Plant Gene最新文献_第4页

Exploring the genetic diversity of common bean germplasm: insights into Andean gene pool variability 探索普通豆类种质资源的遗传多样性：安第斯基因库变异的见解

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-18 DOI: 10.1016/j.plgene.2025.100540

Cecilia Luvizutti Ferreira Silva , Dario Grattapaglia , Paula Arielle Mendes Ribeiro Valdisser , Paula Pereira Torga , Alessandra da Cunha Moraes Rangel , Claudio Brondani , Alexandre Siqueira Guedes Coelho , Tereza Cristina de Oliveira Borba , Rosana Pereira Vianello

Common bean (Phaseolus vulgaris) is among the most widely consumed legumes globally, with Brazil playing a crucial role in preserving and expanding its existing genetic diversity. This study aimed to characterize a subset of 863 common bean accessions from Brazil's Gene Banks, mainly of Andean origin. A germplasm collection was genotyped with 4275 SNPs using the EMBRAPA Multispecies 65KChip. Population structure analysis revealed two main groups: Andean (n = 558) and Middle American (n = 267), along with 38 admixed accessions. Andean group exhibited lower gene diversity (GD = 0.086), and allelic richness (A_R = 1.83) compared to the Middle American group (GD = 0.270, A_R = 1.98). Brazilian landraces in the Andean and Middle American groups showed potentially lower overall diversity, emphasizing the need for conservation efforts to preserve these genetic resources. The Andean Brazilian core collection (n = 221; GD = 0.095) encompasses the active collection diversity evaluated (n = 337; GD = 0.093). A total of 26 SNPs potentially under selection, mainly associated with plant development and defense, were identified. Georeferencing landraces using climate maps identified potentially valuable varieties adapted to drought (e.g., BGF0011779, BGF0012528, BGF0013826) and high temperatures and low-fertility soils (e.g., BGF0016128, BGF0013871), highlighting their relevance for conservation and sustainable use in breeding programs. Accessions' photographs showcased a wide range of morphological diversity, colors, types, shapes, and sizes of beans. Our findings reveal a significant genetic diversity among common bean germplasm, offering practical breeding opportunities and enhancing the value of gene bank collections. Certain landraces show potential for adapting to challenging climatic conditions, making them promising subjects for further adaptation studies.

普通豆（Phaseolus vulgaris）是全球消费最广泛的豆类之一，巴西在保护和扩大其现有遗传多样性方面发挥着至关重要的作用。本研究旨在对来自巴西基因库的863个普通豆品种进行特征分析，这些品种主要来自安第斯山脉。利用EMBRAPA multi - species 65KChip对一份种质进行4275个snp基因分型。种群结构分析显示安第斯（n = 558）和中美洲（n = 267）两个主要种群，以及38个混合种群。安第斯组基因多样性（GD = 0.086）和等位基因丰富度（AR = 1.83）低于中美洲组（GD = 0.270, AR = 1.98）。安第斯山脉和中美洲地区的巴西本土人种显示出潜在的整体多样性较低，这强调了保护这些遗传资源的必要性。安第斯山脉巴西岩心标本（n = 221; GD = 0.095）包含评估的活跃标本多样性（n = 337; GD = 0.093）。共鉴定出26个可能处于选择中的snp，主要与植物发育和防御有关。利用气候图对地方品种进行地理参考，确定了适应干旱（如BGF0011779、BGF0012528、BGF0013826）和高温低肥力土壤（如BGF0016128、BGF0013871）的潜在有价值品种，强调了它们在育种计划中的保护和可持续利用的相关性。这些照片展示了豆类的形态多样性、颜色、类型、形状和大小。我们的研究结果揭示了普通豆类种质资源具有显著的遗传多样性，为实际育种提供了机会，并提高了基因库收藏的价值。某些地方品种显示出适应具有挑战性的气候条件的潜力，使它们成为进一步适应研究的有希望的主题。

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引用次数: 0

Integrating AI in plant science: A review of applications and future prospects 人工智能在植物科学中的应用与展望

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-16 DOI: 10.1016/j.plgene.2025.100542

Imran Khan, Brajesh Kumar Khare

Plant science, which includes crop biology, genetics, and agronomy, is crucial for ensuring food security and enhancing agricultural productivity. As global food demand increases, the field is evolving by incorporating advanced technologies to address challenges such as climate change, disease resistance, and yield improvement. Artificial Intelligence is a key technology driving this transformation, offering new opportunities for innovation and progress in plant science. This review provides a comprehensive overview of the current and future applications of AI in plant science, with a special focus on areas where conventional techniques fall short. Unlike traditional methods that often rely on manual, time-intensive analysis, AI-driven models can learn complex patterns from high-dimensional biological and phenotypic data, automate decision-making, and scale rapidly. It begins with a discussion of the core principles of plant science, followed by an examination of AI technologies and their potential. The paper explores AI's role in plant genomics and breeding, focusing on key areas like genome sequencing, genetic marker identification, and the development of improved crop varieties. Special attention is given to AI-driven approaches in crop improvement, where machine learning models are increasingly used to optimize breeding programs, enhance yield predictions, support phenotypic selection, and address challenges like disease resistance. The review also discusses the challenges of applying AI in plant science, including issues with data quality, model interpretability, and integrating AI into large-scale agricultural practices. Finally, the paper looks ahead to the future of AI in plant science, suggesting directions for further research and development.

包括作物生物学、遗传学和农学在内的植物科学对于确保粮食安全和提高农业生产力至关重要。随着全球粮食需求的增加，该领域正在通过采用先进技术来应对气候变化、抗病性和产量提高等挑战。人工智能是推动这一转变的关键技术，为植物科学的创新和进步提供了新的机遇。本文综述了人工智能在植物科学中的当前和未来应用，并特别关注传统技术不足的领域。与通常依赖于手动、耗时分析的传统方法不同，人工智能驱动的模型可以从高维生物和表型数据中学习复杂的模式，自动化决策，并快速扩展。课程首先讨论植物科学的核心原理，然后考察人工智能技术及其潜力。本文探讨了人工智能在植物基因组学和育种中的作用，重点关注基因组测序、遗传标记鉴定和改良作物品种开发等关键领域。特别关注作物改良中的人工智能驱动方法，其中机器学习模型越来越多地用于优化育种计划，提高产量预测，支持表型选择以及解决诸如抗病等挑战。该综述还讨论了在植物科学中应用人工智能的挑战，包括数据质量、模型可解释性以及将人工智能整合到大规模农业实践中的问题。最后，展望了人工智能在植物科学中的应用前景，提出了进一步研究和发展的方向。

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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 : 2025-08-16 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

Temporal and spatial expression analysis of AtbZIP9 during seed and silique development in Arabidopsis thaliana (L.) Heynh 拟南芥种子和果实发育过程中AtbZIP9的时空表达分析Heynh

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-12 DOI: 10.1016/j.plgene.2025.100536

Jonatan Illescas-Miranda , Victoria Llanos-Casado , Estefanía Contreras, Néstor Carrillo-Barral, Raquel Iglesias-Fernández

In Arabidopsis thaliana, seed dispersal is mediated by the silique, a specialized fruit that undergoes a complex developmental program involving cell division, expansion, and programmed cell death. Transcription factors (TFs) from the bZIP family are key regulators of these transitions. In this study, we focused on the C-group bZIP TF AtbZIP9 to characterize its expression, potential regulatory roles, and functional relevance during silique development and early seedling growth. Promoter-reporter assays and qPCR analyses revealed that AtbZIP9 is broadly expressed, with strong activity in vascular tissues and the funiculus during early and mid-stages of silique development. AtbZIP9 physically interacts with the S1-group member AtbZIP44, as shown by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays, supporting the formation of heterodimeric complexes. Despite the lack of major phenotypic alterations in AtbZIP9 knockout mutants during germination and early development—even under salt stress conditions—its co-expression with AtbZIP44 and the CW-modifying gene AtMAN7 suggests a role in transcriptional regulation during silique development. Recent evidence further links AtbZIP9 to ABA-responsive gene expression and identifies it as a likely component of redundant regulatory networks involving other C-group bZIPs. These findings highlight AtbZIP9 as a candidate transcriptional modulator of silique and seed developmental processes, potentially acting in coordination with AtbZIP44 and other factors.

在拟南芥中，种子的传播是由核介导的，核是一种特殊的果实，经历了一个复杂的发育过程，包括细胞分裂、扩增和程序性细胞死亡。来自bZIP家族的转录因子（TFs）是这些转变的关键调节因子。在这项研究中，我们重点研究了c组bZIP TF AtbZIP9，以表征其在硅酸发育和早期幼苗生长中的表达、潜在的调控作用和功能相关性。启动子报告子分析和qPCR分析显示，AtbZIP9广泛表达，在丝质发育早期和中期的维管组织和索细胞中具有较强的活性。酵母双杂交和双分子荧光互补（BiFC）实验表明，AtbZIP9与s1基团成员AtbZIP44相互作用，支持异二聚体复合物的形成。尽管AtbZIP9基因敲除突变体在萌发和早期发育过程中（甚至在盐胁迫条件下）缺乏主要的表型改变，但它与AtbZIP44和cw修饰基因AtMAN7的共表达表明，在硅藻发育过程中，AtbZIP9基因敲除突变体在转录调控中发挥作用。最近的证据进一步将AtbZIP9与aba反应性基因表达联系起来，并确定它可能是涉及其他c组bzip9的冗余调控网络的组成部分。这些研究结果表明，AtbZIP9可能与AtbZIP44和其他因子协同作用，是硅油和种子发育过程的候选转录调节剂。

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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 : 2025-08-09 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

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 : 2025-08-06 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 : 2025-08-05 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

Harnessing genome editing for the advancement of underutilized crops: A critical review highlighting current progress, challenges and future prospects 利用基因组编辑促进未充分利用的作物：一篇强调当前进展、挑战和未来前景的批判性综述

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-07-30 DOI: 10.1016/j.plgene.2025.100534

Sunandan Swain , Sadhan Debnath , Khalil Khamassi , Kajal Samantara , Parsa Ram , Amarjeet Kumar , Ashok Kumar Mahawer , Tanushri Kaul

Underutilized cereals and legumes are the rich source of important minerals, essential amino acids, vitamins and phytochemicals. These crops possess valuable agronomic and physiological traits, including resilience to harsh climates and the ability to thrive in low-input farming systems. Such characteristics make them vital for agricultural diversification in the face of climate change and biodiversity loss, and they hold significant potential for strengthening global food security and promoting sustainable agriculture. As they possess exceptional nutritional properties, there is a huge need for specific attention to these crops. However, they have been marginalized due to the dominance of high-yielding commercial varieties of major staple food crops, limited adaptability to diverse climatic conditions, insufficient investment, lack of awareness, and monoculture practices. In recent years, advancements in genomics and high throughput sequencing technologies have paved the ways for implementing cutting-edge genomics technologies, like RNA-guided nucleases and other advanced genome editing tools to improve traits such as yield and quality, stress tolerance, nutritional properties and antinutritional factors (ANFs) in these crops. This review mainly focusses on the importance of various underutilized crops, latest progress in gene-editing applications in these crops, major challenges in the implementation of this precise technology for crop improvement including regulatory restrictions and the need for tailored gene-editing approaches to unlock the full potential of these neglected crops. Additionally, it explores strategies to address technical hurdles, such as off-target effects and delivery methods, to enhance the effectiveness of these technologies in agricultural and crop improvement.

未充分利用的谷物和豆类是重要矿物质、必需氨基酸、维生素和植物化学物质的丰富来源。这些作物具有宝贵的农艺和生理特性，包括对恶劣气候的适应能力和在低投入农业系统中茁壮成长的能力。面对气候变化和生物多样性丧失，这些特征对农业多样化至关重要，在加强全球粮食安全和促进可持续农业方面具有巨大潜力。由于它们具有特殊的营养特性，因此非常需要对这些作物进行特别关注。然而，由于主要粮食作物的高产商业品种占主导地位，对多种气候条件的适应性有限，投资不足，缺乏认识和单一栽培做法，它们已被边缘化。近年来，基因组学和高通量测序技术的进步为实施尖端基因组学技术铺平了道路，如rna引导核酸酶和其他先进的基因组编辑工具，以提高这些作物的产量和质量、耐受性、营养特性和抗营养因子（ANFs）等性状。这篇综述主要集中在各种未充分利用的作物的重要性、基因编辑在这些作物中的应用的最新进展、实施这种精确技术进行作物改良的主要挑战，包括监管限制和定制基因编辑方法的需求，以释放这些被忽视的作物的全部潜力。此外，它还探讨了解决技术障碍的战略，如脱靶效应和交付方法，以提高这些技术在农业和作物改良中的有效性。

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引用次数: 0

Genome-wide identification and expression analysis of the OVATE gene family in melon (Cucumis melo L.) 甜瓜（Cucumis melo L.） OVATE基因家族全基因组鉴定及表达分析

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-07-20 DOI: 10.1016/j.plgene.2025.100532

Zixuan Li , Shuaidong Wu , Wenxi Liu , Jiyuan Wang , Yanliang Guo , Congsheng Yan , Yan Wang , Huijun Zhang , Jie Liu

The OVATE gene family (OFP) is widely present in plants and plays a crucial role in regulating growth, development, and plant morphology, particularly in shaping fruit morphology. However, limited research has been conducted on the OFP gene in melon. In this study, we systematically identified and analyzed the entire OFP gene family in the melon genome. By comparing with 20 AtOFP protein sequences, 16 CmOFP genes were identified from the melon genome, and their physicochemical properties were characterized. Phylogenetic relationship analysis revealed that CmOFP and AtOFP could be classified into five subfamilies. Syntenic analysis demonstrated high synteny between Arabidopsis and melon OFP. Additionally, the gene structure and conserved domains of CmOFP were determined, and its predicted tertiary protein structure was elucidated. Through promoter analysis of CmOFP, a total of 30 regulatory elements were identified, showing significant differences in both number and classification among these elements. Expression pattern analysis indicated that the relative expression of CmOFP in the ovary was high and decreased post-pollination. Transcriptome analysis of different melon fruit pulps revealed that plant hormone signal transduction pathways were closely associated with fruit shape determination. Notably, four CmOFP genes exhibited significant differential expression across various fruit shapes, suggesting potential applications in fruit shape improvement. This study provides a theoretical foundation for further exploring the functional roles of CmOFP and their utilization in melon breeding programs.

OVATE基因家族（OFP）广泛存在于植物中，在调节植物的生长发育和形态，特别是果实形态的形成中起着至关重要的作用。然而，对甜瓜中OFP基因的研究有限。在这项研究中，我们系统地鉴定和分析了甜瓜基因组中的整个OFP基因家族。通过比对20个AtOFP蛋白序列，从甜瓜基因组中鉴定出16个CmOFP基因，并对其理化性质进行了分析。系统发育关系分析表明，CmOFP和AtOFP可划分为5个亚科。同源性分析表明拟南芥与甜瓜OFP具有较高的同源性。此外，还确定了CmOFP的基因结构和保守结构域，并对其预测的三级蛋白结构进行了阐释。通过对CmOFP的启动子分析，共鉴定出30个调控元件，这些元件在数量和分类上都存在显著差异。表达谱分析表明，CmOFP在子房中的相对表达量较高，授粉后相对表达量降低。对不同甜瓜果肉的转录组分析表明，植物激素信号转导途径与果实形状的决定密切相关。值得注意的是，4个CmOFP基因在不同果实形状中表现出显著的差异表达，这表明CmOFP基因在改善果实形状方面具有潜在的应用前景。该研究为进一步探索CmOFP的功能作用及其在甜瓜育种中的应用提供了理论基础。

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引用次数: 0

Computational interference of gene regulatory networks on the growth and development of millets 基因调控网络对谷子生长发育的计算干扰

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-07-15 DOI: 10.1016/j.plgene.2025.100531

Lipsa Leena Panigrahi , Gayatri Mishra , Dhaneswar Swain , Gyana Ranjan Rout

Millets are among the cereal crops cultivated for nutrient-rich food. They are generally considered as resilient crops in terms of growth requirements, as they can withstand harsh climatic factors such as unpredictable climate change and nutrient-depleted soils. The present review highlighted that gene regulatory networks are rewired to control the adaptable traits and to understand the transcriptional regulatory system against environmental stress. By combining machine learning, predictive modeling, and multi-omics data to unravel intricate regulatory relationships, computational methods have entirely changed the study of GRNs (gene regulatory networks), making and identifying important transcription factors, co-regulators, and signaling networks. Recent developments in artificial intelligence, systems biology, and bioinformatics have made reconstructing and analyzing millet GRNs, providing new information on blooming mechanisms, nutrient absorption,and drought resistance. Data scarcity, species-specific heterogeneity, and the requirement for high-throughput functional validation. Computational models incorporating transcriptomics, proteomics, and metabolomics help to improve crop improvement by enabling targeted genetic alterations and increasing predictive accuracy. This study discusses critical approaches, accessible datasets, and new developments in computational GRN investigations in millets. Deep learning, CRISPR-based gene editing, and synthetic biology in millet research are among the opportunities to develop new genotypes. By using computational methods to gain a thorough understanding of millet GRNs, it will be possible to create millet varieties that are more nutritious and climate-robust, promoting sustainable agriculture.

小米是一种营养丰富的谷类作物。就生长需求而言，它们通常被认为是适应力强的作物，因为它们可以承受恶劣的气候因素，如不可预测的气候变化和营养枯竭的土壤。本文综述了基因调控网络的重新布线，以控制适应性性状，并了解对环境胁迫的转录调控系统。通过结合机器学习、预测建模和多组学数据来揭示复杂的调控关系，计算方法完全改变了grn（基因调控网络）的研究，制造和识别重要的转录因子、协同调控因子和信号网络。近年来，人工智能、系统生物学和生物信息学的发展使谷子grn得以重构和分析，为谷子开花机制、养分吸收和抗旱性提供了新的信息。数据稀缺性、物种特异性异质性以及对高通量功能验证的需求。结合转录组学、蛋白质组学和代谢组学的计算模型通过实现靶向遗传改变和提高预测准确性来帮助改善作物改良。本研究讨论了小米计算GRN研究的关键方法、可访问的数据集和新发展。小米研究中的深度学习、基于crispr的基因编辑和合成生物学都是开发新基因型的机会。通过使用计算方法来全面了解谷子grn，将有可能创造出更有营养、更适应气候变化的谷子品种，从而促进可持续农业。

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引用次数: 0