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Metabolomic analyses during chayote (Sechium edule var. virens levis) seed germination under the influence of growth regulators 受生长调节剂影响的辣木(Sechium edule var. virens levis)种子萌发过程中的代谢组分析
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-24 DOI: 10.1016/j.cpb.2024.100407
Yeimy C. Ramírez–Rodas , Ma. de Lourdes Arévalo–Galarza , Jorge Cadena–Iñiguez , Ramón M. Soto–Hernández , Cecilia B. Peña–Valdivia , José A. Guerrero–Analco , Juan L. Monribot–Villanueva , Rubén San Miguel-Chávez
The fruit of chayote (Sechium edule) has a recalcitrant seed, as a consequence, viviparism (seed germination inside the fruit) occurs in the first 13 days after harvest. However, at the moment no phytohormone–dependent metabolic changes have been described that would allow us to understand the hormonal relationship during germination. Untargeted and targeted metabolomic analyses were performed on chayote seed treated with plant growth regulators, evaluated in fruits at 7 and 10 days after harvest. Exogenous application of 2–chloroethylphosphonic acid (ethylene releaser) and gibberellic acid3 accelerated germination and viviparism, while auxins and abscisic acid delayed them. Metabolic pathways and possible key metabolites regulating germination were identified, including ethylene, gibberellins, auxins and abscisic acid. This study suggests a likely hormone interaction model during chayote seed germination.
辣木(Sechium edule)的果实具有顽固的种子特性,因此在收获后的头 13 天内就会发生活体萌发(种子在果实内萌发)。然而,目前还没有植物激素依赖性代谢变化的描述,因此我们无法了解萌发过程中的激素关系。我们对使用植物生长调节剂处理过的夏玉米种子进行了非靶向和靶向代谢组学分析,并对收获后 7 天和 10 天的果实进行了评估。外源应用 2-氯乙基膦酸(乙烯释放剂)和赤霉素3 加快了萌发和胎生,而辅酶和脱落酸则延迟了萌发和胎生。研究确定了调节萌芽的代谢途径和可能的关键代谢物,包括乙烯、赤霉素、辅酶和脱落酸。这项研究提出了在油茶籽萌发过程中可能存在的激素相互作用模型。
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引用次数: 0
Arabidopsis B-BOX DOMAIN PROTEIN14/15/16 form a feedback loop with ELONGATED HYPOCOTYL 5 and PHYTOCHROME-INTERACTING FACTORs to regulate hypocotyl elongation 拟南芥 B-BOX DOMAIN PROTEIN14/15/16 与 ELONGATED HYPOCOTYL 5 和 PHYTOCHROME-INTERACTING FACTORs 形成反馈回路,调控下胚轴伸长
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-23 DOI: 10.1016/j.cpb.2024.100395
Zeeshan Nasim , Nouroz Karim , Hendry Susila , Ji Hoon Ahn
Light-regulated developmental processes such as photomorphogenesis and flowering play important roles in the plant life cycle, from seedling emergence to reproduction. Three members of the Arabidopsis thaliana B-BOX DOMAIN PROTEIN (BBX) family, BBX14, BBX15, and BBX16 (hereafter BBX14/15/16), redundantly regulate flowering time, but whether this genetic redundancy also affects the regulation of photomorphogenesis remains unclear. Here, we show that light induces BBX14/15/16 expression primarily in the hypocotyl, where BBX14/15/16 redundantly repress hypocotyl elongation. PHYTOCHROME-INTERACTING FACTORs (PIFs) negatively regulate BBX14/15/16 expression mainly through GOLDEN-LIKE proteins (GLKs); however, analyses of ChIP-seq data showed that PIFs are recruited to the BBX14/15/16 loci and can also regulate these genes independently of GLKs. ELONGATED HYPOCOTYL 5 (HY5), a major regulator of photomorphogenesis, also directly binds to the BBX14/15/16 loci and regulates their expression. Simultaneous knockdown of BBX14/15/16 resulted in significant downregulation of HY5 and upregulation of PIFs, suggesting that these factors participate in a feedback regulatory loop. Indeed, BBX14/15/16 induced HY5 promoter activity by binding to the HY5 promoter. The brassinosteroid-responsive gene TOUCH4 (TCH4) and several auxin-responsive SMALL AUXIN UPREGULATED RNA (SAUR) genes were upregulated in the BBX14/15/16 knockdown plants, suggesting that auxin and brassinosteroids might participate in BBX14/15/16-mediated hypocotyl regulation. Mutating the predicted BBX-binding sites in SAUR4 and TCH4 impaired their regulation by BBX14/15/16. We propose that BBX14/15/16, together with HY5 and PIFs, form a feedback loop that regulates the expression of auxin- and brassinosteroid-related genes to modulate hypocotyl elongation.
光调控的发育过程(如光形态发生和开花)在植物从出苗到繁殖的生命周期中发挥着重要作用。拟南芥 B-BOX DOMAIN PROTEIN(BBX)家族的三个成员 BBX14、BBX15 和 BBX16(以下简称 BBX14/15/16)冗余调控开花时间,但这种遗传冗余是否也影响光形态发生的调控仍不清楚。在这里,我们发现光诱导的 BBX14/15/16 主要在下胚轴中表达,在下胚轴中,BBX14/15/16 冗余地抑制了下胚轴的伸长。细胞互作因子(PIFs)主要通过黄金样蛋白(GLKs)负调控 BBX14/15/16 的表达;然而,对 ChIP-seq 数据的分析表明,PIFs 被招募到 BBX14/15/16 基因座,也能独立于 GLKs 而调控这些基因。光形态发生的主要调控因子 ELONGATED HYPOCOTYL 5(HY5)也直接与 BBX14/15/16 基因座结合并调控其表达。同时敲除 BBX14/15/16 会导致 HY5 的显著下调和 PIFs 的上调,这表明这些因子参与了一个反馈调节环。事实上,BBX14/15/16 通过与 HY5 启动子结合诱导了 HY5 启动子的活性。在 BBX14/15/16 基因敲除的植株中,黄铜类固醇反应基因 TOUCH4(TCH4)和几个辅助素反应基因 SMALL AUXIN UPREGULATED RNA(SAUR)被上调,这表明辅助素和黄铜类固醇可能参与了 BBX14/15/16 介导的下胚轴调控。突变 SAUR4 和 TCH4 中预测的 BBX 结合位点会削弱 BBX14/15/16 对它们的调控。我们认为,BBX14/15/16 与 HY5 和 PIFs 一起形成了一个反馈环,可调节与叶绿素和铜绿素相关基因的表达,从而调节下胚轴的伸长。
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引用次数: 0
Genome-wide identification of TCP transcription factors and functional role of UrTCP4 in regulating terpenoid indole alkaloids biosynthesis in Uncaria rhynchophylla 全基因组范围内 TCP 转录因子的鉴定以及 UrTCP4 在调控 Uncaria rhynchophylla 中萜类吲哚生物碱生物合成中的功能作用
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-22 DOI: 10.1016/j.cpb.2024.100406
Xinghui Liu , Yingying Shao , Detian Mu , Yu Zhou , Jialong He , Huan Zhao , Iain W. Wilson , Yao Zhang , Lina Zhu , Deyou Qiu , Qi Tang
Uncaria rhynchophylla is a widely used Chinese herbal medicine known for its terpenoid indole alkaloids (TIAs), which help in treating hypertension. Teosinte branched 1/cycloidea/proliferating cell factors 1/2 (TCP) TFs have been shown to have a role in the growth and development of plants, but the regulation mechanism of UrTCP in the TIAs biosynthesis pathway is yet unknown. In this study, twenty-six UrTCP genes were identified from the genome of U. rhynchophylla, and these genes were classified into three subgroups based on the phylogenetic analysis. UrTCPs from the same group or subgroup share comparable gene structures and conserved motifs. These 26 UrTCP genes were unevenly distributed throughout 22 chromosomes, and gene segmental duplication occurred. The interspecific co-linearity analysis suggested that UrTCP4 may have an important function in evolutionary process. The expression patterns analysis of UrTCP genes by RT-qPCR showed most UrTCP genes had the highest expression in leaves and stem hooks. The results of co-expression analysis and phylogenetic relationships screened UrTCP4 as the most likely participant in TIAs and its precursor synthesis. Furthermore, the subcellular localization of UrTCP4 indicated that it is located in nucleus. Dual luciferase assays revealed the UrTCP4 protein could activate or repress the transcription of UrLAMT and Ur7-DLH in the TIAs synthesis pathway. Finally, Yeast-one-hybrid assays demonstrated that the UrTCP4 protein can bind to the promoters of UrLAMT and Ur7-DLH. Thus, UrTCP4 may be involved in the regulation of the TIAs biosynthesis pathway. This research establishes a groundwork for elucidating the functions of UrTCP gene family in U. rhynchophylla, offering new insights into the regulation of TIAs.
云芝(Uncaria rhynchophylla)是一种广泛使用的中药,因其萜类吲哚生物碱(TIAs)而闻名,TIAs有助于治疗高血压。Teosinte支链1/cycloidea/增殖细胞因子1/2(TCP)TFs已被证明在植物的生长发育中发挥作用,但UrTCP在TIAs生物合成途径中的调控机制尚不清楚。本研究从 U. rhynchophylla 的基因组中鉴定出 26 个 UrTCP 基因,并根据系统进化分析将这些基因分为三个亚组。同组或亚组中的 UrTCPs 具有相似的基因结构和保守基序。这 26 个 UrTCP 基因不均匀地分布在 22 条染色体上,且存在基因片段重复现象。种间共线性分析表明,UrTCP4在进化过程中可能具有重要功能。通过 RT-qPCR 对 UrTCP 基因的表达模式进行分析,发现大多数 UrTCP 基因在叶片和茎钩中的表达量最高。共表达分析和系统进化关系的结果筛选出 UrTCP4 最有可能参与 TIAs 及其前体的合成。此外,UrTCP4 的亚细胞定位表明它位于细胞核中。双荧光素酶试验显示,UrTCP4 蛋白可激活或抑制 TIAs 合成途径中 UrLAMT 和 Ur7-DLH 的转录。最后,酵母一杂交试验证明,UrTCP4 蛋白能与 UrLAMT 和 Ur7-DLH 的启动子结合。因此,UrTCP4可能参与了TIAs生物合成途径的调控。这项研究为阐明 U. rhynchophylla 中 UrTCP 基因家族的功能奠定了基础,为 TIAs 的调控提供了新的见解。
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引用次数: 0
Phytobioinformatics screening of ayurvedic plants for potential α-glucosidase inhibitors in diabetes management 通过植物生物信息学筛选阿育吠陀植物,寻找潜在的α-葡萄糖苷酶抑制剂,用于治疗糖尿病
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-22 DOI: 10.1016/j.cpb.2024.100404
Hira Khalid , Muhammad Hassan Butt , Aziz ur Rehman Aziz , Iqra Ahmad , Farzana Iqbal , Amen Shamim , Umar Nishan , Riaz Ullah , Mohamed A. Ibrahim , Arlindo Alencar Moura , Mohibullah Shah , Wenwen Sun
The enzyme α-glucosidase in the small intestine regulates blood glucose levels and stimulates the hydrolysis of oligosaccharides and polysaccharides, increasing glucose levels in the body. Inhibiting this enzyme slows glucose digestion and absorption and as a result post-prandial blood glucose levels remain low, causing decreased insulin demand. Here, we investigated the ayurvedic antidiabetic plants and virtually screened an in-house library of 478 phytochemicals of these plants against the human α-glucosidase. We identified 11 secondary metabolites, including palmitic acid α-monoglyceride, (+)-(2 R)-6-propionyloxyethyl-4′,5,7-trihydroxyisoflavanone, Abruquinone E, and Aurantiamide Acetate, among others, showed stronger interactions with the receptor than the native ligand N-acetyl cysteine. Surprisingly, except one, all of these metabolites were from Abrus precatorius L. [Fabaceae] affirming its ethnopharmacological use against diabetes. The stability of the interactions between the ligands and receptor protein was evaluated through Molecular Dynamic (MD) simulation trajectories including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), H bonds, β-factor analysis, and binding energy calculation through MM/GBSA method. The efficacy of top metabolites in inhibiting α-glucosidase is depicted in pharmacophore analysis. A comprehensive pharmacokinetics analysis confirmed the druggability, safety, and efficiency of top drug candidates. Additionally, we predicted the interactions of these top metabolites within the biological system. The medicinal properties described in this study will help develop active drug candidates for therapeutic purposes. Further experiments are recommended to prove the effectiveness of these metabolites in inhibiting the α-glucosidase enzyme for exploring their potential in the treatment of diabetes.
小肠中的α-葡萄糖苷酶能调节血糖水平,刺激低聚糖和多糖的水解,增加体内的葡萄糖含量。抑制这种酶会减缓葡萄糖的消化和吸收,从而使餐后血糖水平保持在较低水平,导致对胰岛素的需求减少。在此,我们对阿育吠陀抗糖尿病植物进行了研究,并对这些植物的 478 种植物化学物质库进行了针对人类 α-葡萄糖苷酶的虚拟筛选。我们发现了 11 种次生代谢物,包括棕榈酸 α-单甘酯、(+)-(2 R)-6- 丙酰氧基乙基-4′,5,7-三羟基异黄烷酮、阿布鲁醌 E 和醋酸金盏花酰胺等,它们与受体的相互作用比原生配体 N-乙酰半胱氨酸更强。令人惊讶的是,除一种代谢物外,所有这些代谢物都来自 Abrus precatorius L. [豆科],这肯定了它在防治糖尿病方面的民族药学用途。通过分子动力学(MD)模拟轨迹,包括均方根偏差(RMSD)、均方根波动(RMSF)、回旋半径(Rg)、H 键、β 因子分析以及 MM/GBSA 方法计算结合能,评估了配体与受体蛋白之间相互作用的稳定性。药代动力学分析表明了顶级代谢物对α-葡萄糖苷酶的抑制作用。全面的药代动力学分析证实了顶级候选药物的可药性、安全性和有效性。此外,我们还预测了这些顶级代谢物在生物系统中的相互作用。本研究中描述的药用特性将有助于开发用于治疗目的的活性候选药物。建议进行进一步的实验,以证明这些代谢物在抑制α-葡萄糖苷酶方面的有效性,从而探索它们在治疗糖尿病方面的潜力。
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引用次数: 0
Genome-wide identification and expression analysis of the SWEET gene family in sweet sorghum (Sorghum dochna) and the role of SdSWEET01 in sugar transport 甜高粱 SWEET 基因家族的全基因组鉴定和表达分析以及 SdSWEET01 在糖运输中的作用
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-22 DOI: 10.1016/j.cpb.2024.100405
Chengcai Pan , Yu Wang , Yiyin Ji , Yang Zhou , Xingyu Jiang
The SWEET sugar transporter plays a fundamental role in plant growth and development. In this study, 18 SWEET genes were identified from sweet sorghum (Sorghum dochna), encoding proteins with 231–336 amino acids, molecular weights from 25.15 to 35.69 kDa, and isoelectric points ranging between 6.41 and 9.69. Phylogenetic analysis categorized these proteins into four distinct subgroups. Examination of spatial expression patterns demonstrated that SdSWEET genes were expressed in a tissue-specific manner. Furthermore, their involvement in responses to various abiotic stresses, including cold, heat, drought, and salinity was observed. A yeast complementation assay verified that SdSWEET01, located on the plasma membrane, selectively transported glucose, sucrose, and galactose, while excluding fructose. Transgenic Arabidopsis expressing SdSWEET01 exhibited enhanced sugar absorption compared to wild-type plants, resulting in increased sensitivity and growth inhibition under high-sugar conditions. The study provides a detailed functional characterization of SdSWEET genes and emphasizes the critical role of SdSWEET01 in regulating sugar transport.
SWEET 糖转运体在植物的生长发育过程中发挥着重要作用。本研究从甜高粱(Sorghum dochna)中鉴定了 18 个 SWEET 基因,这些基因编码的蛋白质具有 231-336 个氨基酸,分子量在 25.15 至 35.69 kDa 之间,等电点在 6.41 至 9.69 之间。系统发生分析将这些蛋白质分为四个不同的亚群。对空间表达模式的研究表明,SdSWEET 基因的表达具有组织特异性。此外,还观察到它们参与了对各种非生物胁迫(包括冷、热、干旱和盐度)的响应。酵母互补试验证实,位于质膜上的 SdSWEET01 可选择性地转运葡萄糖、蔗糖和半乳糖,而不转运果糖。与野生型植物相比,表达 SdSWEET01 的转基因拟南芥表现出更强的糖吸收能力,从而提高了在高糖条件下的敏感性和生长抑制作用。该研究提供了 SdSWEET 基因的详细功能特征,并强调了 SdSWEET01 在调节糖转运中的关键作用。
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引用次数: 0
Multi-functional PGPR Serratia liquefaciens confers enhanced resistance to lead stress and bacterial blight in soybean (Glycine max L.) 多功能 PGPR Serratia liquefaciens 增强了大豆(Glycine max L.)对铅胁迫和细菌性枯萎病的抗性
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-19 DOI: 10.1016/j.cpb.2024.100403
Mohamed A. El-Esawi , Hayssam M. Ali , Ashraf Atef Hatamleh , Munirah Abdullah Al-Dosary , Enas M. El-Ballat
Lead toxicity and bacterial blight disease caused by Pseudomonas savastanoi pv. glycinea have destructive impacts on soybean growth and productivity. Plant growth-promoting rhizobacteria have been used as an eco-friendly approach for augmenting crop growth and stress resistance. The current study investigated the efficacy of Serratia liquefaciens ZM6 strain in enhancing soybean resistance to lead (Pb) stress and bacterial blight. Two pot experiments were performed. In the first pot experiment, soybean plants were inoculated with S. liquefaciens ZM6 and grown under variable Pb stress levels (0, 200 and 400 µM of Pb(NO3)2). In the second experiment, S. liquefaciens-inoculated soybean plants were infected with P. savastanoi pv. glycinea, and disease severity was assessed two weeks post infection. The results revealed that S. liquefaciens strain resisted Pb stress up to 400 µM Pb(NO3)2 and exhibited the highest levels of solubilized phosphate, solubilized zinc, siderophore, indole acetic acid, exopolysaccharide, trehalose and antioxidant enzymes at 400 µM Pb compared to the other treatments. Moreover, Pb stress (200 and 400 µM) significantly decreased the growth, yield, nutrient uptake, gas exchange, and contents of chlorophyll, soluble proteins, sugars, and phenolics of soybean plants. Pb stress also induced the levels of proline, glycine betaine, Pb, oxidative stress markers, antioxidant enzymes, ascorbate, glutathione and expression of stress-responsive genes (CAT, APX, POD, Fe-SOD, CHS7, CHI1A, PAL, IFS2, P5CS and WRKY54) in soybean plants. On the other hand, S. liquefaciens application markedly boosted the growth, yield and levels of nutrients, gas-exchange, chlorophyll, osmolytes, antioxidant enzymes and expression of stress-tolerant genes of Pb-stressed soybean plants. The bacterial inoculation significantly diminished oxidative stress indicators and Pb content in stressed plants. Inoculation of soybean plants with S. liquefaciens also caused significant reductions in blight disease symptoms in P. savastanoi pv. glycinea-infected plants, indicating the efficiency of this strain in controlling harmful blight disease. Overall, this study demonstrated S. liquefaciens ZM6 effectiveness in enhancing soybean resistance to Pb stress and bacterial blight.
铅毒性和由 Pseudomonas savastanoi pv. glycinea 引起的细菌性枯萎病对大豆的生长和产量具有破坏性影响。植物生长促进根瘤菌已被用作提高作物生长和抗逆性的生态友好型方法。本研究调查了 Serratia liquefaciens ZM6 菌株在增强大豆对铅(Pb)胁迫和细菌性枯萎病的抗性方面的功效。研究进行了两次盆栽实验。在第一个盆栽实验中,大豆植株接种了 S. liquefaciens ZM6,并在不同的铅胁迫水平(0、200 和 400 µM 的 Pb(NO3)2)下生长。在第二个实验中,接种了 S. liquefaciens 的大豆植株感染了 P. savastanoi pv. glycinea,并在感染两周后评估了病害严重程度。结果表明,与其他处理相比,S. liquefaciens 菌株能抵抗高达 400 µM Pb(NO3)2 的铅胁迫,并在 400 µM Pb 时表现出最高水平的溶解磷酸盐、溶解锌、苷元、吲哚乙酸、外多糖、三卤糖和抗氧化酶。此外,铅胁迫(200 和 400 µM)显著降低了大豆植株的生长、产量、养分吸收、气体交换以及叶绿素、可溶性蛋白质、糖和酚的含量。铅胁迫还诱导大豆植株中脯氨酸、甘氨酸甜菜碱、铅、氧化胁迫标记物、抗氧化酶、抗坏血酸、谷胱甘肽的水平以及胁迫响应基因(CAT、APX、POD、Fe-SOD、CHS7、CHI1A、PAL、IFS2、P5CS 和 WRKY54)的表达。另一方面,液化大豆酵母菌的应用明显促进了铅胁迫大豆植株的生长、产量和养分、气体交换、叶绿素、渗透溶质、抗氧化酶水平以及抗胁迫基因的表达。接种细菌后,受胁迫植物体内的氧化胁迫指标和铅含量明显降低。给大豆植株接种 S. liquefaciens 还能显著减轻 P. savastanoi pv. glycinea 感染植株的枯萎病症状,这表明该菌株能有效控制有害的枯萎病。总之,这项研究证明了 S. liquefaciens ZM6 在增强大豆对铅胁迫和细菌性枯萎病的抗性方面的有效性。
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引用次数: 0
GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses GRASSIUS 2.0:玉米和其他禾本科植物基因调控信息知识库
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-19 DOI: 10.1016/j.cpb.2024.100396
John Gray , Yi-Hsuan Chu , Ankita Abnave , Fabio Gomez Cano , Yun Sun Lee , Sarah Percival , Nan Jiang , Erich Grotewold
Grass species, which include the major cereal crops maize, wheat, rice, and sugarcane, are an integral part of our global agriculture and source of food and energy for a growing world population. GRASSIUS was established as a knowledgebase for transcription factors (TFs) and coregulators (CoRegs) in maize and several other species in the grass family. TFs are a primary component of the gene regulatory networks (GRNs) and the underlying gene regulatory grids (GRGs) that govern all aspects of plant growth and metabolism. GRASSIUS is the source for all information pertaining to the maize TFome collection, which serves as a powerful resource for the discovery of GRNs in maize and other cereals [1,2]. Here we describe the release of the GRASSIUS 2.0 knowledgebase (www.grassius.org) with updated data, query, and tool features, as well as the ability to expand to accommodate future datasets. The membership and annotation of all TF and CoReg families has been updated and revised to include gene models from v3, v4, and v5, of the maize B73 genome and recent genome versions of rice, sorghum, Brachypodium, and sugarcane. A translation tool enables cross referencing of Gene IDs between versions of the maize genome. Protein-DNA interactions (PDIs) have been added incorporating results derived from various gene- and TF-centered PDI discovery tools and visualized through a new web-based interface. A filtering tools permits the selection and visualization of PDIs within a ± 2 kb distance from the transcriptional start site (TSS) of a gene of interest. A new BLAST (Basic Local Alignment Search Tool) tool facilitates searching of the maize TFome as well as v3, v4, and v5 TF gene model sets. Lastly, we describe the methodology used to implement GRASSIUS 2.0 which can guide others in developing and updating similar plant gene regulatory knowledgebases.
禾本科植物包括主要谷类作物玉米、小麦、水稻和甘蔗,是全球农业不可或缺的一部分,也是不断增长的世界人口的食物和能源来源。GRASSIUS 是作为玉米和其他一些禾本科物种的转录因子(TFs)和核心调控因子(CoRegs)的知识库而建立的。转录因子是基因调控网络(GRN)和底层基因调控网格(GRG)的主要组成部分,而基因调控网络和底层基因调控网格控制着植物生长和新陈代谢的各个方面。GRASSIUS 是与玉米 TFome 收集有关的所有信息的来源,是发现玉米和其他谷物 GRN 的强大资源[1,2]。在此,我们介绍 GRASSIUS 2.0 知识库 (www.grassius.org) 的发布情况,该知识库具有更新的数据、查询和工具功能,并能扩展以适应未来的数据集。所有TF和CoReg家族的成员资格和注释都已更新和修订,以包括玉米B73基因组v3、v4和v5版本的基因模型,以及水稻、高粱、婆婆纳和甘蔗的最新基因组版本。通过翻译工具,可以在不同版本的玉米基因组之间交叉引用基因 ID。还增加了蛋白质-DNA 互作(PDIs),纳入了各种以基因和 TF 为中心的 PDI 发现工具的结果,并通过新的网络界面进行可视化。过滤工具允许选择和可视化距感兴趣基因的转录起始位点(TSS)± 2 kb 范围内的 PDIs。新的 BLAST(基本局部比对搜索工具)工具有助于搜索玉米 TFome 以及 v3、v4 和 v5 TF 基因模型集。最后,我们介绍了实施 GRASSIUS 2.0 所使用的方法,该方法可以指导其他人开发和更新类似的植物基因调控知识库。
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引用次数: 0
The potential applications of cytokinins and cytokinin oxidase/dehydrogenase inhibitors for mitigating abiotic stresses in model and non-model plant species 细胞分裂素和细胞分裂素氧化酶/脱氢酶抑制剂在减轻模式和非模式植物物种的非生物胁迫方面的潜在应用
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-19 DOI: 10.1016/j.cpb.2024.100398
Mxolisi P. Voko , Adeyemi O. Aremu , Nokwanda P. Makunga , Jaroslav Nisler , Karel Doležal , Nqobile A. Masondo
Cytokinins (CKs) are important phytohormones which are used by plants to optimize responses against abiotic stresses such as drought, salinity, temperature and nutrient stresses known to repress germination, and influencing general plant growth and development. Such stresses often trigger phenotypic plasticity and lead to low yields. Yet, the beneficial effect of CKs is counteracted by cytokinin oxidase/dehydrogenase (CKO/CKX, EC 1.5.99.12) enzymes and by N- and/or O-glycosylation. Additionally, research on CKs and CKX is often limited to model plants studied in isolation, and sparsely covers non-model plants exposed to abiotic stresses. Thus, this review explored the role of CKs and CKX inhibitors in mitigating abiotic stresses in model and non-model plants. We also examined possible crosstalk mechanisms of CKs with auxins, polyamines, and other major phytohormones. A detailed literature search was conducted using several databases including Web of Science, Google Scholar, ScienceDirect, Scopus, and PubMed. Upon perception of environmental stimuli, CKs [e.g., N6-(Δ2isopent-2-enyl)adenine (iP), trans-zeatin (tZ) and cis-zeatin (cZ)] induce abiotic stress tolerance in a CK - dependent manner or by forming intermolecular pathways with abscisic acid, ethylene, auxins and polyamines. Regulatory motifs of type-B ARRs code for transcriptional responses via DNA-binding. Inhibitors of CKX (e.g., 3TFM-2HE, INCYDE, F-INCYDE and anisiflupurin) act as promoters of growth and stress-tolerance through the inhibition of catabolic CKXs and regulate an increase in endogenous CKs (e.g., iP, tZ and cZ) in plants. The ability of CKX inhibitors to intercept CKX gene regulation is an indication of their potential applications in agriculture and other industries that rely on plant-based products.
细胞分裂素(CKs)是一种重要的植物激素,植物利用它来优化对干旱、盐度、温度和养分胁迫等非生物胁迫的反应,已知这些胁迫会抑制发芽,并影响植物的整体生长和发育。这些胁迫通常会引发表型可塑性,导致低产。然而,细胞分裂素的有益作用会被细胞分裂素氧化酶/脱氢酶(CKO/CKX,EC 1.5.99.12)以及 N- 和/或 O-糖基化所抵消。此外,有关 CKs 和 CKX 的研究往往局限于孤立研究的模式植物,很少涉及暴露于非生物胁迫的非模式植物。因此,本综述探讨了 CKs 和 CKX 抑制剂在减轻模式植物和非模式植物的非生物胁迫中的作用。我们还研究了 CKs 与辅酶、多胺和其他主要植物激素之间可能存在的串扰机制。我们利用多个数据库(包括 Web of Science、Google Scholar、ScienceDirect、Scopus 和 PubMed)进行了详细的文献检索。在感知环境刺激时,CKs [如 N6-(Δ2-异戊烯基)腺嘌呤(iP)、反式玉米素(tZ)和顺式玉米素(cZ)] 以 CK 依赖性方式或通过与脱落酸、乙烯、辅酶和多胺形成分子间途径诱导非生物胁迫耐受性。B 型 ARR 的调节基团通过 DNA 结合编码转录反应。CKX 抑制剂(如 3TFM-2HE、INCYDE、F-INCYDE 和 anisiflupurin)通过抑制分解代谢的 CKX 起到促进生长和抗逆的作用,并调节植物内源 CK(如 iP、tZ 和 cZ)的增加。CKX 抑制剂能够拦截 CKX 基因调控,这表明它们有可能应用于农业和其他依赖植物产品的行业。
{"title":"The potential applications of cytokinins and cytokinin oxidase/dehydrogenase inhibitors for mitigating abiotic stresses in model and non-model plant species","authors":"Mxolisi P. Voko ,&nbsp;Adeyemi O. Aremu ,&nbsp;Nokwanda P. Makunga ,&nbsp;Jaroslav Nisler ,&nbsp;Karel Doležal ,&nbsp;Nqobile A. Masondo","doi":"10.1016/j.cpb.2024.100398","DOIUrl":"10.1016/j.cpb.2024.100398","url":null,"abstract":"<div><div>Cytokinins (CKs) are important phytohormones which are used by plants to optimize responses against abiotic stresses such as drought, salinity, temperature and nutrient stresses known to repress germination, and influencing general plant growth and development. Such stresses often trigger phenotypic plasticity and lead to low yields. Yet, the beneficial effect of CKs is counteracted by cytokinin oxidase/dehydrogenase (CKO/CKX, EC 1.5.99.12) enzymes and by <em>N</em>- and/or <em>O</em>-glycosylation. Additionally, research on CKs and CKX is often limited to model plants studied in isolation, and sparsely covers non-model plants exposed to abiotic stresses. Thus, this review explored the role of CKs and CKX inhibitors in mitigating abiotic stresses in model and non-model plants. We also examined possible crosstalk mechanisms of CKs with auxins, polyamines, and other major phytohormones. A detailed literature search was conducted using several databases including Web of Science, Google Scholar, ScienceDirect, Scopus, and PubMed. Upon perception of environmental stimuli, CKs [e.g., <em>N</em><sup>6</sup>-(Δ<sup>2</sup>isopent-2-enyl)adenine (iP), <em>trans</em>-zeatin (<em>t</em>Z) and <em>cis</em>-zeatin (<em>c</em>Z)] induce abiotic stress tolerance in a CK - dependent manner or by forming intermolecular pathways with abscisic acid, ethylene, auxins and polyamines. Regulatory motifs of type-B ARRs code for transcriptional responses via DNA-binding. Inhibitors of CKX (e.g., 3TFM-2HE, INCYDE, F-INCYDE and anisiflupurin) act as promoters of growth and stress-tolerance through the inhibition of catabolic CKXs and regulate an increase in endogenous CKs (e.g., iP, <em>t</em>Z and <em>c</em>Z) in plants. The ability of CKX inhibitors to intercept CKX gene regulation is an indication of their potential applications in agriculture and other industries that rely on plant-based products.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100398"},"PeriodicalIF":5.4,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142572304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies 粳稻嵌套关联图谱群体:开发、特征描述及在全基因组关联研究中的应用
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-18 DOI: 10.1016/j.cpb.2024.100401
Bhagwat Nawade , Sang-Ho Chu , Sunhee Kim , Chang-Yong Lee , Jinsong Bao , Yong-Jin Park
Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a japonica nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent varieties and the elite Korean variety Shindongjin. Genetic characterization of KNU_NAM revealed 48,159 polymorphic SNPs, with family counts ranging from 18,787 to 42,578 and an average of 30,019 SNPs per family. Further molecular diversity analysis of KNU_NAM indicated reduced population structure and broad genetic diversity. Genome-wide association studies (GWAS) on five morphological traits identified 47 significant marker-trait associations (MTAs), with a set of 18 MTAs located on chromosome 9. Linkage disequilibrium (LD) block analysis of this region revealed 15 haplotypes and identified five key genes associated with panicle architecture: OsDEP1, OsEATB, OsLGD1, and OsSPL18. Additionally, two non-synonymous MTAs on chromosome 7 were located on the exon of OsPRR37/Ghd7.1, a gene associated with plant height, heading date, and grain number per panicle. Further phenotypic performance analysis of haplotypes from these hotspot regions revealed significant differences in the targeted traits. The study validates the potential of KNU_NAM and GWAS for high-resolution genetic mapping in rice breeding programs, highlighting the utility of these populations for enhancing genetic diversity and improving trait selection in rice.
多亲本制图群体在剖析数量性状和快速鉴定遗传决定因素方面具有巨大潜力。我们建立了一个粳稻嵌套关联作图群体 KNU_NAM,该群体由 880 个品系组成,这些品系来自 10 个著名品种的近交系重组(RIL)家族和韩国优良品种 "新东真"。KNU_NAM 的遗传特征发现了 48,159 个多态 SNPs,家系数从 18,787 个到 42,578 个不等,平均每个家系有 30,019 个 SNPs。对 KNU_NAM 的进一步分子多样性分析表明,种群结构缩小,遗传多样性广泛。对五个形态性状的全基因组关联研究(GWAS)发现了 47 个显著的标记-性状关联(MTAs),其中 18 个 MTAs 位于 9 号染色体上。对该区域的连锁不平衡(LD)区块分析发现了 15 个单倍型,并确定了与圆锥花序结构相关的五个关键基因:OsDEP1、OsEATB、OsLGD1 和 OsSPL18。此外,第 7 号染色体上的两个非同义 MTA 位于 OsPRR37/Ghd7.1 的外显子上,该基因与株高、头期和每圆锥花序的粒数有关。对这些热点区域单倍型的进一步表型表现分析表明,这些单倍型在目标性状上存在显著差异。该研究验证了 KNU_NAM 和 GWAS 在水稻育种计划中用于高分辨率遗传图谱的潜力,强调了这些群体在提高水稻遗传多样性和改进性状选择方面的实用性。
{"title":"Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies","authors":"Bhagwat Nawade ,&nbsp;Sang-Ho Chu ,&nbsp;Sunhee Kim ,&nbsp;Chang-Yong Lee ,&nbsp;Jinsong Bao ,&nbsp;Yong-Jin Park","doi":"10.1016/j.cpb.2024.100401","DOIUrl":"10.1016/j.cpb.2024.100401","url":null,"abstract":"<div><div>Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a <em>japonica</em> nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent varieties and the elite Korean variety Shindongjin. Genetic characterization of KNU_NAM revealed 48,159 polymorphic SNPs, with family counts ranging from 18,787 to 42,578 and an average of 30,019 SNPs per family. Further molecular diversity analysis of KNU_NAM indicated reduced population structure and broad genetic diversity. Genome-wide association studies (GWAS) on five morphological traits identified 47 significant marker-trait associations (MTAs), with a set of 18 MTAs located on chromosome 9. Linkage disequilibrium (LD) block analysis of this region revealed 15 haplotypes and identified five key genes associated with panicle architecture: <em>OsDEP1</em>, <em>OsEATB</em>, <em>OsLGD1</em>, and <em>OsSPL18</em>. Additionally, two non-synonymous MTAs on chromosome 7 were located on the exon of <em>OsPRR37/Ghd7.1</em>, a gene associated with plant height, heading date, and grain number per panicle. Further phenotypic performance analysis of haplotypes from these hotspot regions revealed significant differences in the targeted traits. The study validates the potential of KNU_NAM and GWAS for high-resolution genetic mapping in rice breeding programs, highlighting the utility of these populations for enhancing genetic diversity and improving trait selection in rice.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100401"},"PeriodicalIF":5.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142526926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pyramiding of multiple resistant genes of blast and bacterial blight diseases in the background of rice (Oryza sativa) mega variety BRRI dhan29 水稻(Oryza sativa)超大型品种 BRRI dhan29 背景中抗稻瘟病和细菌性疫病的多抗性基因的金字塔结构
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2024-10-18 DOI: 10.1016/j.cpb.2024.100400
Mohammad Abdul Latif , Sheikh Arafat Islam Nihad, Rakibul Hasan, Lutfur Rahman, Touhidur Rahman Anik, Amal Chandra Manidas, Mamunur Rashid, Mohammad Ashik Iqbal Khan, Rejwan Bhuiyan
Blast and bacterial blight (BB) are the two major rice diseases in the world including Bangladesh. In this study, BB resistance genes (Xa21 and xa13) and blast resistance (Pi9 and Pb1) genes were pyramided into a mega variety, BRRI dhan29 through marker-assisted backcross breeding. IRBB58 was used as a BB-resistant donor and Pi9-US2, and Pb1-US2 were used as blast-resistant donors. Backcross was done between BRRI dhan29 and donor parents to develop BC3F1 population and then selfing was done to develop BC3F6 population. BC3F2 population was genotyped and phenotyped for segregation analysis and BC3F6 was evaluated for genotyping, phenotyping and morphological traits and yields. Chi-square analysis of BC3F2 data revealed that blast and BB resistance followed the single gene mendelian fashion (1:2:1 and 3:1). Two to four gene combinations were found in the advanced lines of the BC3F6 population. The yield of the advanced lines ranged from 6.42 (t ha−1) to 9.5 (t ha−1) and they showed resistant against blast and BB with mean disease scores ranging from 0.67 to 2.33 and 0.33–2.33, respectively. Finally, eight lines having four genes (xa13, Xa21, Pi9 and Pb1) were selected for multilocational (five locations) trials for yield performance and disease reaction. Mean yield data of eight advanced lines of all locations were varied from 6.48±0.15–8.38±0.11 t ha−1 and all the lines showed resistant reactions against blast (score 0.53–1) and BB (score 0.6–0.87) disease. The highest yield was found in BR (Path) 13800-BC3–224–12 (G28, 8.38±0.11 t ha−1) followed by BR (Path) 13800-BC3–134–252 (G26, 8.28±0.08 t ha−1) and BR (Path) 13800-BC3–136–115 (G12, 8.24±0.07 t ha−1). Pyramided advanced lines of this study could be released as BB and blast-resistant varieties or could be utilized as donor parents in resistant breeding.
稻瘟病和细菌性枯萎病(BB)是包括孟加拉国在内的世界两大水稻病害。在这项研究中,通过标记辅助回交育种,将抗BB基因(Xa21和xa13)和抗稻瘟病基因(Pi9和Pb1)构建成一个巨型品种BRRI dhan29。IRBB58 用作抗 BB 供体,Pi9-US2 和 Pb1-US2 用作抗瘟供体。在 BRRI dhan29 和供体亲本之间进行回交,培育出 BC3F1 群体,然后进行自交,培育出 BC3F6 群体。对 BC3F2 群体进行了基因分型和表型分析,对 BC3F6 进行了基因分型、表型、形态性状和产量评估。对 BC3F2 数据的卡方分析表明,稻瘟病和 BB 抗性遵循单基因孟德尔模式(1:2:1 和 3:1)。在 BC3F6 群体的先进品系中发现了 2 至 4 个基因组合。高级品系的产量在 6.42(吨/公顷-1)到 9.5(吨/公顷-1)之间,对稻瘟病和 BB 表现出抗性,平均病害评分分别在 0.67 到 2.33 之间和 0.33 到 2.33 之间。最后,有四个基因(xa13、Xa21、Pi9 和 Pb1)的八个品系被选中进行多地(五个地点)产量和病害反应试验。所有地点的 8 个先进品系的平均产量数据在 6.48±0.15-8.38±0.11 吨/公顷-1 之间,所有品系都表现出对稻瘟病(0.53-1 分)和 BB 病(0.6-0.87 分)的抗性。产量最高的是 BR (Path) 13800-BC3-224-12(G28,8.38±0.11 吨/公顷-1),其次是 BR (Path) 13800-BC3-134-252(G26,8.28±0.08 吨/公顷-1)和 BR (Path) 13800-BC3-136-115(G12,8.24±0.07 吨/公顷-1)。本研究的金字塔型先进品系可作为抗 BB 和抗瘟疫品种发布,也可作为抗性育种的供体亲本。
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引用次数: 0
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Current Plant Biology
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