Wendell J Pereira, Daniel Conde, Noé Perron, Henry W Schmidt, Christopher Dervinis, Rafael E Venado, Jean-Michel Ané, Matias Kirst
The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is fundamental for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: Single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species. Characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations. Single-cell transcriptomics data has enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization. Trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.
{"title":"Investigating biological nitrogen fixation via single-cell transcriptomics.","authors":"Wendell J Pereira, Daniel Conde, Noé Perron, Henry W Schmidt, Christopher Dervinis, Rafael E Venado, Jean-Michel Ané, Matias Kirst","doi":"10.1093/jxb/erae454","DOIUrl":"https://doi.org/10.1093/jxb/erae454","url":null,"abstract":"<p><p>The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is fundamental for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: Single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species. Characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations. Single-cell transcriptomics data has enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization. Trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675844","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}
The increasing frequency and intensity of low-temperature events in temperate and cold rice production regions threaten rice yields under climate change. While process-based crop models can project climate impacts on rice yield, their accuracy under low-temperature conditions has not been well-evaluated. Our six-year chamber experiments revealed that low temperatures reduce spikelet fertility from panicle initiation to flowering, grain number per spike during panicle development, and grain weight during grain filling. We examined the algorithms of spikelet fertility response to temperature used in crop models. Results showed that simulation performance is poor for crop yields if the same function was used at different growth stages outside the booting stage. Indeed, we replaced a parameter spikelet fertility algorithm of the ORYZA model and developed the function of estimating grain number per spike and grain weight. After that, the improved equation algorithm was applied to 10 rice growth models. New functions considered the harmful effects of low temperatures on rice yield at different stages. In addition, the threshold temperatures of the cold tolerance were set for different rice varieties. The improved algorithm enhances the model's ability to simulate rice yields under climate change, providing a more reliable tool for adapting rice production to future climatic challenges.
{"title":"Innovative modeling on the effects of low-temperature stress on rice yields.","authors":"Yanying Shi, Haoyu Ma, Tao Li, Erjing Guo, Tianyi Zhang, Xijuan Zhang, Xianli Yang, Lizhi Wang, Shukun Jiang, Yuhan Deng, Kaixin Guan, Mingzhe Li, Zhijuan Liu, Xiaoguang Yang","doi":"10.1093/jxb/erae452","DOIUrl":"10.1093/jxb/erae452","url":null,"abstract":"<p><p>The increasing frequency and intensity of low-temperature events in temperate and cold rice production regions threaten rice yields under climate change. While process-based crop models can project climate impacts on rice yield, their accuracy under low-temperature conditions has not been well-evaluated. Our six-year chamber experiments revealed that low temperatures reduce spikelet fertility from panicle initiation to flowering, grain number per spike during panicle development, and grain weight during grain filling. We examined the algorithms of spikelet fertility response to temperature used in crop models. Results showed that simulation performance is poor for crop yields if the same function was used at different growth stages outside the booting stage. Indeed, we replaced a parameter spikelet fertility algorithm of the ORYZA model and developed the function of estimating grain number per spike and grain weight. After that, the improved equation algorithm was applied to 10 rice growth models. New functions considered the harmful effects of low temperatures on rice yield at different stages. In addition, the threshold temperatures of the cold tolerance were set for different rice varieties. The improved algorithm enhances the model's ability to simulate rice yields under climate change, providing a more reliable tool for adapting rice production to future climatic challenges.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668157","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}
Juhyeon Lee, Myeong Hoon Kang, Da-Min Choi, Anne Marmagne, Jeehye Park, Heeho Lee, Eunha Gwak, Jong Chan Lee, Jeong-Il Kim, Céline Masclaux-Daubresse, Pyung Ok Lim
During leaf senescence, autophagy plays a critical role by removing damaged cellular components and participating in nutrient remobilization to sink organs. However, how AUTOPHGAY (ATG) genes are regulated during natural leaf senescence remains largely unknown. In this study, we attempted to identify upstream transcriptional regulator(s) of ATGs and their molecular basis during leaf senescence in Arabidopsis through the combined analyses of promoter binding, autophagy flux, and genetic interactions. We found that PIF4 and PIF5 (PIF4/PIF5) directly bind to the promoters of the ATG5, ATG12a, ATG12b, ATG8a, ATG8e, ATG8f, and ATG8g, inducing their transcription. These target ATGs are downregulated in pif4, pif5, and pif4pif5 mutants, resulting in decreased autophagic activity and slower degradation of chloroplast proteins and chlorophyll. Conversely, overexpression of ATG8s accelerated protein degradation with early leaf senescence. Moreover, our data suggests partial suppression of the pif4pif5 phenotype by ATG8a overexpression. PIF4/PIF5 also influences senescence induced by nutrient starvation, another hallmark of the autophagy pathway. Furthermore, we observed that the PIF4/PIF5-ATG regulatory module may contribute to seed maturation. Our study not only unveils transcriptional regulators of autophagy in natural leaf senescence but also underscores the potential role of PIF4/PIF5 as functional regulators in leaf senescence and nutrient remobilization.
{"title":"Phytochrome-interacting factors PIF4 and PIF5 directly regulate autophagy during leaf senescence in Arabidopsis.","authors":"Juhyeon Lee, Myeong Hoon Kang, Da-Min Choi, Anne Marmagne, Jeehye Park, Heeho Lee, Eunha Gwak, Jong Chan Lee, Jeong-Il Kim, Céline Masclaux-Daubresse, Pyung Ok Lim","doi":"10.1093/jxb/erae469","DOIUrl":"https://doi.org/10.1093/jxb/erae469","url":null,"abstract":"<p><p>During leaf senescence, autophagy plays a critical role by removing damaged cellular components and participating in nutrient remobilization to sink organs. However, how AUTOPHGAY (ATG) genes are regulated during natural leaf senescence remains largely unknown. In this study, we attempted to identify upstream transcriptional regulator(s) of ATGs and their molecular basis during leaf senescence in Arabidopsis through the combined analyses of promoter binding, autophagy flux, and genetic interactions. We found that PIF4 and PIF5 (PIF4/PIF5) directly bind to the promoters of the ATG5, ATG12a, ATG12b, ATG8a, ATG8e, ATG8f, and ATG8g, inducing their transcription. These target ATGs are downregulated in pif4, pif5, and pif4pif5 mutants, resulting in decreased autophagic activity and slower degradation of chloroplast proteins and chlorophyll. Conversely, overexpression of ATG8s accelerated protein degradation with early leaf senescence. Moreover, our data suggests partial suppression of the pif4pif5 phenotype by ATG8a overexpression. PIF4/PIF5 also influences senescence induced by nutrient starvation, another hallmark of the autophagy pathway. Furthermore, we observed that the PIF4/PIF5-ATG regulatory module may contribute to seed maturation. Our study not only unveils transcriptional regulators of autophagy in natural leaf senescence but also underscores the potential role of PIF4/PIF5 as functional regulators in leaf senescence and nutrient remobilization.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644059","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}
Virus infection brings about changes in the transcriptome, proteome and metabolome status of the infected plant wherein substantial alterations in the abundance of phytohormones and associated components involved in their signaling pathways have been observed. In the recent years, extensive research in the field of plant virology has showcased the undisputable significance of phytohormone signaling during plant-virus interactions. Apart from acting as growth regulators, phytohormones elicit robust immune response, which restricts the viral multiplication within the plant as well as its propagation by vector. Interestingly, these pathways have been shown to not only act as isolated mechanisms but as complex intertwined regulatory cascades where, the cross-talk among different phytohormones and with other antiviral pathways takes place during plant-virus interplay. Viruses cleverly disrupt phytohormone homeostasis via their multifunctional effectors that seems to be smart approach adopted by viruses to circumvent phytohormone-mediated plant immune responses. In this review, we summarize the current understanding of role of phytohormone signaling pathways during plant-virus interaction in activating antiviral immune responses of plant and also, how viruses exploit these signaling pathways favoring their pathogenesis.
{"title":"Diverse roles of phytohormonal signaling in modulating plant-virus interaction.","authors":"Shambhavi Sharma, Manoj Prasad","doi":"10.1093/jxb/erae468","DOIUrl":"https://doi.org/10.1093/jxb/erae468","url":null,"abstract":"<p><p>Virus infection brings about changes in the transcriptome, proteome and metabolome status of the infected plant wherein substantial alterations in the abundance of phytohormones and associated components involved in their signaling pathways have been observed. In the recent years, extensive research in the field of plant virology has showcased the undisputable significance of phytohormone signaling during plant-virus interactions. Apart from acting as growth regulators, phytohormones elicit robust immune response, which restricts the viral multiplication within the plant as well as its propagation by vector. Interestingly, these pathways have been shown to not only act as isolated mechanisms but as complex intertwined regulatory cascades where, the cross-talk among different phytohormones and with other antiviral pathways takes place during plant-virus interplay. Viruses cleverly disrupt phytohormone homeostasis via their multifunctional effectors that seems to be smart approach adopted by viruses to circumvent phytohormone-mediated plant immune responses. In this review, we summarize the current understanding of role of phytohormone signaling pathways during plant-virus interaction in activating antiviral immune responses of plant and also, how viruses exploit these signaling pathways favoring their pathogenesis.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644057","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}
O Gaju, K J Bloomfield, A C A Negrini, A F Bowerman, D Cullerne, B C Posch, C Bryant, Y Fan, M Spence, B Stone, M Gilliham, R T Furbank, G Molero, B J Pogson, K Mathews, A H Millar, A L Pearson, M P Reynolds, E Stroeher, N L Taylor, M H Turnbull, O K Atkin
An approach to improving radiation use efficiency (RUE) in wheat is to screen for variability in rates of leaf respiration in darkness (Rdark). We used a high-throughput system to quantify variation in Rdark among a diverse range of spring wheat genotypes (301 lines) grown in two countries (Mexico and Australia) and two seasons (2017 and 2018), and in doing so quantify the relative importance of genotype (G) and environment (E) in influencing variations in leaf Rdark. Through careful design, residual (unexplained) variation represented less than 10% of the total observed. Up to a third of the variation in Rdark (and related traits) was under genetic control. This suggests opportunities for breeders to use Rdark as a novel selection tool. In addition, E accounted for more than half of the total variation in area-based rates of Rdark. Here, the day of measurement was crucial, suggesting that day-to-day variations in the environment influence rates of Rdark measured at a common temperature. Overall, this study provides new insights into the role G and E play in determining variation in rates of leaf Rdark of one of the most important cereal crops, with implications for future improvements in carbon use efficiency and yield.
{"title":"Accounting for the impact of genotype and environment on variation in leaf respiration of wheat in Mexico and Australia.","authors":"O Gaju, K J Bloomfield, A C A Negrini, A F Bowerman, D Cullerne, B C Posch, C Bryant, Y Fan, M Spence, B Stone, M Gilliham, R T Furbank, G Molero, B J Pogson, K Mathews, A H Millar, A L Pearson, M P Reynolds, E Stroeher, N L Taylor, M H Turnbull, O K Atkin","doi":"10.1093/jxb/erae449","DOIUrl":"https://doi.org/10.1093/jxb/erae449","url":null,"abstract":"<p><p>An approach to improving radiation use efficiency (RUE) in wheat is to screen for variability in rates of leaf respiration in darkness (Rdark). We used a high-throughput system to quantify variation in Rdark among a diverse range of spring wheat genotypes (301 lines) grown in two countries (Mexico and Australia) and two seasons (2017 and 2018), and in doing so quantify the relative importance of genotype (G) and environment (E) in influencing variations in leaf Rdark. Through careful design, residual (unexplained) variation represented less than 10% of the total observed. Up to a third of the variation in Rdark (and related traits) was under genetic control. This suggests opportunities for breeders to use Rdark as a novel selection tool. In addition, E accounted for more than half of the total variation in area-based rates of Rdark. Here, the day of measurement was crucial, suggesting that day-to-day variations in the environment influence rates of Rdark measured at a common temperature. Overall, this study provides new insights into the role G and E play in determining variation in rates of leaf Rdark of one of the most important cereal crops, with implications for future improvements in carbon use efficiency and yield.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644055","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}
Scott A M McAdam, Anju Manandhar, Cade N Kane, Joel A Mercado-Reyes
The phytohormone abscisic acid (ABA) plays a major role in closing the stomata of angiosperms. However, recent reports of some angiosperm species having a peaking-type ABA dynamic, in which under extreme drought ABA levels decline to pre-stressed levels, raises the possibility that passive stomatal closure by leaf water status alone can occur in species from this lineage. To test this hypothesis, we conducted instantaneous rehydration experiments in the peaking-type species Umbellularia californica through a long-term drought, in which ABA levels declined to pre-stress levels, yet stomata remain closed. We found that when ABA levels were lowest during extreme drought, stomata reopen rapidly to maximum rates of gas exchange on instantaneous rehydration, suggesting that the stomata of U. californica were passively closed by leaf water status alone. This contrasts with leaves early in drought, in which ABA levels were highest and stomata did not reopen on instantaneous rehydration. The transition from ABA-driven stomatal closure to passively driven stomatal closure as drought progresses in this species occurs at very low water potentials facilitated by highly embolism-resistant xylem. These results have important implications for understanding stomatal control during drought in angiosperms.
植物激素脱落酸(ABA)在被子植物气孔关闭过程中起着重要作用。然而,最近有报道称,一些被子植物物种具有峰值型 ABA 动态,在极端干旱情况下,ABA 水平会下降到受压前的水平。为了验证这一假设,我们在峰值型物种加州脐橙(Umbellularia californica)中进行了瞬时补水实验,在长期干旱的情况下,ABA 水平会下降到应激前的水平,但气孔仍然关闭。我们发现,在极端干旱期间,当 ABA 水平最低时,加州脐橙的气孔仅受叶片水分状况的影响而被动关闭,而在瞬时补水时,气孔会迅速重新开放,达到最大气体交换速率。这与干旱初期的叶片形成鲜明对比,干旱初期叶片的 ABA 水平最高,气孔不会在瞬间补水时重新打开。该物种在干旱过程中从 ABA 驱动的气孔关闭过渡到被动驱动的气孔关闭,是在极低的水势下发生的,高度抗栓塞的木质部起到了促进作用。这些结果对于理解被子植物干旱期间的气孔控制具有重要意义。
{"title":"Passive stomatal closure under extreme drought in an angiosperm species.","authors":"Scott A M McAdam, Anju Manandhar, Cade N Kane, Joel A Mercado-Reyes","doi":"10.1093/jxb/erad510","DOIUrl":"10.1093/jxb/erad510","url":null,"abstract":"<p><p>The phytohormone abscisic acid (ABA) plays a major role in closing the stomata of angiosperms. However, recent reports of some angiosperm species having a peaking-type ABA dynamic, in which under extreme drought ABA levels decline to pre-stressed levels, raises the possibility that passive stomatal closure by leaf water status alone can occur in species from this lineage. To test this hypothesis, we conducted instantaneous rehydration experiments in the peaking-type species Umbellularia californica through a long-term drought, in which ABA levels declined to pre-stress levels, yet stomata remain closed. We found that when ABA levels were lowest during extreme drought, stomata reopen rapidly to maximum rates of gas exchange on instantaneous rehydration, suggesting that the stomata of U. californica were passively closed by leaf water status alone. This contrasts with leaves early in drought, in which ABA levels were highest and stomata did not reopen on instantaneous rehydration. The transition from ABA-driven stomatal closure to passively driven stomatal closure as drought progresses in this species occurs at very low water potentials facilitated by highly embolism-resistant xylem. These results have important implications for understanding stomatal control during drought in angiosperms.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6850-6855"},"PeriodicalIF":8.3,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139058409","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}
Yazen Al-Salman, Francisco Javier Cano, Emma Mace, David Jordan, Michael Groszmann, Oula Ghannoum
Environmental change requires more crop production per water use to meet the rising global food demands. However, improving crop intrinsic water use efficiency (iWUE) usually comes at the expense of carbon assimilation. Sorghum is a key crop in many vulnerable agricultural systems with higher tolerance to water stress (WS) than most widely planted crops. To investigate physiological controls on iWUE and its inheritance in sorghum, we screened 89 genotypes selected based on inherited haplotypes from an elite line or five exotics lines, containing a mix of geographical origins and dry versus milder climates, which included different aquaporin (AQP) alleles. We found significant variation among key highly heritable gas exchange and hydraulic traits, with some being significantly affected by variation in haplotypes among parental lines. Plants with a higher proportion of the non-stomatal component of iWUE still maintained iWUE under WS by maintaining photosynthetic capacity, independently of reduction in leaf hydraulic conductance. Haplotypes associated with two AQPs (SbPIP1.1 and SbTIP3.2) influenced iWUE and related traits. These findings expand the range of traits that bridge the trade-off between iWUE and productivity in C4 crops, and provide possible genetic regions that can be targeted for breeding.
{"title":"High water use efficiency due to maintenance of photosynthetic capacity in sorghum under water stress.","authors":"Yazen Al-Salman, Francisco Javier Cano, Emma Mace, David Jordan, Michael Groszmann, Oula Ghannoum","doi":"10.1093/jxb/erae418","DOIUrl":"10.1093/jxb/erae418","url":null,"abstract":"<p><p>Environmental change requires more crop production per water use to meet the rising global food demands. However, improving crop intrinsic water use efficiency (iWUE) usually comes at the expense of carbon assimilation. Sorghum is a key crop in many vulnerable agricultural systems with higher tolerance to water stress (WS) than most widely planted crops. To investigate physiological controls on iWUE and its inheritance in sorghum, we screened 89 genotypes selected based on inherited haplotypes from an elite line or five exotics lines, containing a mix of geographical origins and dry versus milder climates, which included different aquaporin (AQP) alleles. We found significant variation among key highly heritable gas exchange and hydraulic traits, with some being significantly affected by variation in haplotypes among parental lines. Plants with a higher proportion of the non-stomatal component of iWUE still maintained iWUE under WS by maintaining photosynthetic capacity, independently of reduction in leaf hydraulic conductance. Haplotypes associated with two AQPs (SbPIP1.1 and SbTIP3.2) influenced iWUE and related traits. These findings expand the range of traits that bridge the trade-off between iWUE and productivity in C4 crops, and provide possible genetic regions that can be targeted for breeding.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6778-6795"},"PeriodicalIF":5.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11565205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390989","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}
Grace D Tan, Ushasi Chaudhuri, Sebastian Varela, Narendra Ahuja, Andrew D B Leakey
Artificial intelligence and machine learning (AI/ML) can be used to automatically analyze large image datasets. One valuable application of this approach is estimation of plant trait data contained within images. Here we review 39 papers that describe the development and/or application of such models for estimation of stomatal traits from epidermal micrographs. In doing so, we hope to provide plant biologists with a foundational understanding of AI/ML and summarize the current capabilities and limitations of published tools. While most models show human-level performance for stomatal density (SD) quantification at superhuman speed, they are often likely to be limited in how broadly they can be applied across phenotypic diversity associated with genetic, environmental, or developmental variation. Other models can make predictions across greater phenotypic diversity and/or additional stomatal/epidermal traits, but require significantly greater time investment to generate ground-truth data. We discuss the challenges and opportunities presented by AI/ML-enabled computer vision analysis, and make recommendations for future work to advance accelerated stomatal phenotyping.
{"title":"Machine learning-enabled computer vision for plant phenotyping: a primer on AI/ML and a case study on stomatal patterning.","authors":"Grace D Tan, Ushasi Chaudhuri, Sebastian Varela, Narendra Ahuja, Andrew D B Leakey","doi":"10.1093/jxb/erae395","DOIUrl":"10.1093/jxb/erae395","url":null,"abstract":"<p><p>Artificial intelligence and machine learning (AI/ML) can be used to automatically analyze large image datasets. One valuable application of this approach is estimation of plant trait data contained within images. Here we review 39 papers that describe the development and/or application of such models for estimation of stomatal traits from epidermal micrographs. In doing so, we hope to provide plant biologists with a foundational understanding of AI/ML and summarize the current capabilities and limitations of published tools. While most models show human-level performance for stomatal density (SD) quantification at superhuman speed, they are often likely to be limited in how broadly they can be applied across phenotypic diversity associated with genetic, environmental, or developmental variation. Other models can make predictions across greater phenotypic diversity and/or additional stomatal/epidermal traits, but require significantly greater time investment to generate ground-truth data. We discuss the challenges and opportunities presented by AI/ML-enabled computer vision analysis, and make recommendations for future work to advance accelerated stomatal phenotyping.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6683-6703"},"PeriodicalIF":5.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11565210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372033","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}
Ethylene, a plant hormone that significantly influences both plant growth and response to stress, plays a well-established role in stress signaling. However, its impact on stomatal opening and closure during dehydration and rehydration remains relatively unexplored and is still debated. Exogenous ethylene has been proven to induce stomatal closure through a series of signaling pathways, including the accumulation of reactive oxygen species, subsequent synthesis of nitric oxide and hydrogen sulfide, and SLOW ANION CHANNEL-ASSOCIATED 1 activation. Thus, it has been suggested that ethylene might function to induce stomatal closure synergistically with abscisic acid (ABA). Furthermore, it has also been shown that increased ethylene can inhibit ABA- and jasmonic acid-induced stomatal closure, thus hindering drought-induced closure during dehydration. Simultaneously, other stresses, such as chilling, ozone pollution, and K+ deficiency, inhibit drought- and ABA-induced stomatal closure in an ethylene synthesis-dependent manner. However, ethylene has been shown to take on an opposing role during rehydration, preventing stomatal opening in the absence of ABA through its own signaling pathway. These findings offer novel insights into the function of ethylene in stomatal regulation during dehydration and rehydration, giving a better understanding of the mechanisms underlying ethylene-induced stomatal movement in seed plants.
乙烯是一种植物激素,对植物生长和对胁迫的反应都有显著影响,在胁迫信号传导中发挥着公认的作用。然而,乙烯在脱水和补水过程中对气孔开闭的影响仍相对缺乏研究,目前仍存在争议。事实证明,外源乙烯可通过一系列信号通路诱导气孔关闭,包括活性氧(ROS)的积累、一氧化氮(NO)和硫化氢(H2S)的后续合成以及 SLOW ANION CHANNEL-ASSOCIATED 1(SLAC1)的激活。因此,有人认为乙烯可能与脱落酸(ABA)协同诱导气孔关闭。此外,研究还表明,乙烯增加可抑制脱落酸(ABA)和茉莉酸(JA)诱导的气孔关闭,从而阻碍干旱诱导的脱水过程中的气孔关闭。同时,其他胁迫,如寒冷、臭氧污染和 K+ 缺乏,也会通过依赖乙烯合成的方式抑制干旱和 ABA 诱导的气孔关闭。然而,乙烯在补水过程中发挥了相反的作用,在没有 ABA 的情况下通过自身的信号途径阻止气孔开放。这些发现为乙烯在脱水和复水过程中调节气孔的功能提供了新的见解,使人们对乙烯诱导种子植物气孔运动的机制有了更好的了解。
{"title":"Ethylene-mediated stomatal responses to dehydration and rehydration in seed plants.","authors":"Md Mahadi Hasan, Xu-Dong Liu, Guang-Qian Yao, Jianquan Liu, Xiang-Wen Fang","doi":"10.1093/jxb/erae060","DOIUrl":"10.1093/jxb/erae060","url":null,"abstract":"<p><p>Ethylene, a plant hormone that significantly influences both plant growth and response to stress, plays a well-established role in stress signaling. However, its impact on stomatal opening and closure during dehydration and rehydration remains relatively unexplored and is still debated. Exogenous ethylene has been proven to induce stomatal closure through a series of signaling pathways, including the accumulation of reactive oxygen species, subsequent synthesis of nitric oxide and hydrogen sulfide, and SLOW ANION CHANNEL-ASSOCIATED 1 activation. Thus, it has been suggested that ethylene might function to induce stomatal closure synergistically with abscisic acid (ABA). Furthermore, it has also been shown that increased ethylene can inhibit ABA- and jasmonic acid-induced stomatal closure, thus hindering drought-induced closure during dehydration. Simultaneously, other stresses, such as chilling, ozone pollution, and K+ deficiency, inhibit drought- and ABA-induced stomatal closure in an ethylene synthesis-dependent manner. However, ethylene has been shown to take on an opposing role during rehydration, preventing stomatal opening in the absence of ABA through its own signaling pathway. These findings offer novel insights into the function of ethylene in stomatal regulation during dehydration and rehydration, giving a better understanding of the mechanisms underlying ethylene-induced stomatal movement in seed plants.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6719-6732"},"PeriodicalIF":8.3,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898040","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}
Ashley Baldwin, Tamara Lechon, Angela Marchbank, Simon Scofield, Kerstin Lieu, Charlotte L Wilson, Richard A Ludlow, Robert J Herbert, Hans-Wilhelm Nützmann, Hilary J Rogers
Strawberry ripening is non-climacteric, and post-harvest fruit enter senescence and deteriorate rapidly. Chilled storage induces transcriptome wide changes in gene expression, including the down-regulation of aroma related genes. Histone marks are associated with transcriptional activation or repression; the H3K27me3 mark is mainly associated with repression of gene expression. Here genes associated with H3K27me3 were identified through ChIP-seq in ripe red strawberry fruit at harvest and after 5 days of chilled storage in the dark. The number of ChIP peaks increased with storage time, indicating an increased role for this mark in regulation of gene expression following chilled dark storage. Comparing ChIP-seq data to RNA-seq data from the same material identified 440 genes whose expression correlates with H3K27me3 repression. Abiotic stress genes, especially cold stress response genes, were down-regulated during storage. Increased association with the H3K27me3 mark indicates that they may be repressed via this epigenetic mark. Other functional groups included cell wall and carbohydrate metabolism. The association with the H3K27me3 mark of two transcription factors (FaHY5 and FaTRAB1) and FaADH, involved in ester biosynthesis, was validated by ChIP-PCR. These three genes are all down-regulated during storage and indicate a network of H3K27me3 gene repression affecting both anthocyanin and ester biosynthesis.
{"title":"The H3K27me3 histone mark correlates with repression of colour and aroma development post-harvest in strawberry fruit.","authors":"Ashley Baldwin, Tamara Lechon, Angela Marchbank, Simon Scofield, Kerstin Lieu, Charlotte L Wilson, Richard A Ludlow, Robert J Herbert, Hans-Wilhelm Nützmann, Hilary J Rogers","doi":"10.1093/jxb/erae464","DOIUrl":"https://doi.org/10.1093/jxb/erae464","url":null,"abstract":"<p><p>Strawberry ripening is non-climacteric, and post-harvest fruit enter senescence and deteriorate rapidly. Chilled storage induces transcriptome wide changes in gene expression, including the down-regulation of aroma related genes. Histone marks are associated with transcriptional activation or repression; the H3K27me3 mark is mainly associated with repression of gene expression. Here genes associated with H3K27me3 were identified through ChIP-seq in ripe red strawberry fruit at harvest and after 5 days of chilled storage in the dark. The number of ChIP peaks increased with storage time, indicating an increased role for this mark in regulation of gene expression following chilled dark storage. Comparing ChIP-seq data to RNA-seq data from the same material identified 440 genes whose expression correlates with H3K27me3 repression. Abiotic stress genes, especially cold stress response genes, were down-regulated during storage. Increased association with the H3K27me3 mark indicates that they may be repressed via this epigenetic mark. Other functional groups included cell wall and carbohydrate metabolism. The association with the H3K27me3 mark of two transcription factors (FaHY5 and FaTRAB1) and FaADH, involved in ester biosynthesis, was validated by ChIP-PCR. These three genes are all down-regulated during storage and indicate a network of H3K27me3 gene repression affecting both anthocyanin and ester biosynthesis.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639005","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}