Plant Gene最新文献_第5页

In silico analysis and heterologous expression of OsNAC121 shed light on its structure and function in flowering and osmotic stress OsNAC121基因的硅晶分析和异源表达，揭示了其在开花和渗透胁迫中的结构和功能

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-12-01 Epub Date: 2025-08-06 DOI: 10.1016/j.plgene.2025.100537

Nazma Anjum, Ayushi Saini, Bina K. Singh, Amit K. Das, Mrinal K. Maiti

Plant-specific NAC transcription factors (TFs) are key master regulators in multiple vital physiological processes like development, organogenesis, stress tolerance and senescence. Identifying suitable TF is crucial for crop improvement program via biotechnological intervention. In rice (Oryza sativa L.) plant, only 38 out of 151 NAC TFs have been characterized till date. In this study, we have deciphered the in silico structure and in vivo function of OsNAC121 through heterologous expression in Escherichia coli and tobacco systems, and documented its potential role in flowering and osmotic stress. Like a typical NAC TF, OsNAC121 has a highly conserved NAC domain at the N-terminal half, featuring the subdomains A-E with the signature NAC fold comprising the twisted β-barrel between the two α-helices, and a highly variable C-terminal random coil. Analyses revealed that OsNAC121 binds to the consensus NAC binding DNA sequence (NACBS) in silico. In this study we have observed that the bacterially expressed truncated OsNAC121 protein forms tetramers in vitro, but structural modeling and DNA docking strongly support the dimeric form as the biologically relevant DNA-binding unit. Further bioinformatics analysis unravelled that R79 residue and the ⁸⁶WKAT⁸⁹ motif are pivotal for binding to the NACBS. Transgenic tobacco plants constitutively expressing OsNAC121 had elongated stem with reduced stem girth, grew faster, and flowered early, suggesting a role of OsNAC121 in determining the fate of meristematic cells. Transgenic tobacco plants also exhibited susceptibility to both drought and salinity stresses characterized by loss of chlorophyll, stunted height and smaller leaves. Therefore, we conclude that the OsNAC121 plays a crucial role in plant development, flowering time, and stress biology. Research in autologous host rice will elucidate the exact signalling pathway of OsNAC121 involving phytohormones and identify its interacting partners.

植物特异性NAC转录因子（TFs）是植物发育、器官发生、抗逆性和衰老等重要生理过程的主要调控因子。通过生物技术干预确定合适的TF对作物改良计划至关重要。在水稻（Oryza sativa L.）植株中，151个NAC TFs中只有38个已被鉴定。在这项研究中，我们通过在大肠杆菌和烟草系统中的异源表达，破译了OsNAC121的硅结构和体内功能，并记录了其在开花和渗透胁迫中的潜在作用。与典型的NAC TF一样，OsNAC121在n端具有高度保守的NAC结构域，其子结构域a - e具有NAC褶皱特征，NAC褶皱由两个α-螺旋之间的扭曲β-桶组成，c端具有高度可变的随机线圈。分析结果表明，OsNAC121在硅片上与一致的NAC结合DNA序列（NACBS）结合。在本研究中，我们观察到细菌表达的截断的OsNAC121蛋白在体外形成四聚体，但结构建模和DNA对接强烈支持二聚体形式作为生物学相关的DNA结合单元。进一步的生物信息学分析揭示了R79残基和86WKAT89基序是与NACBS结合的关键。组成性表达OsNAC121的转基因烟草植株茎长、茎周缩短、生长更快、开花早，表明OsNAC121在决定分生组织细胞的命运中起着重要作用。转基因烟草还表现出对干旱和盐胁迫的敏感性，其特征是叶绿素丧失、身高发育不良和叶片变小。因此，我们认为OsNAC121在植物发育、开花时间和胁迫生物学中起着至关重要的作用。在自体寄主水稻上的研究将有助于阐明OsNAC121涉及植物激素的确切信号通路，并确定其相互作用的伙伴。

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引用次数: 0

Molecular marker assisted confirmation of a hybrid between Ascocentrum ampullaceum var. auranticum and Rhynchostylis retusa. 分子标记辅助鉴定了壶形散囊草与黄纹花的杂种关系。

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-12-01 Epub Date: 2025-08-05 DOI: 10.1016/j.plgene.2025.100533

Kangabam Soneja Devi , Nandeibam Samarjit Singh , Heisnam Haripriyari Devi , Haobam Sharmila Devi , Huidrom Sunitibala Devi

Two rare and endangered orchids, Rhynchostylis retusa, and Ascocentrum ampullaceum var. auranticum, a narrowly endemic orchid from Manipur, were used for the present study. These two orchids were selected as parents because they have desirable traits like dense and floriferous, colorful, and long-lasting flowers. Our goal is to develop a hybrid species that is intermediate and improved over its parents in terms of floral characteristics by the F1 generation. When A. ampullaceum var. auranticum was the female parent, a 90 % crossability success rate was attained. Half-strength Murashige and Skoog (MS) basal medium with no phytohormones was used for seed germination in vitro and protocorm development of the putative hybrid. The basal medium containing 1 mg/L BAP and 0.5 mg/L NAA showed the highest growth response with 7.57 shoots/explant, 5.90 leaves/explant, and 57.19 PLBs/explant, while the medium enriched with 1 mg/L NAA produced the maximum number of roots (4.95) after 150 days of inoculation. The assessment for rapid determination of genetic purity of the developed hybrid (F1 plants) between A. ampullaceum var. auranticum and R. retusa was carried out by using the molecular markers, SCoT and SSR. The F1 plants' complementing banding patterns, which they inherited from their parents, confirmed that they were pure hybrids. These PCR-based molecular markers could be used for the early assessment of hybridity.

本研究以两种珍稀濒危兰花——蛇纹兰（Rhynchostylis retusa）和曼尼普尔（Manipur）特有的壶形兰（Ascocentrum ampullaceum var. aururanticum）为研究对象。这两种兰花之所以被选为亲本，是因为它们具有致密、多花、色彩鲜艳、开花时间长等令人满意的特点。我们的目标是开发一个杂交物种，是中间和改进其亲本方面的花卉特征的F1代。当壶叶金莲为母本时，杂交成功率达90%。用不含激素的半强度Murashige和Skoog （MS）基础培养基进行离体种子萌发和原球茎发育。BAP含量为1 mg/L、NAA含量为0.5 mg/L的基础培养基在接种150 d后生根数最多，达到7.57根/外植体、5.90叶/外植体和57.19根/外植体；NAA含量为1 mg/L的基础培养基在接种150 d后生根数最多，达到4.95根。利用分子标记、SCoT和SSR等方法，对ampullaceum var. aururanticum和r.r etusa杂交后代（F1植株）的遗传纯度进行了快速鉴定。这些F1植株的互补带状模式从它们的亲本遗传而来，证实了它们是纯杂交种。这些基于pcr的分子标记可用于杂交的早期评估。

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引用次数: 0

Genome-wide analysis of SWEET and TST sugar transporters in sugarbeet: Structural characterization and expression during development and postharvest storage 甜菜SWEET和TST糖转运体的全基因组分析：发育和采后贮藏期间的结构表征和表达

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-12-01 Epub Date: 2025-09-15 DOI: 10.1016/j.plgene.2025.100549

Karen K. Fugate , Fernando L. Finger , Melvin D. Bolton

SWEET (Sugars Will Eventually be Exported Transporter) and TST (Tonoplast Sugar Transporter) genes are implicated in sucrose accumulation and sucrose loss during sugarbeet root production and postharvest storage, although information regarding their identities, structures and expression is limited. Research, therefore, was conducted to identify and structurally characterize sugarbeet SWEET and TST gene families and determine their organ-specific, developmental, and storage-related expression. Sixteen SWEET genes and four TST genes were found in the sugarbeet genome. SWEET genes were notably diverse in genomic and transcriptomic structure, yet shared similarities in protein motifs and structure, whilst TST genes were generally uniform in genomic, transcriptomic, and protein size and structure. Expression analysis revealed high expression of two SWEET genes (SWEET 1, SWEET12) in leaves, relatively low levels of SWEET gene expression in roots throughout all but the earliest stages of development, and a dramatic upregulation of four SWEET genes (SWEET1, SWEET12, SWEET14/N3, SWEET17b) during storage, including a greater than 17,000-fold increase in SWEET14/N3 expression. TST genes were expressed in all tissue types, with most TST expression derived from a single gene (TST2.1) which was highly expressed in roots, minimally expressed in leaves, and elevated in expression during root storage. Overall, these results point to the likely importance of SWEET1 and SWEET12 in leaves and TST2.1 in roots during development when sucrose is actively being accumulated and the likely importance of SWEET14/N3, and possibly SWEET1, SWEET12, SWEET17b, and TST2.1 during storage when vacuolar sequestered sucrose is remobilized and catabolized.

SWEET （Sugars Will最终会被出口的转运蛋白）和TST （tonoplasast Sugar Transporter）基因与甜菜根生产和采后储存期间的蔗糖积累和蔗糖损失有关，尽管关于它们的身份、结构和表达的信息有限。因此，研究人员对甜菜SWEET和TST基因家族进行了鉴定和结构表征，并确定了它们的器官特异性、发育和储存相关表达。在甜菜基因组中发现了16个SWEET基因和4个TST基因。SWEET基因在基因组和转录组结构上具有显著的多样性，但在蛋白质基序和结构上具有相似性，而TST基因在基因组、转录组和蛋白质大小和结构上总体上是一致的。表达分析显示，SWEET基因在叶片中高表达（SWEET1、SWEET12），而在除早期发育阶段外的根系中表达水平相对较低，4个SWEET基因（SWEET1、SWEET12、SWEET14/N3、SWEET17b）在贮藏期间显著上调，其中SWEET14/N3的表达量增加了17000倍以上。TST基因在所有组织类型中均有表达，其中大部分TST表达来源于单一基因（TST2.1），该基因在根中表达量高，在叶中表达量低，在根储存期间表达量升高。总的来说，这些结果表明，在蔗糖积极积累的发育过程中，叶片中的SWEET1和SWEET12以及根中的TST2.1可能很重要，而在液泡封存的蔗糖被再动员和分解代谢的储存过程中，SWEET14/N3以及SWEET1、SWEET12、SWEET17b和TST2.1可能很重要。

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引用次数: 0

Genome-wide identification and expression analysis of UDP-glycosyltransferases genes associated with secondary metabolism during grain development in pearl millet (Pennisetum glaucum) 珍珠粟（Pennisetum glaucum）籽粒发育次生代谢相关udp -糖基转移酶基因全基因组鉴定及表达分析

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-12-01 Epub Date: 2025-08-16 DOI: 10.1016/j.plgene.2025.100541

Adarsh Kumar, Theint Theint Tun, Vinay Kumar

This study focused on analysing the UDP-glycosyltransferase gene family in Pennisetum glaucum, which plays an essential role in plant metabolism and glycosylation of the secondary metabolites. We identified 191 UGTs by performing a BLASTp search against the available pearl millet genome, utilizing amino acid sequences of the conserved plant secondary product glycosyltransferase (PSPG) motif and already reported UGT genes from Arabidopsis and maize. Phylogenetic analysis categorized these genes into 18 groups (A–R), and their genomic distribution was mapped across 10 pearl millet chromosomes. Subcellular localization analysis showed that PglUGT proteins localized to the cytoplasm, chloroplast, and nucleus. Functional annotation was carried out by Gene Ontology (GO) analysis of all the PglUGT genes for biological processes, cellular components, and molecular functions. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that a particular set of PglUGT genes are directly linked with secondary metabolite biosynthesis during seed development. Further, TLC analysis documented the presence of glycoside flavonoids (vitexin and orientin) during different grain development stages: just before milky stage (S1), milky stage (S2–3) and physiological mature (S4). Expression profiling of 20 randomly selected PglUGT genes across different grain developmental stages also showed the elevated expression during these stages, underscoring their potential roles in plant growth and grain development. In conclusion, this study documented the identification and characterization of UGT genes in genome of pearl millet and proposed the potential role of UGTs during seed development.

本研究重点分析了白盆草（Pennisetum glaucum）的udp -糖基转移酶基因家族，该基因在植物代谢和次生代谢产物的糖基化中起重要作用。我们利用保守的植物次生产物糖基转移酶（PSPG）基序的氨基酸序列和已经报道的来自拟南芥和玉米的UGT基因，对可用的珍珠粟基因组进行BLASTp搜索，鉴定出191个UGT。系统发育分析将这些基因分为18个类群（A-R），并确定了它们在10条珍珠粟染色体上的基因组分布。亚细胞定位分析表明，PglUGT蛋白定位于细胞质、叶绿体和细胞核。通过基因本体（Gene Ontology， GO）分析所有PglUGT基因的生物过程、细胞成分和分子功能，进行功能注释。此外，京都基因与基因组百科（KEGG）通路分析表明，一组特定的PglUGT基因与种子发育过程中次生代谢物的生物合成直接相关。此外，TLC分析记录了糖苷类黄酮（牡荆素和东方苷）在籽粒发育的不同阶段的存在：乳白色期（S1），乳白色期（S2-3）和生理成熟（S4）。随机选择的20个PglUGT基因在不同籽粒发育阶段的表达谱也显示出PglUGT基因在籽粒发育阶段的表达水平升高，揭示了其在植物生长和籽粒发育中的潜在作用。综上所述，本研究记录了珍珠谷子基因组中UGT基因的鉴定和特征，并提出了UGT在种子发育中的潜在作用。

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引用次数: 0

Evolutionary and functional insights into ascorbate oxidase genes in the Fabaceae plant family 豆科植物抗坏血酸氧化酶基因的进化和功能研究

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-12-01 Epub Date: 2025-08-09 DOI: 10.1016/j.plgene.2025.100538

Vitória Hirdes Glenzel , João Pedro Carmo Filgueiras , Andreia Carina Turchetto Zolet , Franceli Rodrigues Kulcheski

Ascorbate oxidase (AAO), a multicopper oxidase protein, plays a crucial role in catalyzing the oxidation of ascorbic acid (AA) in the apoplastic space. Despite the extensive attention on AAO functions, a significant gap remains in understanding its evolutionary trajectory and functional intricacies within the Fabaceae family that is recognized for its nutritional and economic importance. Our investigation revealed substantial conservation of the AAO gene family across all 21 studied Fabaceae species. Phylogenetic analysis consistently clustered Fabaceae AAO genes into two well-supported groups, indicating their shared and conserved origin. Similarly, gene structure analyses categorized sequences into two groups based on intronic sizes. Furthermore, motif analysis revealed ten conserved motifs in almost all of the AAO sequences. Notably, chromosomal localization data for Glycine max and Glycine soja AAO genes exhibited a highly similar gene distribution across the genome. Through comprehensive cis-regulatory analysis of G. max AAO genes, we identified binding motifs for transcription factors associated with various biological functions, including development, growth, and responses to biotic and abiotic stresses. Additionally, gene expression analyses unveiled significant variability in AAO gene expression profiles under different environmental stressors, highlighting the dynamic functional role of AAO in response to biotic and abiotic stresses. Our findings facilitated the identification of multiple AAO homologs in Fabaceae species, thereby enhancing our understanding of the functional roles of this gene family.

抗坏血酸氧化酶（AAO）是一种多铜氧化酶蛋白，在胞外空间催化抗坏血酸（AA）的氧化中起重要作用。尽管对AAO功能的广泛关注，但在了解其在豆科家族中的进化轨迹和功能复杂性方面仍存在显着差距，这是公认的营养和经济重要性。我们的研究发现，在所有21个被研究的豆科物种中，AAO基因家族都存在大量的保守性。系统发育分析一致将豆科AAO基因聚为两个支持良好的群体，表明它们具有共同和保守的起源。同样，基因结构分析根据内含子大小将序列分为两组。此外，基序分析在几乎所有的AAO序列中发现了10个保守基序。值得注意的是，甘氨酸max和甘氨酸大豆AAO基因的染色体定位数据显示，基因在基因组中的分布高度相似。通过对G. max AAO基因的全面顺式调控分析，我们确定了与多种生物学功能相关的转录因子的结合基序，包括发育、生长以及对生物和非生物胁迫的反应。此外，基因表达分析揭示了不同环境胁迫下AAO基因表达谱的显著差异，强调了AAO在生物和非生物胁迫下的动态功能作用。我们的发现促进了豆科植物中多个AAO同源物的鉴定，从而增强了我们对该基因家族功能作用的理解。

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引用次数: 0

Genome-wide identification of LOX gene in four cotton species and revealed its function in callus induction and drought tolerance 4种棉花LOX基因的全基因组鉴定及其在愈伤组织诱导和抗旱性中的作用

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-01 Epub Date: 2025-04-30 DOI: 10.1016/j.plgene.2025.100516

Sani Muhammad Tajo , Zhaoe Pan , K.M. Yusuf , Salisu Bello Sadau , Guowei Lv , Shoupu He , Xiaoli Geng , Xiongming Du

Cotton is one of the important fiber crops. Drought is the primary abiotic factor that restricts cotton growth and development and lowers its output. Plant LOX (lipoxygenases) genes catalyze the oxidation of polyunsaturated fatty acids into a variety of functional oxylipins. The LOX gene family has been thoroughly investigated under biotic and abiotic stressors; however, knowledge of their functions on callus induction and regeneration in cotton is still scarce. This study identified 34, 38, 23, and 20 LOX genes in the Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum, and Gossypium raimondii, respectively. The LOX genes were found to be divided into three main categories, 9-LOX, 13-LOX Type I, and 13-LOX Type II. Three accessions of G. hirsutum were used to generate callus from hypocotyl, cotyledon, and shoot tip and we observed that the highest expression of the GhLOX genes were in the hypocotyl callus and most of LOX gene expression was up-regulated in one week callus and decreased in two week and four week callus except in the shoot tip induced callus in Jinmian 498. Virus-induced gene silencing of GhLOX5 (Gh_A02G037000) revealed that the growth of the silenced plant was significantly decreased compared to WT. Excised leaf water loss and relative electrolyte leakage levels were increased about 23 % and 12 % in the GhLOX5 silenced plant when compared to the WT. Compared to the WT, the silenced plant had significantly higher antioxidant activity (25 % in MDA content and 45 % in H₂O₂ content). The importance of LOX genes in drought stress and callus induction is clear, but further research is needed to understand their molecular mechanism.

棉花是重要的纤维作物之一。干旱是制约棉花生长发育、降低棉花产量的主要非生物因素。植物脂氧化酶（LOX）基因催化多不饱和脂肪酸氧化生成多种功能性氧脂素。LOX基因家族在生物和非生物胁迫下已被深入研究；然而，对它们在棉花愈伤组织诱导和再生中的作用还知之甚少。本研究在毛棉、巴氏棉、木棉和雷蒙棉中分别鉴定出34、38、23和20个LOX基因。LOX基因主要分为9-LOX、13-LOX I型和13-LOX II型三大类。以金棉498的3个品种为材料，分别从下胚轴、子叶和茎尖诱导愈伤组织，发现GhLOX基因在下胚轴愈伤组织中表达量最高，除茎尖诱导的愈伤组织外，LOX基因在1周愈伤组织中表达量上调，在2周和4周愈伤组织中表达量下降。病毒诱导的GhLOX5 （Gh_A02G037000）基因沉默显示，与WT相比，沉默植株的生长显著降低。与WT相比，GhLOX5沉默植株的叶片水分流失和相对电解质泄漏水平分别增加了23%和12%。与WT相比，沉默植株的抗氧化活性显著提高（MDA含量为25%，H2O2含量为45%）。LOX基因在干旱胁迫和愈伤组织诱导中的重要性是明确的，但其分子机制有待进一步研究。

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引用次数: 0

Azomite, a volcanic ash-based fertilizer modulates gene expression during photomorphogenesis through phyB-dependent and independent pathways Azomite是一种火山灰肥料，通过phyb依赖和独立的途径调节光形态发生过程中的基因表达

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-01 Epub Date: 2025-06-06 DOI: 10.1016/j.plgene.2025.100523

Elijah Mehlferber , Kent F. McCue , Yang Bi , Robert Reed , Jon Ferrel , Rajnish Khanna

Azomite is a lightly weathered dacitic (rhyolitic) tuff breccia (DTB), it is silicon-based with over 70 minerals and trace elements (micronutrients). In previous studies, application of Azomite increased greenhouse tomato production. In the tomato root endosome, Azomite caused functional shifts from higher abundance of microbes involved in metabolism of 2- to 4- carbon compounds to higher levels of microbes involved in carbohydrate metabolism. This suggested a possible increase in carbohydrate production and shift in exudates involved in microbial recruitment. Parallel studies with 4-day old Arabidopsis seedlings revealed that photosynthetically active radiation was required for Azomite-induced increase in both hypocotyl length and cotyledon area. These data suggested that Azomite may influence growth through changes in photosynthesis, leading to carbohydrate-enriched root exudates and increased growth. Here, we present RNAseq analysis in response to Azomite of 4-day old Arabidopsis seedlings grown either in continuous darkness (Dc) or under continuous red-light (Rc). Significant changes in genes involved in carbon assimilation and nutrient uptake, amongst other functional pathway categories are reported. Comparison with phyB (phytochrome B, red-light photoreceptor) mutant seedlings is shown to determine the overlap between phyB-regulated genes and Azomite-responsive genes. Two concentrations, 0.5 g and 1.0 g of Azomite were included because our previous results with tomato and Arabidopsis exhibited a dose-dependent response. Several genes are identified as responding differentially, including SUBERMAN, a myb-family transcription factor that regulates suberization of the root endodermis. This study advances our understanding of how complex mixtures of micronutrients such as Azomite influence gene expression during plant growth and development.

偶氮石是一种浅风化的英灰质（流纹岩）凝灰岩角砾岩（DTB），它以硅为基，含有70多种矿物质和微量元素（微量元素）。在以往的研究中，偶氮石的施用提高了温室番茄的产量。在番茄根内体中，Azomite引起了从参与2- 4碳化合物代谢的高丰度微生物到参与碳水化合物代谢的高水平微生物的功能转变。这表明碳水化合物的产生可能增加，参与微生物募集的渗出物可能发生变化。对4日龄拟南芥幼苗的平行研究表明，azomia诱导的下胚轴长度和子叶面积的增加都需要光合有效辐射。这些数据表明，Azomite可能通过改变光合作用影响生长，导致富含碳水化合物的根分泌物和生长增加。在这里，我们分析了在连续黑暗（Dc）和连续红光（Rc）下生长4天的拟南芥幼苗对Azomite的响应。据报道，在其他功能途径类别中，参与碳同化和营养吸收的基因发生了重大变化。与phyB（光敏色素B，红色光感受器）突变苗进行比较，可以确定phyB调控基因和azomite响应基因之间的重叠。由于我们之前对番茄和拟南芥的研究结果显示出剂量依赖性，因此我们纳入了0.5 g和1.0 g两种浓度的Azomite。几个基因被确定为有差异的反应，包括SUBERMAN，一个myb家族转录因子，调节根内胚层的suberization。这项研究促进了我们对复杂的微量元素混合物（如Azomite）如何影响植物生长发育过程中的基因表达的理解。

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引用次数: 0

Adaptability of rice to different planting methods: A proof of cumulative transcriptional memory 水稻对不同种植方式的适应性：累积转录记忆的证明

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-01 Epub Date: 2025-04-15 DOI: 10.1016/j.plgene.2025.100515

Karishma Seem , Ayantika Ghosh , Rashmi Varshney , Rakesh Pandey , S. Gopala Krishnan , Trilochan Mohapatra , Suresh Kumar

Plenty of water is required for cultivation of rice by transplanting that is challenging its cultivation, particularly on erratic rainfall or under drought. Direct-sown rice (DSR) is emerging as an alternative to transplanted rice (TPR) to save water. Performance of rice under DSR conditions varies greatly. While the molecular basis of adaptive plasticity of rice is subtle, tolerance to environmental stresses in crops is important for sustainable food production/security. The present study explores the molecular basis of adaptive/genetic plasticity in rice grown by different methods of planting, emphasising the concept of cumulative transcriptional memory. Our findings of comparative RNA-seq analysis highlighted differential gene expression with ∼6130 genes exclusively upregulated in the leaf of Nagina22 (N22) in contrast to only ∼3540 genes upregulated exclusively in the leaf of IR64 grown by dry/direct-sowing. In addition, our findings revealed that numerous genes showing upregulation in N22 were detected downregulated in IR64 that highlight distinct molecular strategies adopted by the rice cultivars. By activating diverse sets of genes coding for transcription factors, growth-regulating factors, translational machinery, nutrient-reservoirs, chromatin organization/epigenetic modifications, cell cycle/division, carbohydrate metabolism, etc., N22 adapts more effectively/efficiently to direct-sown conditions. Complementarity between these factors emerged to play important roles in adaptability of N22 to fluctuating environmental conditions. This helps adjust physio-biochemical responses of N22 to multiple abiotic/biotic stresses experienced under DSR conditions. Thus, our findings make a foundation for the development of molecular markers to facilitate varietal development of DSR for improved water productivity and sustainable agriculture.

水稻的移栽需要大量的水，这给水稻的种植带来了挑战，特别是在降雨不稳定或干旱的情况下。直接播种水稻（DSR）正在成为移栽水稻（TPR）的替代方案，以节约用水。水稻在DSR条件下的性能变化很大。虽然水稻适应性可塑性的分子基础是微妙的，但作物对环境胁迫的耐受性对可持续粮食生产/安全至关重要。本研究探讨了不同种植方式下水稻适应性/遗传可塑性的分子基础，强调了累积转录记忆的概念。我们的比较RNA-seq分析结果突出了Nagina22 （N22）叶片中约6130个基因的差异表达，而通过干播/直播生长的IR64叶片中仅约3540个基因的差异表达。此外，我们的研究结果显示，许多N22上调的基因在IR64中被检测到下调，这突出了水稻品种采用的不同分子策略。N22通过激活转录因子、生长调节因子、翻译机制、营养储备、染色质组织/表观遗传修饰、细胞周期/分裂、碳水化合物代谢等多种编码基因，更有效地适应直接播种条件。这些因子之间的互补性在N22对波动环境条件的适应性中发挥了重要作用。这有助于调节N22在DSR条件下对多种非生物/生物胁迫的生理生化反应。因此，我们的研究结果为开发分子标记来促进DSR品种的发展，提高水分生产力和可持续农业奠定了基础。

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引用次数: 0

Reference gene selection and expression analyses of anthocyanin biosynthetic genes in flower and vegetative tissues of Clivia miniata L. 丁香花及营养组织花青素合成基因的内参基因选择及表达分析。

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-01 Epub Date: 2025-05-30 DOI: 10.1016/j.plgene.2025.100521

Mathabatha F. Maleka , Johan J. Spies

Pigmentation is one of the most variable traits in plants, with flowers typically being the main tissue that displays such diversity. Unlike other horticulturally valuable plants, the genetic basis of flower pigmentation in Clivia species remains poorly understood. Therefore, this study aimed to analyze the expression of numerous anthocyanin biosynthetic genes in flower and vegetative tissues of the most popular Clivia species, Clivia miniata. Such information can facilitate the breeding and biotechnological use of Clivia in the global horticulture value-chain. Initially, we mined a previously assembled C. miniata flower transcriptome for WDR transcripts that are homologous to key pigmentation genes from maize (PAC1) and Arabidopsis thaliana (TTG1). Subsequently, we identified and tested eight candidate reference genes (18S, ACT, EF1α, G6PDH, PP2A, RNPII, TUBα and UBQ) for expression stability in Clivia tissues using geNorm, NormFinder, BestKeeper, and the comparative Delta-Ct method. Homology analysis revealed a transcript encoding a partial protein with specific motifs that are common in pigmentation-related WDR proteins. Further, three reference genes (CmiPP2A, CmiEF1α and Cmi18S) were most stable in tested Clivia tissues. Quantitative real-time PCR (qPCR) analyses of ten anthocyanin biosynthetic genes (CmiDFR, CmiF3H, CmiF3’H, CmiUF3GT, CmibHLH001, CmibHLH002, CmiMYB001, CmiMYB002, CmiMYB003 and CmiWDR001) normalized against the three reference genes revealed that most had relatively higher expression levels in flower than vegetative tissues. Also, expression was generally higher during anthesis than in buds, but some genes remarkably showed marked expression in roots too. Overall, this is the first study to systematically select and validate reference genes for expression analysis of anthocyanin biosynthetic genes in Clivia.

色素沉着是植物中最多变的特征之一，花通常是表现这种多样性的主要组织。与其他有园艺价值的植物不同，Clivia花色素沉着的遗传基础仍然知之甚少。因此，本研究旨在分析众多花青素生物合成基因在最常见的Clivia Clivia miniata的花和营养组织中的表达。这些信息可以促进Clivia在全球园艺价值链中的育种和生物技术应用。首先，我们挖掘了先前组装的小红花转录组，以寻找与玉米（PAC1）和拟南芥（TTG1）的关键色素沉着基因同源的WDR转录本。随后，我们利用geNorm、NormFinder、BestKeeper和比较Delta-Ct方法，鉴定并检测了8个候选内参基因（18S、ACT、EF1α、G6PDH、PP2A、RNPII、TUBα和UBQ）在Clivia组织中的表达稳定性。同源性分析显示，该转录本编码的部分蛋白具有在色素相关WDR蛋白中常见的特定基序。此外，三个内参基因（CmiPP2A、cmif1 α和Cmi18S）在Clivia组织中最稳定。对10个花青素生物合成基因（CmiDFR、CmiF3H、CmiF3'H、cmuf3gt、CmibHLH001、CmibHLH002、CmiMYB001、CmiMYB002、CmiMYB003和CmiWDR001）与3个内参基因进行归一化的实时荧光定量PCR （qPCR）分析显示，大多数花青素生物合成基因在花中的表达水平相对高于营养组织。花期表达量普遍高于花蕾，但部分基因在根中也有显著表达。总的来说，这是第一次系统地选择和验证Clivia花青素生物合成基因表达分析的内参基因。

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引用次数: 0

Revealing drought tolerance mechanisms in Pongamia pinnata through integrated physiological, biochemical, and transcriptomic profiling 通过综合生理、生化和转录组学分析揭示凤梨的耐旱机制

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-01 Epub Date: 2025-06-21 DOI: 10.1016/j.plgene.2025.100527

K. Rajarajan , Sandhya Sharma , Harsha Srivastava , Kumari Arpita , A.K. Handa , A. Arunachalam , S.K. Dhyani

Pongamia pinnata is a promising industrial species for biofuel production. However, the detrimental effects of drought stress on the initial growth phases pose significant challenges to germination and seedling development. This problem impedes the establishment of commercial plantations in drought-prone areas, primarily because of the lack of cultivar stability. To address this issue, understanding their physiochemical and molecular responses is crucial. To elucidate the intricate molecular mechanisms underlying drought tolerance, two contrasting Pongamia genotypes, NRCP9 (tolerant) and NRCP10 (sensitive), were subjected to drought stress and watered conditions. Drought stress significantly reduced the chlorophyll content and relative water content in the NRCP10 (susceptible) genotype. In contrast, drought stress induced greater increases in peroxidase activity and proline accumulation in NRCP9 than in NRCP10. Furthermore, transcriptome analysis revealed a total of 26,195 and 18,742 differentially expressed genes (DEGs) in the tolerant and susceptible genotypes, respectively. Additionally, 128 common DEGs were commonly expressed under drought stress conditions, whereas 10,271 DEGs were commonly expressed under well-watered conditions. Among the DEGs in the TF families, the major were bHLH, NAC, ERF, WRKY, MYB, Trihelix, bZIP, FAR1, B3, C3H, STAT, and C2H2. Furthermore, transcriptome analyses revealed the significant genes involved in hormone biosynthesis, secondary metabolite accumulation, cofactor and carbon metabolism, and MAPK signaling. Additionally, the selected genes were validated by qRT-PCR, the transcriptome analysis and expression patterns were found to be corresponded. These findings reveal Pongamia's stress-adaptive mechanism and shed light on the physicochemical and differential gene responses to drought stress.

凤尾花是一种很有前途的生物燃料工业树种。然而，干旱胁迫对幼苗生长初期的不利影响对种子萌发和幼苗发育构成了重大挑战。这个问题阻碍了在干旱易发地区建立商业种植园，主要是因为缺乏品种稳定性。为了解决这个问题，了解它们的物理化学和分子反应是至关重要的。为了阐明干旱耐旱性的复杂分子机制，研究了两种不同基因型——NRCP9（耐旱性）和NRCP10（敏感性）——在干旱胁迫和水分条件下的差异。干旱胁迫显著降低了NRCP10（易感）基因型的叶绿素含量和相对含水量。相比之下，干旱胁迫诱导NRCP9过氧化物酶活性和脯氨酸积累的增加幅度大于NRCP10。此外，转录组分析显示，耐受性基因型和易感基因型分别有26,195和18,742个差异表达基因（deg）。此外，干旱胁迫条件下共有128个基因表达，而水分充足条件下共有10271个基因表达。TF家族的deg主要为bHLH、NAC、ERF、WRKY、MYB、Trihelix、bZIP、FAR1、B3、C3H、STAT和C2H2。此外，转录组分析还揭示了参与激素生物合成、次生代谢物积累、辅因子和碳代谢以及MAPK信号传导的重要基因。此外，对所选基因进行qRT-PCR验证，发现转录组分析和表达模式相对应。这些研究结果揭示了干旱胁迫对蓬棉的胁迫适应机制，揭示了干旱胁迫对蓬棉的理化和差异基因反应。

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引用次数: 0