Pub Date : 2024-10-09DOI: 10.1016/j.envexpbot.2024.106000
Salt-alkaline stress adversely affects growth and productivity of soybean. In the event of global climate change, the effects of elevated CO2 concentration (eCO2) and salt-alkaline stress on soybean remain unclear. This study investigated the combined effects of elevated CO2 concentration (700 μmol·moL−1) and salt-alkaline stress on soybean growth, gas exchange, pigments profiles, antioxidative enzyme activities, osmolyte accumulation, Na+ and K+ contents, and genes involved in ion homeostasis. This study suggested that eCO2 improved plant physiological performance due to the greater net photosynthetic rate (+212.49 %) and water use efficiency (+92.86 %). Both salt-alkaline stress and eCO2 significantly increased catalase (CAT) activity in leaves and stems, significantly increased superoxide dismutase (SOD) activity in stems, and significantly increased peroxidase (POD) activity in whole plants of soybean. eCO2 significantly inhibited Na+ absorption as indicated by decreased Na+ contents in whole plants under salt-alkaline stress accompanied by lower relative electrical conductivity, thus reducing osmotic and ionic stress. eCO2 induced enhancement of expressions of gene encoding the ion transporter of GmHKT1;2, GmHKT1;5, GmHKT1;6, GmNHX5, and GmSOS1 in stems mediated Na+ and K+ transport, thus benefiting to keep ions homeostasis. These results suggest that eCO2 contributes to enhancing soybean tolerance to saline-alkaline stress.
{"title":"Elevated CO2 concentration enhances plant growth, photosynthesis, and ion homeostasis of soybean under salt-alkaline stress","authors":"","doi":"10.1016/j.envexpbot.2024.106000","DOIUrl":"10.1016/j.envexpbot.2024.106000","url":null,"abstract":"<div><div>Salt-alkaline stress adversely affects growth and productivity of soybean. In the event of global climate change, the effects of elevated CO<sub>2</sub> concentration (<em>e</em>CO<sub>2</sub>) and salt-alkaline stress on soybean remain unclear. This study investigated the combined effects of elevated CO<sub>2</sub> concentration (700 μmol·moL<sup>−1</sup>) and salt-alkaline stress on soybean growth, gas exchange, pigments profiles, antioxidative enzyme activities, osmolyte accumulation, Na<sup>+</sup> and K<sup>+</sup> contents, and genes involved in ion homeostasis. This study suggested that <em>e</em>CO<sub>2</sub> improved plant physiological performance due to the greater net photosynthetic rate (+212.49 %) and water use efficiency (+92.86 %). Both salt-alkaline stress and <em>e</em>CO<sub>2</sub> significantly increased catalase (CAT) activity in leaves and stems, significantly increased superoxide dismutase (SOD) activity in stems, and significantly increased peroxidase (POD) activity in whole plants of soybean. <em>e</em>CO<sub>2</sub> significantly inhibited Na<sup>+</sup> absorption as indicated by decreased Na<sup>+</sup> contents in whole plants under salt-alkaline stress accompanied by lower relative electrical conductivity, thus reducing osmotic and ionic stress. <em>e</em>CO<sub>2</sub> induced enhancement of expressions of gene encoding the ion transporter of <em>GmHKT1;2</em>, <em>GmHKT1;5</em>, <em>GmHKT1;6</em>, <em>GmNHX5</em>, and <em>GmSOS1</em> in stems mediated Na<sup>+</sup> and K<sup>+</sup> transport, thus benefiting to keep ions homeostasis. These results suggest that <em>e</em>CO<sub>2</sub> contributes to enhancing soybean tolerance to saline-alkaline stress.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445404","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 : 2024-10-09DOI: 10.1016/j.envexpbot.2024.105982
In the context of current climate change, alkaline salinity is increasingly challenging crop yields, especially in arid and semiarid regions. Alkaline salinity is more detrimental to plant performance than neutral salinity and tolerance to neutral salinity may not confer tolerance to alkaline salinity. The mechanisms behind are still poorly understood. This study aims to identify physiological and genetic traits underlying this differential tolerance to neutral and alkaline salinity by exploiting the variation present in natural populations (demes) of Arabidopsis thaliana. Growth, photosynthesis, phytohormone and mineral nutrient profiles, plant water status and transcriptomic changes were analyzed in four demes with contrasting tolerance to neutral and alkaline salinity. Results of this novel holistic approach suggest low internal Fe use efficiency caused by bicarbonate as a driver of enhanced sensitivity to alkaline salinity in plants adapted to neutral salinity prompting photosynthesis inhibition and alteration of the plant’s carbon budget for primary and secondary metabolism. Moreover, alkaline salinity specifically altered the auxin and jasmonic acid signaling pathways, while sustained ABA biosynthesis was an adaptive trait under neutral salinity. Exploring the genes with non-shared expression trends between salinity types, we identified sequence variation at the BGAL4 locus associated with advantageous responses to each type of salinity. Weighted correlation network analysis (WGCNA) validated the significant involvement of gene co-expression modules targeted by the enrichment analyses, highlighting the hubs correlated with favorable responses to both salinity types. Overall, the present study points out the complex physiological and genetic mechanisms responsible for plant tolerance to alkaline salinity and proposes target genes for breeding strategies under alkaline saline soils.
在当前气候变化的背景下,碱性盐度对作物产量的挑战越来越大,尤其是在干旱和半干旱地区。与中性盐度相比,碱性盐度更不利于植物生长,而耐受中性盐度未必就能耐受碱性盐度。人们对其背后的机理仍然知之甚少。本研究旨在利用拟南芥自然种群(demes)中存在的变异,找出对中性和碱性盐度的不同耐受性的生理和遗传特征。研究人员分析了对中性和碱性盐度耐受性截然不同的四个种群的生长、光合作用、植物激素和矿质营养概况、植物水分状态和转录组变化。这种新颖的整体方法的结果表明,碳酸氢盐导致的内部铁利用效率低是适应中性盐度的植物对碱性盐度敏感性增强的驱动因素,这促使光合作用受到抑制,并改变了植物初级和次级代谢的碳预算。此外,碱性盐度特异性地改变了辅助素和茉莉酸信号通路,而持续的 ABA 生物合成是中性盐度下的一种适应性特征。在探索盐度类型间非共享表达趋势的基因时,我们发现 BGAL4 基因座上的序列变异与对每种盐度类型的优势反应有关。加权相关网络分析(WGCNA)验证了富集分析所针对的基因共表达模块的显著参与,突出了与对两种盐度类型的有利响应相关的中心。总之,本研究指出了植物耐碱盐度的复杂生理和遗传机制,并提出了碱性盐碱地育种策略的目标基因。
{"title":"At the core of salinity: Divergent transcriptomic responses to neutral and alkaline salinity in Arabidopsis thaliana","authors":"","doi":"10.1016/j.envexpbot.2024.105982","DOIUrl":"10.1016/j.envexpbot.2024.105982","url":null,"abstract":"<div><div>In the context of current climate change, alkaline salinity is increasingly challenging crop yields, especially in arid and semiarid regions. Alkaline salinity is more detrimental to plant performance than neutral salinity and tolerance to neutral salinity may not confer tolerance to alkaline salinity. The mechanisms behind are still poorly understood. This study aims to identify physiological and genetic traits underlying this differential tolerance to neutral and alkaline salinity by exploiting the variation present in natural populations (demes) of <em>Arabidopsis thaliana</em>. Growth, photosynthesis, phytohormone and mineral nutrient profiles, plant water status and transcriptomic changes were analyzed in four demes with contrasting tolerance to neutral and alkaline salinity. Results of this novel holistic approach suggest low internal Fe use efficiency caused by bicarbonate as a driver of enhanced sensitivity to alkaline salinity in plants adapted to neutral salinity prompting photosynthesis inhibition and alteration of the plant’s carbon budget for primary and secondary metabolism. Moreover, alkaline salinity specifically altered the auxin and jasmonic acid signaling pathways, while sustained ABA biosynthesis was an adaptive trait under neutral salinity. Exploring the genes with non-shared expression trends between salinity types, we identified sequence variation at the <em>BGAL4</em> locus associated with advantageous responses to each type of salinity. Weighted correlation network analysis (WGCNA) validated the significant involvement of gene co-expression modules targeted by the enrichment analyses, highlighting the hubs correlated with favorable responses to both salinity types. Overall, the present study points out the complex physiological and genetic mechanisms responsible for plant tolerance to alkaline salinity and proposes target genes for breeding strategies under alkaline saline soils.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445405","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}
Pub Date : 2024-10-09DOI: 10.1016/j.envexpbot.2024.105998
Under current and future climate scenarios, identifying drought-resistant tree species, tree genotypes, and beneficial interactions between trees and their root-associated soil microbiomes is becoming more imperative for maintaining tree health and sustaining increasingly vulnerable forests. We designed a genotype x soil x watering x time glasshouse experiment using Pinus radiata as a model tree to assess the magnitude of the effect of host genotype and root-associated soil microbiome on the phenotype response (functional traits, metabolome, nutrients) under drought. We identified the shikimate pathway as a critical metabolic pathway for Pinus radiata drought resistance, with the shikimic acid intermediate being one of the strongest drought signals, besides downstream metabolites such as flavonoids and phenylpropanoids. Overall, we found that the host genotype diversity was a key actor in the observed phenotype response of P. radiata to drought. In contrast, the microbiome was attributed a minor supporting role. Contrary to our hypothesis, dry soils could not support drought-sensitive genotypes under drought stress. Instead, the drought-resistant genotype was able to leverage locally adaptive bacteria to match local selective drought pressures at the expense of tree growth. This highlights the significance of finding specific combinations of tree genotype and mutualistic microbial communities that would thrive under future environmental pressures.
{"title":"Host genetics shapes Pinus radiata phenotypic plasticity under drought and is linked with root-associated soil microbiome shifts","authors":"","doi":"10.1016/j.envexpbot.2024.105998","DOIUrl":"10.1016/j.envexpbot.2024.105998","url":null,"abstract":"<div><div>Under current and future climate scenarios, identifying drought-resistant tree species, tree genotypes, and beneficial interactions between trees and their root-associated soil microbiomes is becoming more imperative for maintaining tree health and sustaining increasingly vulnerable forests. We designed a genotype x soil x watering x time glasshouse experiment using <em>Pinus radiata</em> as a model tree to assess the magnitude of the effect of host genotype and root-associated soil microbiome on the phenotype response (functional traits, metabolome, nutrients) under drought. We identified the shikimate pathway as a critical metabolic pathway for <em>Pinus radiata</em> drought resistance, with the shikimic acid intermediate being one of the strongest drought signals, besides downstream metabolites such as flavonoids and phenylpropanoids. Overall, we found that the host genotype diversity was a key actor in the observed phenotype response of <em>P. radiata</em> to drought. In contrast, the microbiome was attributed a minor supporting role. Contrary to our hypothesis, dry soils could not support drought-sensitive genotypes under drought stress. Instead, the drought-resistant genotype was able to leverage locally adaptive bacteria to match local selective drought pressures at the expense of tree growth. This highlights the significance of finding specific combinations of tree genotype and mutualistic microbial communities that would thrive under future environmental pressures.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142535792","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 : 2024-10-06DOI: 10.1016/j.envexpbot.2024.105999
<div><div>The physiological and molecular mechanisms underlying salt-alkali tolerance in <em>Medicago sativa</em> are of significant importance for the development of animal husbandry on salt-alkali lands and the restoration of vegetation in such areas. This study utilized salt-alkali tolerance <em>Medicago sativa</em> 'Zhaodong' (ZD) and salt-alkali sensitive variety <em>M. sativa</em> 'Zhongmu No.1′ (ZM) as materials. Physiological analyses, transcriptomic sequencing, and hormone-targeted metabolomics techniques were employed to investigate the differential responses of the two alfalfa varieties to NaHCO<sub>3</sub> stress in terms of morphology, photosynthetic functionality, and oxidative damage indicators. Additionally, weighted gene co-expression network analysis (WGCNA) was utilized to elucidate key mechanisms underlying salt-alkali tolerance in alfalfa. The results indicate that NaHCO<sub>3</sub> stress leads to photosynthetic inhibition and oxidative damage in alfalfa leaves. Under NaHCO<sub>3</sub> stress, PSI in alfalfa leaves exhibits higher stability compared to PSII. The salt-alkali tolerance alfalfa variety ZD demonstrates stronger tolerance compared to the salt-alkali sensitive variety ZM. Furthermore, differentially expressed genes (DEGs) between the two varieties under NaHCO<sub>3</sub> stress are primarily enriched in KEGG pathways such as chlorophyll synthesis, photosynthesis, carbon fixation, and plant hormone synthesis and signaling. Weighted gene co-expression network analysis (WGCNA) was conducted based on physiological and transcriptomic data. Most differentially expressed genes (DEGs) in the top two modules with the highest correlation to physiological indicators such as photosynthesis are enriched in hormone synthesis and signal transduction pathways. Additionally, key transcription factors involved in hormone signal transduction were identified within these modules, such as <em>MYC2</em> and <em>ABI5</em>, which regulate jasmonic acid (JA) and abscisic acid (ABA) signaling, respectively. These findings suggest that plant hormone signaling may play a critical role in regulating salt-alkali tolerance in alfalfa. Further analysis was conducted on plant hormone levels and gene expression involved in biosynthesis and signal transduction processes. The results indicate that NaHCO<sub>3</sub> stress leads to significant accumulation of ABA and JA content in alfalfa leaves. The biosynthesis and signal transduction pathways of ABA and JA are activated under NaHCO<sub>3</sub> stress. Additionally, the salt-alkali tolerance alfalfa variety ZD exhibits a more sensitive response to ABA and JA signals compared to ZM. Salicylic acid (SA) shows a positive response to NaHCO<sub>3</sub> stress only in the ZD variety, which may be one of the key reasons for its stronger salt-alkali tolerance. Under NaHCO<sub>3</sub> stress, overall growth-promoting hormones (IAA, GA, CK) are downregulated in ZD but upregulated in ZM, indicating that the s
盐碱地上的畜牧业发展和植被恢复对盐碱地上的畜牧业发展和植被恢复具有重要意义。本研究以耐盐碱品种Medicago sativa'Zhaodong'(ZD)和盐碱敏感品种M.通过生理分析、转录组测序和激素靶向代谢组学技术,研究了两个紫花苜蓿品种在形态、光合功能和氧化损伤指标等方面对NaHCO3胁迫的不同响应。此外,还利用加权基因共表达网络分析(WGCNA)阐明了紫花苜蓿耐盐碱的关键机制。结果表明,NaHCO3胁迫会导致苜蓿叶片光合作用受抑制和氧化损伤。在 NaHCO3 胁迫下,苜蓿叶片中的 PSI 比 PSII 表现出更高的稳定性。与盐碱敏感品种 ZM 相比,耐盐碱紫花苜蓿品种 ZD 表现出更强的耐受性。此外,两个品种在 NaHCO3 胁迫下的差异表达基因(DEGs)主要富集在 KEGG 通路中,如叶绿素合成、光合作用、碳固定以及植物激素合成和信号转导。根据生理和转录组数据进行了加权基因共表达网络分析(WGCNA)。在与光合作用等生理指标相关性最高的前两个模块中,大多数差异表达基因(DEGs)都富集在激素合成和信号转导途径中。此外,在这些模块中还发现了参与激素信号转导的关键转录因子,如分别调控茉莉酸(JA)和脱落酸(ABA)信号转导的 MYC2 和 ABI5。这些研究结果表明,植物激素信号转导可能在调节紫花苜蓿的耐盐碱能力方面起着关键作用。研究人员进一步分析了植物激素水平以及生物合成和信号转导过程中的基因表达。结果表明,NaHCO3 胁迫会导致紫花苜蓿叶片中 ABA 和 JA 含量的显著积累。在 NaHCO3 胁迫下,ABA 和 JA 的生物合成和信号转导途径被激活。此外,与 ZM 相比,耐盐碱紫花苜蓿品种 ZD 对 ABA 和 JA 信号表现出更敏感的反应。只有 ZD 品种的水杨酸(SA)对 NaHCO3 胁迫表现出积极反应,这可能是其耐盐碱性更强的关键原因之一。在NaHCO3胁迫下,促进生长的激素(IAA、GA、CK)在ZD中整体下调,而在ZM中上调,表明耐盐碱紫花苜蓿品种ZD主要通过调节促进生长激素和胁迫相关激素的比例来调节生长和抗性之间的平衡,以应对NaHCO3胁迫。该研究揭示了激素信号在调节苜蓿应对盐碱胁迫的光合功能中起着关键作用,为苜蓿耐盐碱分子育种提供了理论依据和线索。
{"title":"Hormonal signaling regulates photosynthetic function of alfalfa (Medicago sativa L.) under NaHCO3 stress","authors":"","doi":"10.1016/j.envexpbot.2024.105999","DOIUrl":"10.1016/j.envexpbot.2024.105999","url":null,"abstract":"<div><div>The physiological and molecular mechanisms underlying salt-alkali tolerance in <em>Medicago sativa</em> are of significant importance for the development of animal husbandry on salt-alkali lands and the restoration of vegetation in such areas. This study utilized salt-alkali tolerance <em>Medicago sativa</em> 'Zhaodong' (ZD) and salt-alkali sensitive variety <em>M. sativa</em> 'Zhongmu No.1′ (ZM) as materials. Physiological analyses, transcriptomic sequencing, and hormone-targeted metabolomics techniques were employed to investigate the differential responses of the two alfalfa varieties to NaHCO<sub>3</sub> stress in terms of morphology, photosynthetic functionality, and oxidative damage indicators. Additionally, weighted gene co-expression network analysis (WGCNA) was utilized to elucidate key mechanisms underlying salt-alkali tolerance in alfalfa. The results indicate that NaHCO<sub>3</sub> stress leads to photosynthetic inhibition and oxidative damage in alfalfa leaves. Under NaHCO<sub>3</sub> stress, PSI in alfalfa leaves exhibits higher stability compared to PSII. The salt-alkali tolerance alfalfa variety ZD demonstrates stronger tolerance compared to the salt-alkali sensitive variety ZM. Furthermore, differentially expressed genes (DEGs) between the two varieties under NaHCO<sub>3</sub> stress are primarily enriched in KEGG pathways such as chlorophyll synthesis, photosynthesis, carbon fixation, and plant hormone synthesis and signaling. Weighted gene co-expression network analysis (WGCNA) was conducted based on physiological and transcriptomic data. Most differentially expressed genes (DEGs) in the top two modules with the highest correlation to physiological indicators such as photosynthesis are enriched in hormone synthesis and signal transduction pathways. Additionally, key transcription factors involved in hormone signal transduction were identified within these modules, such as <em>MYC2</em> and <em>ABI5</em>, which regulate jasmonic acid (JA) and abscisic acid (ABA) signaling, respectively. These findings suggest that plant hormone signaling may play a critical role in regulating salt-alkali tolerance in alfalfa. Further analysis was conducted on plant hormone levels and gene expression involved in biosynthesis and signal transduction processes. The results indicate that NaHCO<sub>3</sub> stress leads to significant accumulation of ABA and JA content in alfalfa leaves. The biosynthesis and signal transduction pathways of ABA and JA are activated under NaHCO<sub>3</sub> stress. Additionally, the salt-alkali tolerance alfalfa variety ZD exhibits a more sensitive response to ABA and JA signals compared to ZM. Salicylic acid (SA) shows a positive response to NaHCO<sub>3</sub> stress only in the ZD variety, which may be one of the key reasons for its stronger salt-alkali tolerance. Under NaHCO<sub>3</sub> stress, overall growth-promoting hormones (IAA, GA, CK) are downregulated in ZD but upregulated in ZM, indicating that the s","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422888","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 : 2024-10-05DOI: 10.1016/j.envexpbot.2024.106002
The common bean (Phaseolus vulgaris), a widely consumed legume in Ecuador, boasts low economic value, significant nutritional contributions, and a remarkable capacity to enhance soil fertility. Despite these attributes, its field productivity often needs to improve, with the water deficit emerging as a primary hindrance. Consequently, genetic enhancements have been incorporated into select varieties, conferring tolerance to specific levels of water scarcity stress. This study aimed to elucidate the distinctions in protein expression patterns responding to water deficiency stress across nine bean varieties. Protein patterns were scrutinized through two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and selected protein spots were subjected to mass spectrometry analysis (MALDI-TOF MS/RP-LC-MS/MS). A comprehensive identification of 111 proteins was achieved and categorized based on their respective functions. Noteworthy among these were the desiccation-protectant protein (LEA14) and Desiccation-related protein PCC13–62, identified as proteins associated with the response to abiotic stress, particularly prevalent in the INIAP_473 cultivar. These findings underscore the potential for targeted genetic improvements to mitigate the impact of water deficit stress on common bean cultivation, contributing to enhanced agricultural resilience and productivity.
{"title":"Proteomic analysis of storage proteins in Phaseolus vulgaris associated with resistance to water stress","authors":"","doi":"10.1016/j.envexpbot.2024.106002","DOIUrl":"10.1016/j.envexpbot.2024.106002","url":null,"abstract":"<div><div>The common bean (<em>Phaseolus vulgaris</em>), a widely consumed legume in Ecuador, boasts low economic value, significant nutritional contributions, and a remarkable capacity to enhance soil fertility. Despite these attributes, its field productivity often needs to improve, with the water deficit emerging as a primary hindrance. Consequently, genetic enhancements have been incorporated into select varieties, conferring tolerance to specific levels of water scarcity stress. This study aimed to elucidate the distinctions in protein expression patterns responding to water deficiency stress across nine bean varieties. Protein patterns were scrutinized through two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and selected protein spots were subjected to mass spectrometry analysis (MALDI-TOF MS/RP-LC-MS/MS). A comprehensive identification of 111 proteins was achieved and categorized based on their respective functions. Noteworthy among these were the desiccation-protectant protein (LEA14) and Desiccation-related protein PCC13–62, identified as proteins associated with the response to abiotic stress, particularly prevalent in the INIAP_473 cultivar. These findings underscore the potential for targeted genetic improvements to mitigate the impact of water deficit stress on common bean cultivation, contributing to enhanced agricultural resilience and productivity.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142444896","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}
Pub Date : 2024-10-05DOI: 10.1016/j.envexpbot.2024.106001
Salt stress upregulates osmoprotectants proline and melatonin in plants, and their exogenous application under salt stress can protect them from stress. While melatonin-induced plant epigenetic reprogramming is known in plants, such a mechanism is yet to be identified in the case of proline. The studies conducted so far used proline and melatonin along with one or more stress factors to look into their stress-alleviating effects. We investigated the impact of externally applied proline and melatonin on the methylation of promoter sequences of proline and melatonin biosynthesis genes in 14-day-old rice plants using a combination of biochemical, bioinformatics, and molecular techniques. Our findings demonstrate that exogenously applied proline and melatonin elevate endogenous levels of these compounds in rice, mimicking stress conditions in plants, as the biochemical assays corroborated the activation of antioxidant systems, particularly ascorbate peroxidase (APX) and catalase (CAT). Bioinformatics analysis unveiled multiple stress-responsive transcription factor binding sites on gene promoters associated with proline and melatonin biosynthesis pathways. Restriction analysis using the isoschizomer pair MspI/HpaII revealed distinct cytosine methylations at the restriction sites on the promoters analyzed in plants treated with proline and melatonin compared to the control. Differential methylation identified in the promoter sequences were matching with the biosynthesis of proline and melatonin and also the antioxidant enzyme levels. These observations are consistent with previous transcriptome data of proline and melatonin biosynthesis genes, providing insights into underlying regulatory mechanisms of proline and melatonin biosynthesis, their role in epigenome control during abiotic stress, and the evolution of various stress-tolerant varieties.
{"title":"Elevated proline and melatonin alter the methylation pattern in the promoter of their biosynthesis genes in rice","authors":"","doi":"10.1016/j.envexpbot.2024.106001","DOIUrl":"10.1016/j.envexpbot.2024.106001","url":null,"abstract":"<div><div>Salt stress upregulates osmoprotectants proline and melatonin in plants, and their exogenous application under salt stress can protect them from stress. While melatonin-induced plant epigenetic reprogramming is known in plants, such a mechanism is yet to be identified in the case of proline. The studies conducted so far used proline and melatonin along with one or more stress factors to look into their stress-alleviating effects. We investigated the impact of externally applied proline and melatonin on the methylation of promoter sequences of proline and melatonin biosynthesis genes in 14-day-old rice plants using a combination of biochemical, bioinformatics, and molecular techniques. Our findings demonstrate that exogenously applied proline and melatonin elevate endogenous levels of these compounds in rice, mimicking stress conditions in plants, as the biochemical assays corroborated the activation of antioxidant systems, particularly ascorbate peroxidase (APX) and catalase (CAT). Bioinformatics analysis unveiled multiple stress-responsive transcription factor binding sites on gene promoters associated with proline and melatonin biosynthesis pathways. Restriction analysis using the isoschizomer pair <em>MspI/HpaII</em> revealed distinct cytosine methylations at the restriction sites on the promoters analyzed in plants treated with proline and melatonin compared to the control. Differential methylation identified in the promoter sequences were matching with the biosynthesis of proline and melatonin and also the antioxidant enzyme levels. These observations are consistent with previous transcriptome data of proline and melatonin biosynthesis genes, providing insights into underlying regulatory mechanisms of proline and melatonin biosynthesis, their role in epigenome control during abiotic stress, and the evolution of various stress-tolerant varieties.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422523","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 : 2024-10-05DOI: 10.1016/j.envexpbot.2024.105991
Hirschfeldia incana L., a member of the Brassicaceae family commonly found in Mediterranean regions, is known for its capacity to withstand and accumulate heavy metals, particularly lead (Pb) both in soil environments and hydroponic systems. This plant has been used as a model to study plant responses to heavy metals. Nonetheless, the molecular mechanisms underlying its tolerance and heavy metal accumulation are not fully understood, partly because of the limited knowledge about its genome. In this study, the genome of H. incana was sequenced, assembled, characterized, and annotated. Approximately 8.6 Gpb of data were generated using Oxford Nanopore Technology (ONT), resulting in a genome assembly of 390 Mb, comprising 5196 contigs with an N50 exceeding 131 kb. The genome had a BUSCO score of 97.2 %, with 38,454 genes and a repetition content of 38.25 %. Subsequently, the assembled genome was annotated using several databases including GO, InterPro, MetaCyc, PANTHER, Pfam, Reactome, SUPERFAMILY, and KEGG. This annotation yielded 22,661 GO terms and 143 KEGG maps. A comparative genomic analysis between H. incana and six Brassicaceae species (five hyperaccumulators of heavy metals and one non-hyperaccumulator) was also conducted. This analysis revealed that H. incana shares a substantial proportion of orthologous genes (89.7 % of orthogroups) with six Brassicaceae species. The generated phylogenetic tree suggests that H. incana is closely related to B. juncea, B. napus, and B. oleracea, indicating a common ancestry and potentially shared genetic factors contributing to hyperaccumulation in these species. Moreover, the copy number of twenty-nine genes involved in heavy metal tolerance and accumulation mechanisms in H. incana and six brassicaceae were assayed. This analysis revealed that H. incana and other hyperaccumulator species possess a higher copy number of genes related to heavy metal tolerance than the sensitive plant A. thaliana. Notably, the variation in gene copy numbers highlights their potential role in the adaptation of H. incana to heavy metal stress. This study provides a comprehensive genomic framework that enhance our understanding of H. incana adaptation to heavy metal stress, and offers valuable data for further genomic investigations of the molecular mechanisms of heavy metal tolerance and accumulation in plants.
Hirschfeldia incana L.是一种常见于地中海地区的十字花科植物,以其在土壤环境和水培系统中承受和积累重金属(尤其是铅(Pb))的能力而闻名。这种植物已被用作研究植物对重金属反应的模型。然而,人们对其耐受性和重金属积累的分子机制并不完全了解,部分原因是对其基因组的了解有限。本研究对 H. incana 的基因组进行了测序、组装、表征和注释。利用牛津纳米孔技术(ONT)生成了约 8.6 Gpb 的数据,最终完成了 390 Mb 的基因组组装,包括 5196 个 N50 超过 131 kb 的等位基因。该基因组的 BUSCO 得分为 97.2%,有 38,454 个基因,重复率为 38.25%。随后,利用多个数据库对组装好的基因组进行了注释,包括 GO、InterPro、MetaCyc、PANTHER、Pfam、Reactome、SUPERFAMILY 和 KEGG。这一注释产生了 22,661 个 GO 术语和 143 个 KEGG 图谱。还对 H. incana 和六种十字花科植物(五种重金属高积累植物和一种非高积累植物)进行了基因组比较分析。该分析表明,H. incana 与 6 个十字花科物种有大量的同源基因(89.7% 的同源组)。生成的系统发生树表明,H. incana 与 B. juncea、B. napus 和 B. oleracea 亲缘关系密切,表明这些物种具有共同的祖先,并可能具有导致高积累的遗传因素。此外,还检测了 H. incana 和六种芸香科植物中 29 个涉及重金属耐受性和积累机制的基因的拷贝数。分析结果显示,与敏感植物大丽花(A. thaliana)相比,白花蛇舌草(H. incana)和其他高积累物种具有更高的重金属耐受基因拷贝数。值得注意的是,基因拷贝数的变化突显了它们在 H. incana 适应重金属胁迫过程中的潜在作用。这项研究提供了一个全面的基因组框架,加深了我们对 H. incana 适应重金属胁迫的理解,并为进一步研究植物重金属耐受性和积累的分子机制提供了宝贵的基因组数据。
{"title":"Genome architecture of the heavy metal tolerant and accumulator Hirschfeldia incana: Insights from genome sequencing, assembly, and comparative analysis","authors":"","doi":"10.1016/j.envexpbot.2024.105991","DOIUrl":"10.1016/j.envexpbot.2024.105991","url":null,"abstract":"<div><div><em>Hirschfeldia incana</em> L., a member of the Brassicaceae family commonly found in Mediterranean regions, is known for its capacity to withstand and accumulate heavy metals, particularly lead (Pb) both in soil environments and hydroponic systems. This plant has been used as a model to study plant responses to heavy metals. Nonetheless, the molecular mechanisms underlying its tolerance and heavy metal accumulation are not fully understood, partly because of the limited knowledge about its genome. In this study, the genome of <em>H. incana</em> was sequenced, assembled, characterized, and annotated. Approximately 8.6 Gpb of data were generated using Oxford Nanopore Technology (ONT), resulting in a genome assembly of 390 Mb, comprising 5196 contigs with an N50 exceeding 131 kb. The genome had a BUSCO score of 97.2 %, with 38,454 genes and a repetition content of 38.25 %. Subsequently, the assembled genome was annotated using several databases including GO, InterPro, MetaCyc, PANTHER, Pfam, Reactome, SUPERFAMILY, and KEGG. This annotation yielded 22,661 GO terms and 143 KEGG maps. A comparative genomic analysis between <em>H. incana</em> and six Brassicaceae species (five hyperaccumulators of heavy metals and one non-hyperaccumulator) was also conducted. This analysis revealed that <em>H. incana</em> shares a substantial proportion of orthologous genes (89.7 % of orthogroups) with six Brassicaceae species. The generated phylogenetic tree suggests that <em>H. incana</em> is closely related to <em>B. juncea, B. napus,</em> and <em>B. oleracea</em>, indicating a common ancestry and potentially shared genetic factors contributing to hyperaccumulation in these species. Moreover, the copy number of twenty-nine genes involved in heavy metal tolerance and accumulation mechanisms in <em>H. incana</em> and six brassicaceae were assayed. This analysis revealed that <em>H. incana</em> and other hyperaccumulator species possess a higher copy number of genes related to heavy metal tolerance than the sensitive plant <em>A. thaliana</em>. Notably, the variation in gene copy numbers highlights their potential role in the adaptation of <em>H. incana</em> to heavy metal stress. This study provides a comprehensive genomic framework that enhance our understanding of <em>H. incana</em> adaptation to heavy metal stress, and offers valuable data for further genomic investigations of the molecular mechanisms of heavy metal tolerance and accumulation in plants.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422889","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 : 2024-10-04DOI: 10.1016/j.envexpbot.2024.105986
Dry and hot climates severely impact wheat yields, necessitating the development of innovative solutions to accelerate the breeding and selection of more adaptable durum wheat genotypes. The aim of this study was to identify new wheat ecotypes that can bridge the gap between commercial varieties and adaptability to ongoing climate change. In this study, advanced genomic and phenomic techniques were combined to characterize a set of durum wheat landraces derived from single seed descent (SSD). This approach enabled the identification of novel variability in the TdHsp26-A1 and -B1 genes. As a result, 38 durum wheat genotypes were analyzed using targeted enrichment PCR, leading to the identification of 17 novel haplotype combinations with SNPs in the TdHsp26 genes. The response of these SSD haplotypes to heat stress was characterized at both the seedling and tillering growth stages. Phenotypic analysis of contrasting genotypes led to the selection of two distinct genotypes: SSD69 and SSD397. During heat stress, SSD69 exhibited altered accumulation of H2O2 and MDA content under both growth conditions, providing new insights into the oxidative response to heat stress. Additionally, this work identifies phenotypic traits that are suitable for detecting differences between variants. The geographic distribution of the different alleles aligned with the spread of durum wheat from its center of origin.
{"title":"From landraces to haplotypes, exploiting a genomic and phenomic approach to identify heat tolerant genotypes within durum wheat landraces","authors":"","doi":"10.1016/j.envexpbot.2024.105986","DOIUrl":"10.1016/j.envexpbot.2024.105986","url":null,"abstract":"<div><div>Dry and hot climates severely impact wheat yields, necessitating the development of innovative solutions to accelerate the breeding and selection of more adaptable durum wheat genotypes. The aim of this study was to identify new wheat ecotypes that can bridge the gap between commercial varieties and adaptability to ongoing climate change. In this study, advanced genomic and phenomic techniques were combined to characterize a set of durum wheat landraces derived from single seed descent (SSD). This approach enabled the identification of novel variability in the <em>TdHsp26-A1</em> and <em>-B1</em> genes. As a result, 38 durum wheat genotypes were analyzed using targeted enrichment PCR, leading to the identification of 17 novel haplotype combinations with SNPs in the TdHsp26 genes. The response of these SSD haplotypes to heat stress was characterized at both the seedling and tillering growth stages. Phenotypic analysis of contrasting genotypes led to the selection of two distinct genotypes: SSD69 and SSD397. During heat stress, SSD69 exhibited altered accumulation of H<sub>2</sub>O<sub>2</sub> and MDA content under both growth conditions, providing new insights into the oxidative response to heat stress. Additionally, this work identifies phenotypic traits that are suitable for detecting differences between variants. The geographic distribution of the different alleles aligned with the spread of durum wheat from its center of origin.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422883","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}
Pub Date : 2024-10-02DOI: 10.1016/j.envexpbot.2024.105989
Ankyrin repeat (ANK) proteins are crucial for cell growth, development, and response to hormones and environmental stress. However, there has been little research done to clarify the roles of ANK proteins in sorghum. In this study, 142 ANK genes of sorghum were identified and classified into 12 subfamilies according to the conserved domains. The cis-elements analysis revealed a substantial presence of stress-responsive elements within the promoter region of SbANK genes. After treated with drought, salt, and abscisic acid, SbANK56 showed the highest expression levels among family members by using quantitative real-time PCR (qRT-PCR) analysis. The survival rate was significantly improved by the overexpression of SbANK56 compared to wild type (WT) under drought conditions. SbANK56 overexpressing plants displayed lower malondialdehyde and higher proline contents compared to WT plants under drought conditions. Additionally, the expression levels of drought-associated genes were significantly increased in SbANK56 transgenic plants. Importantly, the analysis of natural variation in SbANK56 revealed a significant positive correlation between SbANK56Hap4 and both its differential expression and drought stress tolerance. Taken together, our results provide some evidence for improving drought tolerance in sorghum through breeding initiatives while also advancing our knowledge of the evolutionary trends and functional mechanisms underlying ANK genes.
{"title":"Comprehensive analysis of ankyrin repeat gene family revealed SbANK56 confers drought tolerance in sorghum","authors":"","doi":"10.1016/j.envexpbot.2024.105989","DOIUrl":"10.1016/j.envexpbot.2024.105989","url":null,"abstract":"<div><div>Ankyrin repeat (ANK) proteins are crucial for cell growth, development, and response to hormones and environmental stress. However, there has been little research done to clarify the roles of ANK proteins in sorghum. In this study, 142 <em>ANK</em> genes of sorghum were identified and classified into 12 subfamilies according to the conserved domains. The <em>cis</em>-elements analysis revealed a substantial presence of stress-responsive elements within the promoter region of <em>SbANK</em> genes. After treated with drought, salt, and abscisic acid, <em>SbANK56</em> showed the highest expression levels among family members by using quantitative real-time PCR (qRT-PCR) analysis. The survival rate was significantly improved by the overexpression of <em>SbANK56</em> compared to wild type (WT) under drought conditions. <em>SbANK56</em> overexpressing plants displayed lower malondialdehyde and higher proline contents compared to WT plants under drought conditions. Additionally, the expression levels of drought-associated genes were significantly increased in <em>SbANK56</em> transgenic plants. Importantly, the analysis of natural variation in <em>SbANK56</em> revealed a significant positive correlation between <em>SbANK56</em><sub>Hap4</sub> and both its differential expression and drought stress tolerance. Taken together, our results provide some evidence for improving drought tolerance in sorghum through breeding initiatives while also advancing our knowledge of the evolutionary trends and functional mechanisms underlying ANK genes.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422881","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 : 2024-09-28DOI: 10.1016/j.envexpbot.2024.105987
The invasive green algae Caulerpa taxifolia (M. Vahl) C. Agardh, 1817 and Caulerpa cylindracea Sonder, 1845 are widely diffused in the Mediterranean Sea, where they compete for space with the endemic seagrass Posidonia oceanica (Linnaeus) Delile, 1813, a keystone species in Mediterranean marine biodiversity. The present study aims to explore the possible effects of bioactive metabolites from the invasive algae on the seagrass, which may imply an allelopathic action. In particular, the study focuses on the effects of the algal alkaloid caulerpin and the sesquiterpene caulerpenyne. Changes in leaf growth, chlorophyll content, and leaf protein expression of P. oceanica genets under treatments were evaluated after 28 days of cultivation in mesocosms. Caulerpenyne strongly inhibited the growth of adult leaves and the formation of new ones, while inducing the elongation of the intermediate leaves and increased total chlorophyll content; on the contrary, caulerpin did not significantly influence leaf growth and the formation of new ones. A total of 107 differentially accumulated proteins common to the two treatments were also identified using the proteomic approach. Both molecules induced cells to maintain homeostasis, enhancing the amino acid metabolism or fatty acid biosynthesis. Despite these disruptions, P. oceanica demonstrated a more efficient response to stress induced by caulerpin, stimulating the biosynthesis of essential amino acids to maintain cellular homeostasis and mitigate damage caused by reactive oxygen species (ROS). Overall, obtained results supports the possible role of caulerpenyne, and not caulerpin, as an effector in allelopathic interactions among invasive Caulerpa species and P. oceanica in the Mediterranean.
{"title":"Physiological and proteomic responses of Posidonia oceanica to phytotoxins of invasive Caulerpa species","authors":"","doi":"10.1016/j.envexpbot.2024.105987","DOIUrl":"10.1016/j.envexpbot.2024.105987","url":null,"abstract":"<div><div>The invasive green algae <em>Caulerpa taxifolia</em> (M. Vahl) C. Agardh, 1817 and <em>Caulerpa cylindracea</em> Sonder, 1845 are widely diffused in the Mediterranean Sea, where they compete for space with the endemic seagrass <em>Posidonia oceanica</em> (Linnaeus) Delile, 1813, a keystone species in Mediterranean marine biodiversity. The present study aims to explore the possible effects of bioactive metabolites from the invasive algae on the seagrass, which may imply an allelopathic action. In particular, the study focuses on the effects of the algal alkaloid caulerpin and the sesquiterpene caulerpenyne. Changes in leaf growth, chlorophyll content, and leaf protein expression of <em>P. oceanica</em> genets under treatments were evaluated after 28 days of cultivation in mesocosms. Caulerpenyne strongly inhibited the growth of adult leaves and the formation of new ones, while inducing the elongation of the intermediate leaves and increased total chlorophyll content; on the contrary, caulerpin did not significantly influence leaf growth and the formation of new ones. A total of 107 differentially accumulated proteins common to the two treatments were also identified using the proteomic approach. Both molecules induced cells to maintain homeostasis, enhancing the amino acid metabolism or fatty acid biosynthesis. Despite these disruptions, <em>P. oceanica</em> demonstrated a more efficient response to stress induced by caulerpin, stimulating the biosynthesis of essential amino acids to maintain cellular homeostasis and mitigate damage caused by reactive oxygen species (ROS). Overall, obtained results supports the possible role of caulerpenyne, and not caulerpin, as an effector in allelopathic interactions among invasive <em>Caulerpa</em> species and <em>P. oceanica</em> in the Mediterranean.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422879","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}