, also referred to as storability, is therefore an essential trait. As a major staple crop, rice (Oryza sativa L.) has been widely studied to identify the genetic determinants of seed longevity, primarily through QTL mapping and molecular analyses. However, integrated multi-omics data remain limited, especially compared to advances made for other seed physiological features (e.g., dry quiescence, germination). This study investigates the molecular determinants of rice seed longevity under varying storage conditions using controlled deterioration treatments (CDTs) at 25 °C (no deterioration), 40 °C (reduction of germination speed and uniformity) and 45 °C (loss of germinative capacity) under high relative humidity. Through physiological characterizationand multi-omics analyses, we identified key metabolic pathways and genetic factors associated with seed aging. By integrating transcriptomic, proteomic, and metabolomic data, we pinpointed specific pathways critical to seed viability loss. CDTs revealed that only a small number of genes and proteins are significantly affected. In particular, our results highlight a major impact of CDTs on the GABA shunt and mitochondrial factors as the DEAD-box ATP-dependent RNA helicase 9. Altogether, this work opens the way for in-depth functional studies on a small number of mitochondria-related genes involved in rice seed longevity.
{"title":"Combined “omics” and physiological approaches highlight the roles of the GABA shunt and mitochondria-related functions in rice seed longevity","authors":"Julia Zinsmeister , Naoto Sano , Imen Lounifi , Steven P.C. Groot , Dongli He , Mathilde Lagesse , Sandrine Balzergue , Stéphanie Huguet , Romain Huguet , Boris Collet , Gwendal Cueff , Gilles Clément , Loïc Rajjou , Marc Galland","doi":"10.1016/j.plaphy.2026.111094","DOIUrl":"10.1016/j.plaphy.2026.111094","url":null,"abstract":"<div><div>In the context of global warming, the ability of seeds to withstand higher temperatures and humidity during dry storage is critical to maintain food production. Seed longevity, also referred to as storability, is therefore an essential trait. As a major staple crop, rice (<em>Oryza sativa L.</em>) has been widely studied to identify the genetic determinants of seed longevity, primarily through QTL mapping and molecular analyses. However, integrated multi-omics data remain limited, especially compared to advances made for other seed physiological features (e.g., dry quiescence, germination). This study investigates the molecular determinants of rice seed longevity under varying storage conditions using controlled deterioration treatments (CDTs) at 25 °C (no deterioration), 40 °C (reduction of germination speed and uniformity) and 45 °C (loss of germinative capacity) under high relative humidity. Through physiological characterizationand multi-omics analyses, we identified key metabolic pathways and genetic factors associated with seed aging. By integrating transcriptomic, proteomic, and metabolomic data, we pinpointed specific pathways critical to seed viability loss. CDTs revealed that only a small number of genes and proteins are significantly affected. In particular, our results highlight a major impact of CDTs on the GABA shunt and mitochondrial factors as the DEAD-box ATP-dependent RNA helicase 9. Altogether, this work opens the way for in-depth functional studies on a small number of mitochondria-related genes involved in rice seed longevity.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"232 ","pages":"Article 111094"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1016/j.plaphy.2026.111059
Min Gao , Shiqing Jia , Ziyu Chang , Rudan Xue , Congzhen Yan , Zihan Meng , Wenya Gong , Shuang Sun , Han Sun , Baohua Zhao , Zhao Zhang
Light is a crucial regulatory factor for astaxanthin biosynthesis in microalgae under non-stress and abiotic stresses. However, its physiological impacts, molecular mechanisms and signaling pathway remain unclear. The present study showed that light could significantly promote the cell proliferation, nitrogen redistribution and astaxanthin accumulation via Target of Rapamycin (TOR) signaling pathway under nitrogen starvation condition. Compared with the dark condition, the cell density, protein content, astaxanthin content and TOR activity increased by 22 %, 100 %, 136 % and 335 % under 200 μmol m2 s−1 light intensity. But the above induction effects were significantly impaired by the inhibition of the TOR signaling pathway. Interestingly, the level of reactive oxygen species (ROS) was not positive regulator in light-induced astaxanthin accumulation, as it was decreased by light under nitrogen starvation condition. Comparative transcriptome analysis revealed that TOR-mediated light exposure upregulated the expression of key genes involved in energy production pathways, as well as carotenoid biosynthesis. Weighted gene co-expression network analysis identified genes such as MYB3R and bZIP as potential key regulatory genes downstream of TOR, contributing to high light-induced cell proliferation and carotenoid production. The whole-genome DNA methylation analysis suggested that TOR was involved in the suppression of global DNA methylation under high light, potentially facilitating gene expression. This study emphasized the regulatory mechanisms of TOR mediated light-induced astaxanthin accumulation, providing theoretical basis and induction strategy for astaxanthin production.
光是微藻在非胁迫和非生物胁迫下虾青素合成的重要调控因子。然而，其生理作用、分子机制和信号通路尚不清楚。本研究表明，在氮饥饿条件下，光可通过Rapamycin靶蛋白（Target of Rapamycin， TOR）信号通路显著促进细胞增殖、氮再分配和虾青素积累。与暗处理相比，200 μmol m2 s-1光强下，细胞密度、蛋白质含量、虾青素含量和TOR活性分别提高了22%、100%、136%和335%。但上述诱导作用因抑制TOR信号通路而明显减弱。有趣的是，活性氧（ROS）水平不是光诱导虾青素积累的正调节因子，在氮饥饿条件下，活性氧水平降低。比较转录组分析显示，tor介导的光暴露上调了参与能量产生途径和类胡萝卜素生物合成的关键基因的表达。加权基因共表达网络分析发现，MYB3R和bZIP等基因是TOR下游潜在的关键调控基因，参与高光诱导细胞增殖和类胡萝卜素的产生。全基因组DNA甲基化分析表明，TOR参与了强光下整体DNA甲基化的抑制，可能促进基因表达。本研究强调了TOR介导光诱导虾青素积累的调控机制，为虾青素的产生提供了理论依据和诱导策略。
{"title":"Light boosts cell proliferation and astaxanthin accumulation in nitrogen-starved Chromochloris zofingiensis via TOR signaling pathway","authors":"Min Gao , Shiqing Jia , Ziyu Chang , Rudan Xue , Congzhen Yan , Zihan Meng , Wenya Gong , Shuang Sun , Han Sun , Baohua Zhao , Zhao Zhang","doi":"10.1016/j.plaphy.2026.111059","DOIUrl":"10.1016/j.plaphy.2026.111059","url":null,"abstract":"<div><div>Light is a crucial regulatory factor for astaxanthin biosynthesis in microalgae under non-stress and abiotic stresses. However, its physiological impacts, molecular mechanisms and signaling pathway remain unclear. The present study showed that light could significantly promote the cell proliferation, nitrogen redistribution and astaxanthin accumulation via Target of Rapamycin (TOR) signaling pathway under nitrogen starvation condition. Compared with the dark condition, the cell density, protein content, astaxanthin content and TOR activity increased by 22 %, 100 %, 136 % and 335 % under 200 μmol m<sup>2</sup> s<sup>−1</sup> light intensity. But the above induction effects were significantly impaired by the inhibition of the TOR signaling pathway. Interestingly, the level of reactive oxygen species (ROS) was not positive regulator in light-induced astaxanthin accumulation, as it was decreased by light under nitrogen starvation condition. Comparative transcriptome analysis revealed that TOR-mediated light exposure upregulated the expression of key genes involved in energy production pathways, as well as carotenoid biosynthesis. Weighted gene co-expression network analysis identified genes such as MYB3R and bZIP as potential key regulatory genes downstream of TOR, contributing to high light-induced cell proliferation and carotenoid production. The whole-genome DNA methylation analysis suggested that TOR was involved in the suppression of global DNA methylation under high light, potentially facilitating gene expression. This study emphasized the regulatory mechanisms of TOR mediated light-induced astaxanthin accumulation, providing theoretical basis and induction strategy for astaxanthin production.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"231 ","pages":"Article 111059"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146066192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1016/j.plaphy.2026.111051
Guanqun Chen , Junyan Song , Yuanshan Zhang , Xiaohui Shen , Junsong Pan , Jian Pan
Carotenoids are widely distributed pigments that confer yellow and orange hues in flowers and fruits. Petunia hybrida and Calibrachoa hybrida, two closely related ornamental species, display distinct yellow flower pigmentation patterns. We developed a new Petunia inbred line '1408' (Pet-Yel) with vibrant yellow corollas, although they remained lighter than those of the deep-yellow Calibrachoa hybrid line '821H3' (Cal-Yel). In this study, we investigated the molecular and metabolic basis underlying yellow corolla coloration between them. By pair comparison of carotenoid metabolites between white and yellow corollas in each species, the formation of yellow corollas was primarily due to a significant increase in the levels of phytoene, β-carotene and violaxanthin. Esterified xanthophylls were notably enriched in Cal-Yel, suggesting enhanced xanthophyll esterification and improved pigment stability. To explore the underlying genetic mechanisms, we performed de novo transcriptome sequencing of Cal-Yel and conducted comparative analyses with published Petunia genome assemblies. Cal-Yel exhibited fewer gene copies in the carotenoid biosynthesis pathway but showed higher expression of key genes including PSY1-1, BCH1, and XES1, consistent with its elevated carotenoid accumulation. Notably, BCH1 and BCH2 exhibited completely opposite expression patterns between the two yellow varieties, and ChBCH1 was identified as a potential key regulator. Functional validation via transgenic overexpression of ChBCH1 in Petunia resulted in a significant increase in zeaxanthin and β-cryptoxanthin content and enhanced yellow pigmentation. These results suggest that distinct transcriptional regulatory networks and enzymatic activities underlie the yellow pigmentation in Petunia and Calibrachoa. Our findings provide new insights into carotenoid metabolism and offer genetic resources for the molecular breeding of yellow-flowered ornamental plants.
{"title":"Comparative transcriptome and metabolome analyses identified key genes for carotenoid metabolic variation in Petunia and Calibrachoa","authors":"Guanqun Chen , Junyan Song , Yuanshan Zhang , Xiaohui Shen , Junsong Pan , Jian Pan","doi":"10.1016/j.plaphy.2026.111051","DOIUrl":"10.1016/j.plaphy.2026.111051","url":null,"abstract":"<div><div>Carotenoids are widely distributed pigments that confer yellow and orange hues in flowers and fruits. <em>Petunia hybrida</em> and <em>Calibrachoa hybrida</em>, two closely related ornamental species, display distinct yellow flower pigmentation patterns. We developed a new <em>Petunia</em> inbred line '1408' (Pet-Yel) with vibrant yellow corollas, although they remained lighter than those of the deep-yellow <em>Calibrachoa</em> hybrid line '821H3' (Cal-Yel). In this study, we investigated the molecular and metabolic basis underlying yellow corolla coloration between them. By pair comparison of carotenoid metabolites between white and yellow corollas in each species, the formation of yellow corollas was primarily due to a significant increase in the levels of phytoene, β-carotene and violaxanthin. Esterified xanthophylls were notably enriched in Cal-Yel, suggesting enhanced xanthophyll esterification and improved pigment stability. To explore the underlying genetic mechanisms, we performed <em>de novo</em> transcriptome sequencing of Cal-Yel and conducted comparative analyses with published <em>Petunia</em> genome assemblies. Cal-Yel exhibited fewer gene copies in the carotenoid biosynthesis pathway but showed higher expression of key genes including <em>PSY1-1</em>, <em>BCH1</em>, and <em>XES1</em>, consistent with its elevated carotenoid accumulation. Notably, <em>BCH1</em> and <em>BCH2</em> exhibited completely opposite expression patterns between the two yellow varieties, and <em>ChBCH1</em> was identified as a potential key regulator. Functional validation via transgenic overexpression of <em>ChBCH1</em> in <em>Petunia</em> resulted in a significant increase in zeaxanthin and β-cryptoxanthin content and enhanced yellow pigmentation. These results suggest that distinct transcriptional regulatory networks and enzymatic activities underlie the yellow pigmentation in <em>Petunia</em> and <em>Calibrachoa</em>. Our findings provide new insights into carotenoid metabolism and offer genetic resources for the molecular breeding of yellow-flowered ornamental plants.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"231 ","pages":"Article 111051"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1016/j.plaphy.2026.111082
Peng Chen, Xu Wang, Meiling Qu, Caijin Wang, Dengjie Luo
RNA N6-methyladenosine (m6A) modification, the most abundant epigenetic modification in eukaryotic mRNAs, regulates gene expression via modulating mRNA translation, degradation, and other post-transcriptional processes, and is critical for plant growth, development, and abiotic stress responses. Soybean (Glycine max), a globally vital food and oil crop, suffers severe yield and quality losses under salt and drought stresses; however, the functions of m6A regulatory genes, especially methyltransferases, in soybean abiotic stress responses remain largely uncharacterized. In this study, four GmFIP37 genes were identified in the soybean genome. Bioinformatic analyses revealed that GmFIP37 proteins have conserved physicochemical properties, harbor the core WTAP functional domain, and their promoters contain abundant abiotic stress-responsive cis-acting elements. Expression pattern analysis showed GmFIP37 are ubiquitously expressed across soybean tissues (with the highest expression in stems and roots) and are rapidly induced under salt and PEG (drought-mimic) stresses. Subcellular localization assays confirmed GmFIP37 localizes to the nucleus. Functional validation demonstrated that heterologous expression of GmFIP37c in the yeast Saccharomyces cerevisiae strain INVSc1 significantly enhanced yeast tolerance to salt and drought stresses. Overexpression of GmFIP37c in soybean hairy root composite plants increased total root m6A content, improved growth traits (e.g., root length, root surface area, plant height), and enhanced salt tolerance via increasing antioxidant enzyme (SOD, POD) activities and osmolyte (proline, betaine) contents while reducing reactive oxygen species (ROS) accumulation. Conversely, virus-induced gene silencing (VIGS) of GmFIP37c in soybean reduced salt and drought tolerance. Additionally, heterologous overexpression of GmFIP37c in Arabidopsis thaliana promoted seedling growth and improved tolerance to both stresses. Collectively, our findings indicate that GmFIP37 acts as a key component of the soybean m6A methyltransferase complex and positively regulates soybean responses to salt and drought stresses by modulating m6A modification. This study provides novel insights into the epigenetic regulatory mechanisms underlying soybean abiotic stress tolerance and lays a foundation for the genetic improvement of stress-resistant soybean varieties.
{"title":"GmFIP37, a core m6A methyltransferase in soybean (Glycine max), confers salt and drought tolerance via synergistic regulation of m6A modification and antioxidant-osmolyte homeostasis","authors":"Peng Chen, Xu Wang, Meiling Qu, Caijin Wang, Dengjie Luo","doi":"10.1016/j.plaphy.2026.111082","DOIUrl":"10.1016/j.plaphy.2026.111082","url":null,"abstract":"<div><div>RNA N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) modification, the most abundant epigenetic modification in eukaryotic mRNAs, regulates gene expression via modulating mRNA translation, degradation, and other post-transcriptional processes, and is critical for plant growth, development, and abiotic stress responses. Soybean (<em>Glycine max</em>), a globally vital food and oil crop, suffers severe yield and quality losses under salt and drought stresses; however, the functions of m<sup>6</sup>A regulatory genes, especially methyltransferases, in soybean abiotic stress responses remain largely uncharacterized. In this study, four GmFIP37 genes were identified in the soybean genome. Bioinformatic analyses revealed that GmFIP37 proteins have conserved physicochemical properties, harbor the core WTAP functional domain, and their promoters contain abundant abiotic stress-responsive cis-acting elements. Expression pattern analysis showed <em>GmFIP37</em> are ubiquitously expressed across soybean tissues (with the highest expression in stems and roots) and are rapidly induced under salt and PEG (drought-mimic) stresses. Subcellular localization assays confirmed GmFIP37 localizes to the nucleus. Functional validation demonstrated that heterologous expression of GmFIP37c in the yeast <em>Saccharomyces cerevisiae</em> strain INVSc1 significantly enhanced yeast tolerance to salt and drought stresses. Overexpression of <em>GmFIP37c</em> in soybean hairy root composite plants increased total root m<sup>6</sup>A content, improved growth traits (e.g., root length, root surface area, plant height), and enhanced salt tolerance via increasing antioxidant enzyme (SOD, POD) activities and osmolyte (proline, betaine) contents while reducing reactive oxygen species (ROS) accumulation. Conversely, virus-induced gene silencing (VIGS) of <em>GmFIP37c</em> in soybean reduced salt and drought tolerance. Additionally, heterologous overexpression of <em>GmFIP37c</em> in <em>Arabidopsis thaliana</em> promoted seedling growth and improved tolerance to both stresses. Collectively, our findings indicate that GmFIP37 acts as a key component of the soybean m<sup>6</sup>A methyltransferase complex and positively regulates soybean responses to salt and drought stresses by modulating m<sup>6</sup>A modification. This study provides novel insights into the epigenetic regulatory mechanisms underlying soybean abiotic stress tolerance and lays a foundation for the genetic improvement of stress-resistant soybean varieties.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"231 ","pages":"Article 111082"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1016/j.plaphy.2026.111070
Satyam Rastogi , Sonal Srivastava , Akhand P. Singh , Srishti Kar , Shashank Kumar Mishra , Sumit Yadav , Poonam C. Singh , Sandip Kumar Behera , Suchi Srivastava
Plants are constantly exposed to wide variety of soil-borne phytopathogens, with Fusarium oxysporum being a major obstacle to crop productivity. Conventional control methods primarily rely on fumigants and chemical pesticides, which disrupt soil microbial communities and the ecosystem balance. When pathogens infect, plants activate stress responses such as strengthening of cell walls, regulation of reactive oxygen species, and production of antimicrobial compounds, often through metabolic reprogramming. Given the limitations of chemical pesticides and the soil-borne nature of the pathogen, this study investigates the mechanism of biocontrol agents (BCAs) as a sustainable strategy for managing Fusarium wilt in chickpea (Cicer arietinum). Two BCAs, Paenibacillus lentimorbus (NBRI-CHM12) and Bacillus amyloliquefaciens (NBRI-SN13), were tested for their antagonistic effects against F. oxysporum. Their effectiveness was evaluated under both greenhouse and microplot conditions to understand their role in disease suppression. Metabolomic analysis of chickpea plants identified specific saccharide derivatives linked to each BCA. CHM12 was associated with fructose, glucose, galactose, ribofuranose, glucopyranoside, xylopyranose, malic acid, arabitol, ribitol, hexadecanoic acid, and oleic acid; while, SN13 was linked with mannose, xylofuranose, sorbopyranose, glucopyranoside, galactopyranoside, xylitol, and trimethyl ester of glucitol. These findings indicate different defense mechanisms activated by each BCA. Both BCAs modulated cell wall hydrolases and antioxidant systems, improved soil microbial health, and notably decreased Fusarium-associated zearalenone levels in seeds by 77.3 % (CHM12) and 77.5 % (SN13) under greenhouse conditions. Overall, the results revealed the distinct pathways by which P. lentimorbus and B. amyloliquefaciens work and demonstrated their potential as biopesticides for sustainable control of Fusarium wilt in chickpea.
{"title":"Deciphering the potential of biocontrol agents for managing mycotoxin in chickpea: Mechanistic insights and functional dynamics","authors":"Satyam Rastogi , Sonal Srivastava , Akhand P. Singh , Srishti Kar , Shashank Kumar Mishra , Sumit Yadav , Poonam C. Singh , Sandip Kumar Behera , Suchi Srivastava","doi":"10.1016/j.plaphy.2026.111070","DOIUrl":"10.1016/j.plaphy.2026.111070","url":null,"abstract":"<div><div>Plants are constantly exposed to wide variety of soil-borne phytopathogens, with <em>Fusarium oxysporum</em> being a major obstacle to crop productivity. Conventional control methods primarily rely on fumigants and chemical pesticides, which disrupt soil microbial communities and the ecosystem balance. When pathogens infect, plants activate stress responses such as strengthening of cell walls, regulation of reactive oxygen species, and production of antimicrobial compounds, often through metabolic reprogramming. Given the limitations of chemical pesticides and the soil-borne nature of the pathogen, this study investigates the mechanism of biocontrol agents (BCAs) as a sustainable strategy for managing Fusarium wilt in chickpea (<em>Cicer arietinum</em>). Two BCAs, <em>Paenibacillus lentimorbus</em> (NBRI-CHM12) and <em>Bacillus amyloliquefaciens</em> (NBRI-SN13), were tested for their antagonistic effects against <em>F. oxysporum</em>. Their effectiveness was evaluated under both greenhouse and microplot conditions to understand their role in disease suppression. Metabolomic analysis of chickpea plants identified specific saccharide derivatives linked to each BCA. CHM12 was associated with fructose, glucose, galactose, ribofuranose, glucopyranoside, xylopyranose, malic acid, arabitol, ribitol, hexadecanoic acid, and oleic acid; while, SN13 was linked with mannose, xylofuranose, sorbopyranose, glucopyranoside, galactopyranoside, xylitol, and trimethyl ester of glucitol. These findings indicate different defense mechanisms activated by each BCA. Both BCAs modulated cell wall hydrolases and antioxidant systems, improved soil microbial health, and notably decreased <em>Fusarium</em>-associated zearalenone levels in seeds by 77.3 % (CHM12) and 77.5 % (SN13) under greenhouse conditions. Overall, the results revealed the distinct pathways by which <em>P. lentimorbus</em> and <em>B. amyloliquefaciens</em> work and demonstrated their potential as biopesticides for sustainable control of Fusarium wilt in chickpea.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"231 ","pages":"Article 111070"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1016/j.plaphy.2026.111078
Tao Tang , Jinyu Wu , Juan Fu , Yuqing Wang , Guang Qiao , Yi Hong , Tian Tian
The Flowering locus T (FT) is pivotal in integrating photoperiod signals to regulate plant floral transition and flowering. The FT protein is generally synthesized in leaves and translocated to the shoot apical meristem, where it interacts with FD to initiate flowering. Light intensity as a component of photoperiod signaling and a dynamically fluctuating factor in field light environments, however, the molecular mechanisms by which FT integrates changes in light intensity to regulate flowering in Chinese cherry remain unclear. Morphological analysis of flower buds and electron microscopic examination of pollen structures demonstrated that rain shelter (RS) extended the flowering period and enhanced the quantity and quality of flower buds. The expression levels of CpFT and CpFD genes were significantly up-regulated in various tissues under RS in the field. Based on these findings, it is hypothesized that FT exhibits a distinct response mechanism to changes in the light environment, thereby facilitating the regulation of floral induction under low-light conditions. Subsequently, plasmid recombination was carried out using seamless cloning technology, and tobacco was genetically transformed through leaf disc transformation. In addition, the ectopic overexpression of CpFT in tobacco promoted the expression of floral induction key genes, leading to the flowering time being advanced by 5–8 days, increased the number of flower buds and lateral buds, and staining rate increased by 58 % and the germination rate rose by 7 times. Furthermore, yeast two-hybrid and luciferase complementation assays confirmed the interaction between CpFT and CpFD. Combined with field observations of the ‘Manaohong’ cherry, these findings revealed that CpFT and CpFD constitute a signaling module in response to light intensity. This module positively regulates reproductive transitions and flowering time in cherries under low-light conditions, serving as a valuable reference for supplementing FT and FD to regulate floral induction in response to changes in the light environment.
开花位点T （flower locus T， FT）是整合光周期信号调控植物成花转变和开花的关键。FT蛋白通常在叶片中合成，并转运到茎尖分生组织，在那里它与FD相互作用，启动开花。光强作为光周期信号的一个组成部分，在田间光环境中是一个动态波动的因子，然而，FT整合光强变化调控中国樱桃开花的分子机制尚不清楚。花蕾形态分析和花粉结构电镜分析表明，遮阳棚延长了花期，提高了花蕾的数量和质量。田间RS处理下，CpFT和CpFD基因在各组织中的表达水平均显著上调。基于这些发现，我们假设FT对光环境的变化表现出独特的响应机制，从而促进了弱光条件下花诱导的调节。随后，利用无缝克隆技术进行质粒重组，通过叶片转化对烟草进行遗传转化。此外，CpFT在烟草中的异位过表达促进了花诱导关键基因的表达，导致开花时间提前5-8天，花芽和侧芽数量增加，染色率提高58%，发芽率提高7倍。此外，酵母双杂交和荧光素酶互补实验证实了CpFT和CpFD之间的相互作用。结合田间观察，这些发现表明CpFT和CpFD构成了一个响应光强的信号模块。该模块正向调节弱光条件下樱桃的生殖过渡和开花时间，为补充FT和FD调节花诱导响应光环境变化提供了有价值的参考。
{"title":"Ectopic overexpression of CpFT from ‘Manaohong’ cherry: Promoting floral induction and floral organ development in tobacco under rain shelter cultivation","authors":"Tao Tang , Jinyu Wu , Juan Fu , Yuqing Wang , Guang Qiao , Yi Hong , Tian Tian","doi":"10.1016/j.plaphy.2026.111078","DOIUrl":"10.1016/j.plaphy.2026.111078","url":null,"abstract":"<div><div>The <em>Flowering locus T</em> (<em>FT</em>) is pivotal in integrating photoperiod signals to regulate plant floral transition and flowering. The FT protein is generally synthesized in leaves and translocated to the shoot apical meristem, where it interacts with FD to initiate flowering. Light intensity as a component of photoperiod signaling and a dynamically fluctuating factor in field light environments, however, the molecular mechanisms by which <em>FT</em> integrates changes in light intensity to regulate flowering in Chinese cherry remain unclear. Morphological analysis of flower buds and electron microscopic examination of pollen structures demonstrated that rain shelter (RS) extended the flowering period and enhanced the quantity and quality of flower buds. The expression levels of <em>CpFT</em> and <em>CpFD</em> genes were significantly up-regulated in various tissues under RS in the field. Based on these findings, it is hypothesized that <em>FT</em> exhibits a distinct response mechanism to changes in the light environment, thereby facilitating the regulation of floral induction under low-light conditions. Subsequently, plasmid recombination was carried out using seamless cloning technology, and tobacco was genetically transformed through leaf disc transformation. In addition, the ectopic overexpression of <em>CpFT</em> in tobacco promoted the expression of floral induction key genes, leading to the flowering time being advanced by 5–8 days, increased the number of flower buds and lateral buds, and staining rate increased by 58 % and the germination rate rose by 7 times. Furthermore, yeast two-hybrid and luciferase complementation assays confirmed the interaction between CpFT and CpFD. Combined with field observations of the ‘Manaohong’ cherry, these findings revealed that CpFT and CpFD constitute a signaling module in response to light intensity. This module positively regulates reproductive transitions and flowering time in cherries under low-light conditions, serving as a valuable reference for supplementing <em>FT</em> and <em>FD</em> to regulate floral induction in response to changes in the light environment.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"231 ","pages":"Article 111078"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1016/j.plaphy.2026.111063
Yuwei Li , Chunyao Cui , Xiukai Zhang , Weile Lei , Junying Wang , Xiping Wang , Zhi Li
Grape white rot caused by Coniella species is one of the most serious fungal diseases of grape, leading to yield losses and quality reduction. Utilizing or breeding white rot–resistant grapevine is an important disease management strategy. This study evaluated the Coniella vitis resistance of 53 grape genotypes from 13 grape species and two interspecific hybrids. Most genotypes were susceptible, and disease resistance did not depend on grape species. No correlation was found between the C. vitis resistance of grape fruit and leaves. The resistant genotype ‘Shine Muscat’ and susceptible genotype ‘Manicure Finger’ were selected for cytological and metabolic studies. Compared with the susceptible genotype ‘Manicure Finger,’ the resistant genotype ‘Shine Muscat’ exhibited lower conidial germination rates and fewer infective hyphae in its leaf and berry tissues after inoculation with C. vitis as revealed by microscopy observation. After inoculation with C. vitis, the susceptible grape genotype showed higher H2O2 content in its leaf and berry tissues than the resistant grape genotype. Polyphenolic metabolites substantially accumulated in the berries of the susceptible genotype ‘Manicure Finger.’ Protocatechuic acid, catechin, epicatechin, and hyperoside significantly inhibited the conidial germination of C. vitis in a concentration-independent manner and exhibited a significant control effect on the white rot in grape leaves and berries. The findings of this work lay the foundation for breeding C. vitis–resistant grapes and enhance the understanding of the defense responses to C. vitis in different grape varieties.
{"title":"Cytological and metabolic mechanisms underlying grapevine resistance to Coniella vitis","authors":"Yuwei Li , Chunyao Cui , Xiukai Zhang , Weile Lei , Junying Wang , Xiping Wang , Zhi Li","doi":"10.1016/j.plaphy.2026.111063","DOIUrl":"10.1016/j.plaphy.2026.111063","url":null,"abstract":"<div><div>Grape white rot caused by <em>Coniella</em> species is one of the most serious fungal diseases of grape, leading to yield losses and quality reduction. Utilizing or breeding white rot–resistant grapevine is an important disease management strategy. This study evaluated the <em>Coniella vitis</em> resistance of 53 grape genotypes from 13 grape species and two interspecific hybrids. Most genotypes were susceptible, and disease resistance did not depend on grape species. No correlation was found between the <em>C. vitis</em> resistance of grape fruit and leaves. The resistant genotype ‘Shine Muscat’ and susceptible genotype ‘Manicure Finger’ were selected for cytological and metabolic studies. Compared with the susceptible genotype ‘Manicure Finger,’ the resistant genotype ‘Shine Muscat’ exhibited lower conidial germination rates and fewer infective hyphae in its leaf and berry tissues after inoculation with <em>C. vitis</em> as revealed by microscopy observation. After inoculation with <em>C. vitis</em>, the susceptible grape genotype showed higher H<sub>2</sub>O<sub>2</sub> content in its leaf and berry tissues than the resistant grape genotype. Polyphenolic metabolites substantially accumulated in the berries of the susceptible genotype ‘Manicure Finger.’ Protocatechuic acid, catechin, epicatechin, and hyperoside significantly inhibited the conidial germination of <em>C. vitis</em> in a concentration-independent manner and exhibited a significant control effect on the white rot in grape leaves and berries. The findings of this work lay the foundation for breeding <em>C. vitis</em>–resistant grapes and enhance the understanding of the defense responses to <em>C. vitis</em> in different grape varieties.</div></div>","PeriodicalId":20234,"journal":{"name":"Plant Physiology and Biochemistry","volume":"231 ","pages":"Article 111063"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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