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CORONATINE INSENSITIVE 1-mediated repression of immunity-related genes in Arabidopsis roots is overcome upon infection with Verticillium longisporum.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-13 DOI: 10.1093/jxb/eraf056
Louisa Ulrich, Johanna Schmitz, Corinna Thurow, Christiane Gatz

Verticillium longisporum is a soil-borne fungal pathogen causing vascular disease predominantly in Brassicaceae. We have reported previously that the receptor of the plant defense hormone jasmonoyl-isoleucine (JA-Ile), CORONATINE INSENSITIVE 1 (COI1), is required in roots for efficient proliferation of the fungus in the shoot implicating a mobile root-borne signal that influences the outcome of the disease in shoots. This susceptibility-promoting COI1 function is independent from JA-Ile. To explore the underlying mechanism we compared the root transcriptome of coi1 with the transcriptomes of the susceptible JA-Ile-deficient allene oxide synthase (aos) mutant and susceptible wild-type (WT) plants. The biggest difference between the transcriptomes of coi1 versus WT and aos was due to 316 immunity-related genes that were constitutively higher expressed in coi1 as compared to the susceptible genotypes. Interfering with the expression of a subgroup of these genes partially suppressed the coi1-mediated tolerance phenotype. We therefore hypothesize that secreted defense compounds encoded by genes constitutively expressed in coi1 are transported to the shoot with the transpiration stream where they accumulate to interfere with fungal growth. We furthermore report that 149 of the 316 COI1-repressed genes are induced in WT and aos upon infection reaching similar levels as in mock-treated coi1. These were not further induced in coi1 upon infection. Thus, the repressive effect of COI1 is either lifted or overridden upon infection with V. longisporum.

{"title":"CORONATINE INSENSITIVE 1-mediated repression of immunity-related genes in Arabidopsis roots is overcome upon infection with Verticillium longisporum.","authors":"Louisa Ulrich, Johanna Schmitz, Corinna Thurow, Christiane Gatz","doi":"10.1093/jxb/eraf056","DOIUrl":"https://doi.org/10.1093/jxb/eraf056","url":null,"abstract":"<p><p>Verticillium longisporum is a soil-borne fungal pathogen causing vascular disease predominantly in Brassicaceae. We have reported previously that the receptor of the plant defense hormone jasmonoyl-isoleucine (JA-Ile), CORONATINE INSENSITIVE 1 (COI1), is required in roots for efficient proliferation of the fungus in the shoot implicating a mobile root-borne signal that influences the outcome of the disease in shoots. This susceptibility-promoting COI1 function is independent from JA-Ile. To explore the underlying mechanism we compared the root transcriptome of coi1 with the transcriptomes of the susceptible JA-Ile-deficient allene oxide synthase (aos) mutant and susceptible wild-type (WT) plants. The biggest difference between the transcriptomes of coi1 versus WT and aos was due to 316 immunity-related genes that were constitutively higher expressed in coi1 as compared to the susceptible genotypes. Interfering with the expression of a subgroup of these genes partially suppressed the coi1-mediated tolerance phenotype. We therefore hypothesize that secreted defense compounds encoded by genes constitutively expressed in coi1 are transported to the shoot with the transpiration stream where they accumulate to interfere with fungal growth. We furthermore report that 149 of the 316 COI1-repressed genes are induced in WT and aos upon infection reaching similar levels as in mock-treated coi1. These were not further induced in coi1 upon infection. Thus, the repressive effect of COI1 is either lifted or overridden upon infection with V. longisporum.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143408559","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}
引用次数: 0
Gene expression driving ethylene biosynthesis and signaling pathways in ripening tomato fruit; a kinetic modelling approach.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-13 DOI: 10.1093/jxb/eraf055
Thao Minh Viet Nguyen, Dinh Thi Tran, Clara I Mata, Bram Van de Poel, Bart M Nicolaï, Maarten L A T M Hertog

Ethylene biosynthesis and signaling are pivotal pathways in various plant aging processes, including fruit ripening. Kinetic models can be used to better understand metabolic pathways, but modeling of the ethylene-related pathways is limited and the link between these pathways remains unsolved. A transcriptomics-based kinetic model was developed, consisting of ordinary differential equations describing ethylene biosynthesis and signaling pathways in tomato during fruit development and ripening, both on- and off-vine. This model was calibrated against a large volume of transcriptomic, proteomic and metabolic data during on-vine fruit development and ripening of tomato fruit grown in winter and summer. The model was validated using data on off-vine ripening of mature green harvested fruit grown in the same seasons. The ethylene biosynthesis pathway under different conditions appeared to be largely driven by gene expression levels. The ethylene-regulation of fruit ripening of a heat tolerant tomato grown in different seasons is identical but with quantitative differences at the targeted omics levels. This is reflected by some of the same parameters with distinct values for summer and winter fruit. The current model is the first attempt to model the ethylene signaling pathway starting from gene expression, the various protein - protein interactions, including the link with ethylene production, internal ethylene levels and the binding to its receptors.

{"title":"Gene expression driving ethylene biosynthesis and signaling pathways in ripening tomato fruit; a kinetic modelling approach.","authors":"Thao Minh Viet Nguyen, Dinh Thi Tran, Clara I Mata, Bram Van de Poel, Bart M Nicolaï, Maarten L A T M Hertog","doi":"10.1093/jxb/eraf055","DOIUrl":"https://doi.org/10.1093/jxb/eraf055","url":null,"abstract":"<p><p>Ethylene biosynthesis and signaling are pivotal pathways in various plant aging processes, including fruit ripening. Kinetic models can be used to better understand metabolic pathways, but modeling of the ethylene-related pathways is limited and the link between these pathways remains unsolved. A transcriptomics-based kinetic model was developed, consisting of ordinary differential equations describing ethylene biosynthesis and signaling pathways in tomato during fruit development and ripening, both on- and off-vine. This model was calibrated against a large volume of transcriptomic, proteomic and metabolic data during on-vine fruit development and ripening of tomato fruit grown in winter and summer. The model was validated using data on off-vine ripening of mature green harvested fruit grown in the same seasons. The ethylene biosynthesis pathway under different conditions appeared to be largely driven by gene expression levels. The ethylene-regulation of fruit ripening of a heat tolerant tomato grown in different seasons is identical but with quantitative differences at the targeted omics levels. This is reflected by some of the same parameters with distinct values for summer and winter fruit. The current model is the first attempt to model the ethylene signaling pathway starting from gene expression, the various protein - protein interactions, including the link with ethylene production, internal ethylene levels and the binding to its receptors.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143408564","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}
引用次数: 0
Binary division of plastids involves ER-mediation.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-13 DOI: 10.1093/jxb/eraf064
Puja Puspa Ghosh, Thomas Kadanthottu Kunjumon, Jaideep Mathur

Plastids divide through binary division, involving the cytosolic protein Accumulation and Replication of Chloroplast 5 (ARC5), suggested to constrict and sever the plastid envelope membrane. However, the mechanisms involved in ARC5 recruitment to the mid-plastid division site and the final separation of daughter plastids are not fully understood. Using time-lapse imaging of Arabidopsis thaliana stable transgenics expressing fluorescently tagged endoplasmic reticulum (ER) and ARC5 proteins, we investigated the role played by the ER in the late stages of plastid division. Our observations establish that prior to its mid-plastid localization at the division-plane, ARC5 associates with ER membranes. ARC5-ER association generates an ER band around the plastid mid-plane that persists throughout division. Progressive tightening of the ER-band narrows the plastid middle to form an isthmus. Concomitantly, tandem plastid - ER dynamics facilitated by membrane contact sites (MCSs) move and rotate the dividing plastid and ultimately lead to the separation of daughter plastids. Our findings strongly indicate a pivotal role for the ER in facilitating plastid division.

{"title":"Binary division of plastids involves ER-mediation.","authors":"Puja Puspa Ghosh, Thomas Kadanthottu Kunjumon, Jaideep Mathur","doi":"10.1093/jxb/eraf064","DOIUrl":"https://doi.org/10.1093/jxb/eraf064","url":null,"abstract":"<p><p>Plastids divide through binary division, involving the cytosolic protein Accumulation and Replication of Chloroplast 5 (ARC5), suggested to constrict and sever the plastid envelope membrane. However, the mechanisms involved in ARC5 recruitment to the mid-plastid division site and the final separation of daughter plastids are not fully understood. Using time-lapse imaging of Arabidopsis thaliana stable transgenics expressing fluorescently tagged endoplasmic reticulum (ER) and ARC5 proteins, we investigated the role played by the ER in the late stages of plastid division. Our observations establish that prior to its mid-plastid localization at the division-plane, ARC5 associates with ER membranes. ARC5-ER association generates an ER band around the plastid mid-plane that persists throughout division. Progressive tightening of the ER-band narrows the plastid middle to form an isthmus. Concomitantly, tandem plastid - ER dynamics facilitated by membrane contact sites (MCSs) move and rotate the dividing plastid and ultimately lead to the separation of daughter plastids. Our findings strongly indicate a pivotal role for the ER in facilitating plastid division.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414441","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}
引用次数: 0
LIPID RICH 1 Modulates Allocation of Carbon between Starch and Triacylglycerol in Arabidopsis Leaves.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-08 DOI: 10.1093/jxb/eraf048
Mebae Yamaguchi, Shuji Shigenobu, Katsushi Yamaguchi, Yasuhiro Higashi, Yozo Okazaki, Kazuki Saito, Emi Mishiro-Sato, Keiko Kano, Ryosuke Sugiyama, Mami Yamazaki, Shigeo S Sugano, Shuichi Fukuyoshi, Haruko Ueda, Ikuko Hara-Nishimura, Takashi L Shimada

Plants accumulate starch and triacylglycerols (TAGs) as carbon sources. Leaves primarily store starch in chloroplasts, with some TAGs stored in lipid droplets, but how carbon resource allocation is regulated in leaves during cellular metabolism is largely unknown. Using a forward genetics approach, we isolated an Arabidopsis thaliana mutant with more lipid droplets in its leaves than the wild type, named lipid rich 1 (liri1). The overaccumulation of lipid droplets was caused by the loss of function in the causal gene, encoding an uncharacterized protein. TAG levels were five-fold higher and starch levels two-fold lower in the leaves of liri1 than the wild type. LIRI1 localized to the chloroplasts, and the contents of chloroplast membrane lipids were 20% higher in liri1 leaves than in wild-type leaves. Co-immunoprecipitation assays revealed that LIRI1 interacts with acetyl-coenzyme A carboxylase carboxyltransferase alpha subunit (an enzyme for fatty acid biosynthesis) and starch synthase 4 (an enzyme for starch biosynthesis). In isotope tracer experiments using [1-13C]-sodium acetate, more 13C was incorporated into TAGs in liri1 leaves than in wild-type leaves. Moreover, liri1 plants showed growth defects and irregular chloroplasts. These results suggest that LIRI1 affects the carbon trade-off to inhibit lipid production in leaves.

{"title":"LIPID RICH 1 Modulates Allocation of Carbon between Starch and Triacylglycerol in Arabidopsis Leaves.","authors":"Mebae Yamaguchi, Shuji Shigenobu, Katsushi Yamaguchi, Yasuhiro Higashi, Yozo Okazaki, Kazuki Saito, Emi Mishiro-Sato, Keiko Kano, Ryosuke Sugiyama, Mami Yamazaki, Shigeo S Sugano, Shuichi Fukuyoshi, Haruko Ueda, Ikuko Hara-Nishimura, Takashi L Shimada","doi":"10.1093/jxb/eraf048","DOIUrl":"https://doi.org/10.1093/jxb/eraf048","url":null,"abstract":"<p><p>Plants accumulate starch and triacylglycerols (TAGs) as carbon sources. Leaves primarily store starch in chloroplasts, with some TAGs stored in lipid droplets, but how carbon resource allocation is regulated in leaves during cellular metabolism is largely unknown. Using a forward genetics approach, we isolated an Arabidopsis thaliana mutant with more lipid droplets in its leaves than the wild type, named lipid rich 1 (liri1). The overaccumulation of lipid droplets was caused by the loss of function in the causal gene, encoding an uncharacterized protein. TAG levels were five-fold higher and starch levels two-fold lower in the leaves of liri1 than the wild type. LIRI1 localized to the chloroplasts, and the contents of chloroplast membrane lipids were 20% higher in liri1 leaves than in wild-type leaves. Co-immunoprecipitation assays revealed that LIRI1 interacts with acetyl-coenzyme A carboxylase carboxyltransferase alpha subunit (an enzyme for fatty acid biosynthesis) and starch synthase 4 (an enzyme for starch biosynthesis). In isotope tracer experiments using [1-13C]-sodium acetate, more 13C was incorporated into TAGs in liri1 leaves than in wild-type leaves. Moreover, liri1 plants showed growth defects and irregular chloroplasts. These results suggest that LIRI1 affects the carbon trade-off to inhibit lipid production in leaves.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374339","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}
引用次数: 0
Integrating cold hardiness and deacclimation resistance demonstrates a conserved response to chilling accumulation in grapevines.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-08 DOI: 10.1093/jxb/eraf045
Jason P Londo, Al P Kovaleski

To survive the harsh conditions of winter, woody perennial species such as grapevine have adapted to use environmental cues to trigger physiological changes to induce dormancy, acquire cold hardiness, and measure the length of winter to properly time spring budbreak. Human induced climate change disrupts these cues by prolonging warm temperatures in fall, reducing the depth and consistency of midwinter, and triggering early budbreak through false spring events. We evaluated variation in dormant bud cold hardiness and chilling hour requirements of 31 different grapevine varieties over 3 years. Differential thermal analysis was used to track changes in cold hardiness and deacclimation resistance was assessed throughout the season to track dormancy progression. Results demonstrate wide variation in maximum deacclimation rate (1.03 - 2.87 °C/day) among varieties under forcing conditions. Significant correlations were noted between wild species distributions or cultivar provenance with cold hardiness and deacclimation rates, demonstrating the likely climate-adaptive nature of these traits. When integrated with variation in cold hardiness, these rates revealed a relationship between winter cold hardiness, changes in deacclimation rate and budbreak phenology. Standardizing rates among varieties as deacclimation potential demonstrated a conserved response to chilling exposure among varieties that alters our interpretation of the concept of high and low chill varieties and chilling requirement in grapevine.

{"title":"Integrating cold hardiness and deacclimation resistance demonstrates a conserved response to chilling accumulation in grapevines.","authors":"Jason P Londo, Al P Kovaleski","doi":"10.1093/jxb/eraf045","DOIUrl":"https://doi.org/10.1093/jxb/eraf045","url":null,"abstract":"<p><p>To survive the harsh conditions of winter, woody perennial species such as grapevine have adapted to use environmental cues to trigger physiological changes to induce dormancy, acquire cold hardiness, and measure the length of winter to properly time spring budbreak. Human induced climate change disrupts these cues by prolonging warm temperatures in fall, reducing the depth and consistency of midwinter, and triggering early budbreak through false spring events. We evaluated variation in dormant bud cold hardiness and chilling hour requirements of 31 different grapevine varieties over 3 years. Differential thermal analysis was used to track changes in cold hardiness and deacclimation resistance was assessed throughout the season to track dormancy progression. Results demonstrate wide variation in maximum deacclimation rate (1.03 - 2.87 °C/day) among varieties under forcing conditions. Significant correlations were noted between wild species distributions or cultivar provenance with cold hardiness and deacclimation rates, demonstrating the likely climate-adaptive nature of these traits. When integrated with variation in cold hardiness, these rates revealed a relationship between winter cold hardiness, changes in deacclimation rate and budbreak phenology. Standardizing rates among varieties as deacclimation potential demonstrated a conserved response to chilling exposure among varieties that alters our interpretation of the concept of high and low chill varieties and chilling requirement in grapevine.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374268","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}
引用次数: 0
Ethylene signaling is essential for mycorrhiza-induced resistance against chewing herbivores in tomato.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-08 DOI: 10.1093/jxb/eraf053
Javier Lidoy, Javier Rivero, Živa Ramšak, Marko Petek, Maja Križnik, Victor Flors, Juan A Lopez-Raez, Ainhoa Martinez-Medina, Kristina Gruden, Maria J Pozo

Arbuscular mycorrhizal (AM) symbiosis can prime plant defenses, leading to mycorrhiza-induced resistance (MIR) against different attackers, including insect herbivores. Still, our knowledge of the complex molecular regulation leading to MIR is very limited. Here, we show that the AM fungus Funneliformis mosseae protects tomato plants against two different chewing herbivores, Spodoptera exigua and Manduca sexta. We explore the underlying molecular mechanism through genome-wide transcriptional profiling, bioinformatics network analyses, and functional bioassays. Herbivore-triggered JA-regulated defenses were primed in leaves of mycorrhizal plants, while ET biosynthesis and signaling were also higher both before and after herbivory. We hypothesized that fine-tuned ET signaling is required for the primed defensive response leading to MIR. ET is a complex regulator of plant responses to stress and is generally considered a negative regulator of plant defenses against herbivory. However, ET-deficient or insensitive lines did not show AM-primed JA biosynthesis or defense response, and were unable to develop MIR against any of the herbivores. Thus, we demonstrate that hormone crosstalk is central to the priming of plant immunity by beneficial microbes, with ET fine-tuning being essential for the primed JA biosynthesis and boosted defenses leading to MIR in tomato.

{"title":"Ethylene signaling is essential for mycorrhiza-induced resistance against chewing herbivores in tomato.","authors":"Javier Lidoy, Javier Rivero, Živa Ramšak, Marko Petek, Maja Križnik, Victor Flors, Juan A Lopez-Raez, Ainhoa Martinez-Medina, Kristina Gruden, Maria J Pozo","doi":"10.1093/jxb/eraf053","DOIUrl":"https://doi.org/10.1093/jxb/eraf053","url":null,"abstract":"<p><p>Arbuscular mycorrhizal (AM) symbiosis can prime plant defenses, leading to mycorrhiza-induced resistance (MIR) against different attackers, including insect herbivores. Still, our knowledge of the complex molecular regulation leading to MIR is very limited. Here, we show that the AM fungus Funneliformis mosseae protects tomato plants against two different chewing herbivores, Spodoptera exigua and Manduca sexta. We explore the underlying molecular mechanism through genome-wide transcriptional profiling, bioinformatics network analyses, and functional bioassays. Herbivore-triggered JA-regulated defenses were primed in leaves of mycorrhizal plants, while ET biosynthesis and signaling were also higher both before and after herbivory. We hypothesized that fine-tuned ET signaling is required for the primed defensive response leading to MIR. ET is a complex regulator of plant responses to stress and is generally considered a negative regulator of plant defenses against herbivory. However, ET-deficient or insensitive lines did not show AM-primed JA biosynthesis or defense response, and were unable to develop MIR against any of the herbivores. Thus, we demonstrate that hormone crosstalk is central to the priming of plant immunity by beneficial microbes, with ET fine-tuning being essential for the primed JA biosynthesis and boosted defenses leading to MIR in tomato.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374266","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}
引用次数: 0
Gene-Based Model To Predict Heading Date In Wheat Based On Allelic Characterization And Environmental Drivers.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-07 DOI: 10.1093/jxb/eraf049
Mariana R Jardón, Santiago Alvarez-Prado, Leonardo Vanzetti, Fernanda G Gonzalez, Thomas Pérez-Gianmarco, Dionisio Gómez, Román A Serrago, Jorge Dubcovsky, Maria Elena Fernandez Long, Daniel J Miralles

While numerous wheat phenology prediction models are available, most of them are constrained to using variety-dependent coefficients. The overarching objective of this study was to calibrate a gene-based model to predict wheat heading date that allows breeders to select specific gene combinations that would head within the optimal window for a given environment independently of varietal genetic background. A dataset with a total of 49 Argentine wheat cultivars and two recombinant inbred lines was chosen to cover a wide range of allelic combinations for major vernalization, photoperiod, and earliness per-se genes. The model was validated using independent data from an Argentine wheat trial network that includes sites from a wide latitudinal range. Ultimately, using this gene-based model, simulations were made to identify optimal gene combinations (ideotypes) × site combinations in contrasting locations. The selected model accurately predicted heading date with an overall median error of 4.6 days. This gene-based crop model for wheat phenology allowed the identification of groups of gene combinations predicted to head within a low-risk window and can be adapted to predict other phenological stages based on accessible climatic information and publicly available molecular markers, facilitating its adoption in wheat-growing regions worldwide.

{"title":"Gene-Based Model To Predict Heading Date In Wheat Based On Allelic Characterization And Environmental Drivers.","authors":"Mariana R Jardón, Santiago Alvarez-Prado, Leonardo Vanzetti, Fernanda G Gonzalez, Thomas Pérez-Gianmarco, Dionisio Gómez, Román A Serrago, Jorge Dubcovsky, Maria Elena Fernandez Long, Daniel J Miralles","doi":"10.1093/jxb/eraf049","DOIUrl":"https://doi.org/10.1093/jxb/eraf049","url":null,"abstract":"<p><p>While numerous wheat phenology prediction models are available, most of them are constrained to using variety-dependent coefficients. The overarching objective of this study was to calibrate a gene-based model to predict wheat heading date that allows breeders to select specific gene combinations that would head within the optimal window for a given environment independently of varietal genetic background. A dataset with a total of 49 Argentine wheat cultivars and two recombinant inbred lines was chosen to cover a wide range of allelic combinations for major vernalization, photoperiod, and earliness per-se genes. The model was validated using independent data from an Argentine wheat trial network that includes sites from a wide latitudinal range. Ultimately, using this gene-based model, simulations were made to identify optimal gene combinations (ideotypes) × site combinations in contrasting locations. The selected model accurately predicted heading date with an overall median error of 4.6 days. This gene-based crop model for wheat phenology allowed the identification of groups of gene combinations predicted to head within a low-risk window and can be adapted to predict other phenological stages based on accessible climatic information and publicly available molecular markers, facilitating its adoption in wheat-growing regions worldwide.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143365029","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}
引用次数: 0
Making the most of canopy light: shade avoidance under a fluctuating spectrum and irradiance. 充分利用树冠光:在波动的光谱和辐照度条件下避免遮荫。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-07 DOI: 10.1093/jxb/erae334
Romina Sellaro, Maxime Durand, Pedro J Aphalo, Jorge J Casal

In the field, plants face constantly changing light conditions caused by both atmospheric effects and neighbouring vegetation. This interplay creates a complex, fluctuating light environment within plant canopies. Shade-intolerant species rely on light cues from competitors to trigger shade avoidance responses, ensuring access to light for photosynthesis. While research often uses controlled growth chambers with steady light to study shade avoidance responses, the influence of light fluctuations in real-world settings remains unclear. This review examines the dynamic light environments found in woodlands, grasslands, and crops. We explore how plants respond to some fluctuations but not others, analyse the potential reasons for these differences, and discuss the possible molecular mechanisms regulating this sensitivity. We propose that studying shade avoidance responses under fluctuating light conditions offers a valuable tool to explore the intricate regulatory network behind them.

在野外,植物面临的光照条件因大气影响和邻近植被而不断变化。这种相互作用在植物树冠内形成了复杂多变的光照环境。不耐阴的物种依靠来自竞争者的光照线索来触发避阴反应,确保获得光照进行光合作用。虽然研究通常使用稳定光照的受控生长室来研究避阴反应,但实际环境中光照波动的影响仍不清楚。本综述探讨了林地、草地和农作物中的动态光照环境。我们探讨了植物如何对某些波动而非其他波动做出反应,分析了造成这些差异的潜在原因,并讨论了调节这种敏感性的可能分子机制。我们认为,研究光照波动条件下的避阴反应为探索其背后错综复杂的调控网络提供了宝贵的工具。
{"title":"Making the most of canopy light: shade avoidance under a fluctuating spectrum and irradiance.","authors":"Romina Sellaro, Maxime Durand, Pedro J Aphalo, Jorge J Casal","doi":"10.1093/jxb/erae334","DOIUrl":"10.1093/jxb/erae334","url":null,"abstract":"<p><p>In the field, plants face constantly changing light conditions caused by both atmospheric effects and neighbouring vegetation. This interplay creates a complex, fluctuating light environment within plant canopies. Shade-intolerant species rely on light cues from competitors to trigger shade avoidance responses, ensuring access to light for photosynthesis. While research often uses controlled growth chambers with steady light to study shade avoidance responses, the influence of light fluctuations in real-world settings remains unclear. This review examines the dynamic light environments found in woodlands, grasslands, and crops. We explore how plants respond to some fluctuations but not others, analyse the potential reasons for these differences, and discuss the possible molecular mechanisms regulating this sensitivity. We propose that studying shade avoidance responses under fluctuating light conditions offers a valuable tool to explore the intricate regulatory network behind them.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"712-729"},"PeriodicalIF":5.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11805590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141889454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Lights, location, action: shade avoidance signalling over spatial scales. 灯光、位置、行动:空间尺度上的避阴信号。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-07 DOI: 10.1093/jxb/erae217
Pierre Gautrat, Sanne E A Matton, Lisa Oskam, Siddhant S Shetty, Kyra J van der Velde, Ronald Pierik

Plants growing in dense vegetation need to flexibly position their photosynthetic organs to ensure optimal light capture in a competitive environment. They do so through a suite of developmental responses referred to as the shade avoidance syndrome. Below ground, root development is also adjusted in response to above-ground neighbour proximity. Canopies are dynamic and complex environments with heterogeneous light cues in the far-red, red, blue, and UV spectrum, which can be perceived by photoreceptors in spatially separated plant tissues. Molecular regulation of plant architecture adjustment via PHYTOCHROME-INTERACTING FACTOR transcription factors and growth-related hormones such as auxin, gibberellic acid, brassinosteroids, and abscisic acid were historically studied without much attention to spatial or tissue-specific context. Recent developments and technologies have, however, sparked strong interest in spatially explicit understanding of shade avoidance regulation. Other environmental factors such as temperature and nutrient availability interact with the molecular shade avoidance regulation network, often depending on the spatial location of the signals, and the responding organs. Here, we review recent advances in how plants respond to heterogeneous light cues and integrate these with other environmental signals.

生长在茂密植被丛中的植物需要灵活调整光合器官的位置,以确保在竞争激烈的环境中获得最佳光照。它们通过一系列发育反应来实现这一目标,这些反应被称为 "避阴综合症"。在地下,根系的发育也会根据地上相邻植物的接近程度进行调整。树冠是一个动态的复杂环境,具有远红、红、蓝和紫外线光谱的异质光线索,空间上分离的植物组织可通过光感受器感知这些光线索。通过 PHYTOCHROME-INTERACTING FACTOR(PIF)转录因子和生长相关激素(如辅酶、赤霉素、铜固醇和脱落酸)对植物结构调整进行分子调控的研究历来都不太关注空间或组织特异性背景。然而,最近的发展和技术引发了人们对从空间角度了解避阴调节的浓厚兴趣。温度和养分供应等其他环境因素与分子遮荫调节网络相互作用,通常取决于信号的空间位置和响应器官。在此,我们旨在回顾植物如何对异质光线索做出反应并将其与其他环境信号整合的最新进展。
{"title":"Lights, location, action: shade avoidance signalling over spatial scales.","authors":"Pierre Gautrat, Sanne E A Matton, Lisa Oskam, Siddhant S Shetty, Kyra J van der Velde, Ronald Pierik","doi":"10.1093/jxb/erae217","DOIUrl":"10.1093/jxb/erae217","url":null,"abstract":"<p><p>Plants growing in dense vegetation need to flexibly position their photosynthetic organs to ensure optimal light capture in a competitive environment. They do so through a suite of developmental responses referred to as the shade avoidance syndrome. Below ground, root development is also adjusted in response to above-ground neighbour proximity. Canopies are dynamic and complex environments with heterogeneous light cues in the far-red, red, blue, and UV spectrum, which can be perceived by photoreceptors in spatially separated plant tissues. Molecular regulation of plant architecture adjustment via PHYTOCHROME-INTERACTING FACTOR transcription factors and growth-related hormones such as auxin, gibberellic acid, brassinosteroids, and abscisic acid were historically studied without much attention to spatial or tissue-specific context. Recent developments and technologies have, however, sparked strong interest in spatially explicit understanding of shade avoidance regulation. Other environmental factors such as temperature and nutrient availability interact with the molecular shade avoidance regulation network, often depending on the spatial location of the signals, and the responding organs. Here, we review recent advances in how plants respond to heterogeneous light cues and integrate these with other environmental signals.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"695-711"},"PeriodicalIF":5.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11805592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction to: Hyperspectral imaging for chloroplast movement detection.
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-02-07 DOI: 10.1093/jxb/eraf043
{"title":"Correction to: Hyperspectral imaging for chloroplast movement detection.","authors":"","doi":"10.1093/jxb/eraf043","DOIUrl":"https://doi.org/10.1093/jxb/eraf043","url":null,"abstract":"","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370834","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}
引用次数: 0
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Journal of Experimental Botany
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