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Elevated CO2 concentration enhances plant growth, photosynthesis, and ion homeostasis of soybean under salt-alkaline stress 二氧化碳浓度升高可促进盐碱胁迫下大豆的植物生长、光合作用和离子平衡
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-09 DOI: 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.
盐碱胁迫对大豆的生长和产量有不利影响。在全球气候变化的情况下,二氧化碳浓度(eCO2)升高和盐碱胁迫对大豆的影响仍不清楚。本研究调查了二氧化碳浓度升高(700 μmol-moL-1)和盐碱胁迫对大豆生长、气体交换、色素谱、抗氧化酶活性、渗透溶质积累、Na+和K+含量以及离子平衡相关基因的综合影响。该研究表明,eCO2 可提高净光合速率(+212.49 %)和水分利用效率(+92.86 %),从而改善植物的生理表现。盐碱胁迫和 eCO2 都能显著提高大豆叶片和茎中过氧化氢酶(CAT)的活性,显著提高茎中超氧化物歧化酶(SOD)的活性,显著提高全株过氧化物酶(POD)的活性。eCO2 能显著抑制 Na+ 的吸收,表现在盐碱胁迫下整株植物中 Na+ 含量降低,同时相对电导率降低,从而减轻渗透胁迫和离子胁迫。这些结果表明,eCO2 有助于提高大豆对盐碱胁迫的耐受性。
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引用次数: 0
At the core of salinity: Divergent transcriptomic responses to neutral and alkaline salinity in Arabidopsis thaliana 盐度的核心:拟南芥对中性和碱性盐度的不同转录组反应
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-09 DOI: 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。
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引用次数: 0
Host genetics shapes Pinus radiata phenotypic plasticity under drought and is linked with root-associated soil microbiome shifts 宿主遗传塑造了黑松在干旱条件下的表型可塑性,并与根系相关的土壤微生物群变化有关
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-09 DOI: 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.
在当前和未来的气候条件下,确定抗旱树种、树木基因型以及树木与其根系相关土壤微生物群之间的有益相互作用,对于维护树木健康和维持日益脆弱的森林变得越来越重要。我们设计了一个基因型×土壤×浇水×时间的玻璃温室实验,以辐射松为模型树,评估宿主基因型和根相关土壤微生物组对干旱下表型响应(功能性状、代谢组、养分)的影响程度。我们发现莽草酸途径是辐射松抗旱的关键代谢途径,其中莽草酸中间体是最强的干旱信号之一,此外还有黄酮类和苯丙类等下游代谢产物。总之,我们发现宿主基因型多样性是所观察到的辐射松对干旱的表型响应的关键因素。相比之下,微生物组只起了次要的辅助作用。与我们的假设相反,在干旱胁迫下,干燥的土壤无法支持对干旱敏感的基因型。相反,抗旱基因型能够利用当地的适应性细菌来应对当地的选择性干旱压力,但却牺牲了树木的生长。这凸显了找到树木基因型与互生微生物群落的特定组合,从而在未来环境压力下茁壮成长的重要性。
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引用次数: 0
Hormonal signaling regulates photosynthetic function of alfalfa (Medicago sativa L.) under NaHCO3 stress 激素信号调节 NaHCO3 胁迫下紫花苜蓿(Medicago sativa L. )的光合功能
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-06 DOI: 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":"&lt;div&gt;&lt;div&gt;The physiological and molecular mechanisms underlying salt-alkali tolerance in &lt;em&gt;Medicago sativa&lt;/em&gt; 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 &lt;em&gt;Medicago sativa&lt;/em&gt; 'Zhaodong' (ZD) and salt-alkali sensitive variety &lt;em&gt;M. sativa&lt;/em&gt; '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&lt;sub&gt;3&lt;/sub&gt; 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&lt;sub&gt;3&lt;/sub&gt; stress leads to photosynthetic inhibition and oxidative damage in alfalfa leaves. Under NaHCO&lt;sub&gt;3&lt;/sub&gt; 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&lt;sub&gt;3&lt;/sub&gt; 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 &lt;em&gt;MYC2&lt;/em&gt; and &lt;em&gt;ABI5&lt;/em&gt;, 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&lt;sub&gt;3&lt;/sub&gt; 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&lt;sub&gt;3&lt;/sub&gt; 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&lt;sub&gt;3&lt;/sub&gt; stress only in the ZD variety, which may be one of the key reasons for its stronger salt-alkali tolerance. Under NaHCO&lt;sub&gt;3&lt;/sub&gt; 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}
引用次数: 0
Proteomic analysis of storage proteins in Phaseolus vulgaris associated with resistance to water stress 与抗水胁迫有关的普通相思豆贮藏蛋白的蛋白质组分析
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-05 DOI: 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.
蚕豆(Phaseolus vulgaris)是厄瓜多尔人广泛食用的豆科植物,经济价值低,营养价值高,具有显著的提高土壤肥力的能力。尽管具有这些特性,但其田间生产力往往需要提高,而缺水则是主要障碍。因此,人们对部分品种进行了基因改良,使其能够耐受特定程度的缺水胁迫。本研究旨在阐明九个豆类品种在应对缺水胁迫时蛋白质表达模式的差异。通过二维聚丙烯酰胺凝胶电泳(2D-PAGE)对蛋白质模式进行了仔细研究,并对选定的蛋白质点进行了质谱分析(MALDI-TOF MS/RP-LC-MS/MS)。对 111 种蛋白质进行了全面鉴定,并根据其各自的功能进行了分类。其中值得注意的是干燥保护蛋白(LEA14)和干燥相关蛋白 PCC13-62,它们被鉴定为与非生物胁迫响应相关的蛋白质,在 INIAP_473 栽培品种中尤其普遍。这些发现强调了有针对性的遗传改良的潜力,以减轻缺水胁迫对普通豆类种植的影响,从而提高农业的抗逆性和生产力。
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引用次数: 0
Elevated proline and melatonin alter the methylation pattern in the promoter of their biosynthesis genes in rice 脯氨酸和褪黑激素的升高改变了水稻中其生物合成基因启动子的甲基化模式
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-05 DOI: 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.
盐胁迫会上调植物体内的渗透保护剂脯氨酸和褪黑激素,在盐胁迫下外源施用这两种物质可以保护植物免受胁迫。褪黑激素诱导的植物表观遗传重编程在植物中已为人所知,但脯氨酸的这种机制尚未确定。迄今为止进行的研究使用脯氨酸和褪黑激素以及一种或多种胁迫因子来研究它们的胁迫缓解效应。我们结合生化、生物信息学和分子技术,研究了外源脯氨酸和褪黑激素对 14 天水稻植株中脯氨酸和褪黑激素生物合成基因启动子序列甲基化的影响。我们的研究结果表明,外源施加的脯氨酸和褪黑激素会提高水稻中这些化合物的内源水平,模拟植物的胁迫条件,因为生化检测证实了抗氧化系统的激活,特别是抗坏血酸过氧化物酶(APX)和过氧化氢酶(CAT)。生物信息学分析揭示了与脯氨酸和褪黑激素生物合成途径相关的基因启动子上的多个应激反应转录因子结合位点。使用同源异构体对 MspI/HpaII 进行限制分析发现,与对照组相比,使用脯氨酸和褪黑激素处理的植物启动子上的限制位点存在不同的胞嘧啶甲基化。在启动子序列中发现的甲基化差异与脯氨酸和褪黑激素的生物合成以及抗氧化酶水平相匹配。这些观察结果与之前脯氨酸和褪黑激素生物合成基因的转录组数据一致,有助于深入了解脯氨酸和褪黑激素生物合成的潜在调控机制、它们在非生物胁迫期间表观基因组调控中的作用以及各种抗逆品种的进化。
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引用次数: 0
Genome architecture of the heavy metal tolerant and accumulator Hirschfeldia incana: Insights from genome sequencing, assembly, and comparative analysis 重金属耐受者和积累者 Hirschfeldia incana 的基因组结构:基因组测序、组装和比较分析的启示
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-05 DOI: 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。
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引用次数: 0
From landraces to haplotypes, exploiting a genomic and phenomic approach to identify heat tolerant genotypes within durum wheat landraces 从陆地小麦到单倍型,利用基因组学和表型学方法鉴定硬质小麦陆地小麦中的耐热基因型
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-04 DOI: 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.
干燥和炎热的气候严重影响小麦产量,因此有必要开发创新解决方案,加快培育和选育适应性更强的硬粒小麦基因型。本研究的目的是确定新的小麦生态型,以弥补商业品种与适应正在发生的气候变化之间的差距。在这项研究中,结合了先进的基因组学和表型组学技术,对一组源自单粒种子后裔(SSD)的硬质小麦陆地品系进行了表征。这种方法能够鉴定 TdHsp26-A1 和 -B1 基因的新变异。因此,利用定向富集 PCR 分析了 38 种硬质小麦基因型,从而鉴定出 17 种带有 TdHsp26 基因 SNPs 的新型单倍型组合。这些 SSD 单倍型在幼苗和分蘖生长阶段对热胁迫的反应均有特征。通过对对比基因型的表型分析,筛选出了两种不同的基因型:SSD69 和 SSD397。在热胁迫期间,SSD69 在两种生长条件下都表现出 H2O2 和 MDA 含量积累的改变,为了解热胁迫的氧化反应提供了新的视角。此外,这项研究还发现了适合检测变体间差异的表型特征。不同等位基因的地理分布与硬质小麦从其原产地中心扩散的情况一致。
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引用次数: 0
Comprehensive analysis of ankyrin repeat gene family revealed SbANK56 confers drought tolerance in sorghum 全面分析杏仁蛋白重复基因家族发现 SbANK56 能赋予高粱耐旱性
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-10-02 DOI: 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.
安基蛋白重复序列(ANK)蛋白对细胞的生长、发育以及对激素和环境压力的反应至关重要。然而,关于 ANK 蛋白在高粱中的作用的研究却很少。本研究鉴定了 142 个高粱 ANK 基因,并根据保守结构域将其分为 12 个亚族。顺式元件分析表明,在SbANK基因的启动子区域存在大量胁迫响应元件。通过实时定量 PCR(qRT-PCR)分析,SbANK56 在干旱、盐分和脱落酸处理后的表达水平在家族成员中最高。与野生型(WT)相比,过表达 SbANK56 能明显提高干旱条件下的存活率。在干旱条件下,与 WT 植物相比,过表达 SbANK56 的植物丙二醛含量更低,脯氨酸含量更高。此外,SbANK56 转基因植株中干旱相关基因的表达水平也显著增加。重要的是,对 SbANK56 自然变异的分析表明,SbANK56Hap4 与其差异表达和干旱胁迫耐受性之间存在明显的正相关。总之,我们的研究结果为通过育种措施提高高粱的抗旱性提供了一些证据,同时也增进了我们对 ANK 基因的进化趋势和功能机制的了解。
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引用次数: 0
Physiological and proteomic responses of Posidonia oceanica to phytotoxins of invasive Caulerpa species Posidonia oceanica 对入侵 Caulerpa 物种的植物毒素的生理和蛋白质组反应
IF 4.5 2区 生物学 Q2 ENVIRONMENTAL SCIENCES Pub Date : 2024-09-28 DOI: 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.
入侵绿藻 Caulerpa taxifolia (M. Vahl) C. Agardh, 1817 和 Caulerpa cylindracea Sonder, 1845 广泛分布于地中海,与当地特有的海草 Posidonia oceanica (Linnaeus) Delile, 1813 争夺空间,后者是地中海海洋生物多样性的关键物种。本研究旨在探索入侵藻类的生物活性代谢物对海草可能产生的影响,这可能意味着一种等效作用。研究重点尤其放在藻类生物碱 caulerpin 和倍半萜 caulerpenyne 的影响上。在中置培养箱中培养 28 天后,对处理下的大洋洲豚草属植物的叶片生长、叶绿素含量和叶片蛋白质表达的变化进行了评估。Caulerpenyne强烈抑制了成叶的生长和新叶的形成,同时诱导了中间叶的伸长并增加了叶绿素总含量;相反,caulerpin对叶片生长和新叶形成没有显著影响。利用蛋白质组学方法还鉴定了两种处理共有的 107 种不同积累的蛋白质。这两种分子都能诱导细胞保持平衡,加强氨基酸代谢或脂肪酸的生物合成。尽管存在这些干扰,但海洋豚鼠对 caulerpin 诱导的压力表现出更有效的反应,刺激必需氨基酸的生物合成,以维持细胞稳态,减轻活性氧(ROS)造成的损伤。总之,研究结果表明,在地中海地区入侵蕨类植物和大洋洲蕨之间的等位病理相互作用中,可能起作用的是caulerpenyne,而不是caulerpin。
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引用次数: 0
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Environmental and Experimental Botany
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