Plant Gene最新文献_第4页

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 : 2025-09-15 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

Flower development in Brassica rapa: Linking anatomy, physiology, transcriptomics, and metabolomics 油菜花的发育：解剖学、生理学、转录组学和代谢组学的联系

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-12 DOI: 10.1016/j.plgene.2025.100545

Waseem Ahmad Lone, Rayees Ahmad Rather, Tahira Akhtar Bhat, Umer Majeed Wani, Riffat John

Flowering is essential to most plants, and is regulated by environmental and internal signals. This study investigates the molecular mechanisms regulating flower development in Brassica rapa L. by performing, anatomical studies, RNA sequencing, analysis of photosynthetic parameters and metabolomics at different developmental stages. We conducted RNA sequencing and analysed 47,135 genes across three pairwise comparisons: Vegetative vs. Pre-Bolting, Pre-Bolting vs. Bolting, and Bolting vs. Post-Bolting. The greatest differential gene expression was observed between the vegetative and pre-bolting stages, with significant changes in 3618 genes. Functional enrichment analysis revealed that photosynthesis, circadian rhythm regulation, response to environmental stimuli, and glucosinolate biosynthesis were the most enriched biological processes during floral transition. Photosynthetic parameters showed a significant increase from the vegetative to bolting stages, peaking from pre-bolting to bolting, and decreasing post-bolting. Metabolomic analysis identified 23 metabolites with significant changes during development. Key metabolites such as campesterol and gamma sitosterol increased during bolting, indicating a role in promoting floral meristem formation. Our study identified several key regulatory genes involved in the photoperiod, circadian clock, and gibberellin pathways, such as GIGANTEA (GI), SOC1, and ELF3. Upregulation of these genes from pre-bolting to bolting stages correlated with enhanced photosynthetic activity and gene expression related to light signaling, carbohydrate metabolism, carbon metabolism, and glucosinolate biosynthesis. These findings provide a comprehensive view of the transcriptional changes and regulatory networks governing the transition from vegetative growth to flowering in B. rapa L., highlighting the integration of environmental and internal cues in this complex process.

开花对大多数植物来说是必不可少的，并受到环境和内部信号的调节。本研究通过解剖研究、RNA测序、光合参数分析和代谢组学分析，探讨了油菜不同发育阶段花发育的分子调控机制。我们进行了RNA测序，并通过三个两两比较分析了47,135个基因：营养与预抽苔、预抽苔与抽苔、抽苔与抽苔后。营养期和抽苔期基因表达差异最大，有3618个基因表达差异显著。功能富集分析表明，光合作用、昼夜节律调节、对环境刺激的响应和硫代葡萄糖苷生物合成是花转化过程中富集程度最高的生物过程。光合参数从营养期到抽苔期显著增加，从抽苔前到抽苔期达到峰值，抽苔后下降。代谢组学分析发现23种代谢物在发育过程中发生了显著变化。油菜甾醇和谷甾醇等关键代谢物在抽苔过程中增加，表明其在促进花分生组织形成中起作用。我们的研究确定了几个参与光周期、生物钟和赤霉素途径的关键调控基因，如GIGANTEA （GI）、SOC1和ELF3。从抽苔前到抽苔期，这些基因的上调与光合活性的增强以及与光信号、碳水化合物代谢、碳代谢和硫代葡萄糖苷生物合成相关的基因表达有关。这些发现为植物从营养生长到开花的转录变化和调控网络提供了一个全面的视角，强调了这一复杂过程中环境和内部线索的整合。

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引用次数: 0

Genome-wide identification and transcriptome-based expression analysis of hybrid sugarcane calmodulin-binding transcription activators under drought 干旱条件下杂交甘蔗钙调素结合转录激活因子的全基因组鉴定和转录组表达分析

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-11 DOI: 10.1016/j.plgene.2025.100547

Vitor Luciano Costa da Silva , Ana Maria Martinez , Maqsood Alam , Muhammad Noman , Antonio Chalfun-Junior

As the highly demanding complex genome of the hybrid sugarcane cultivar became publicly available recently (2023), it opened avenues to further study this important crop at molecular level. We are interested in digging the multiple stress responsive transcription factors family, the Calmodulin-Binding Transcription Activator (CAMTA) of sugarcane. This manuscript presents a comprehensive study of ScCAMTA family based on the latest sugarcane genome sequence information. Within the 10 gb genome, through HMM model prepared from sorghum CAMTA common domains, we found 48 genes, 46 out of which carry all the CAMTA-associated domains including CG-1, TIG, IQ and Ank. The phylogenetic analysis clustered then into seven classes. Keeping sorghum as reference, we named them as ScCAMTA1 – ScCAMTA7, while each one representing a class having 5–7 copies such as ScCAMTA1A – ScCAMTA1E, present in each sub-genome (chromosome) within the hybrid sugarcane. In parallel to determining their physico-chemical attributes, miRNA targets, protein interaction network and genome collinearity, we observed evolutionary conservation in gene structures, protein domains, and motif organization across the phylogenetic classes. Promoter analysis revealed the presence of multiple stress-responsive cis-regulatory elements, such as MBS (drought) and MYB (salinity), suggesting their direct involvement in stress adaptation. MicroRNA target analysis predicted 20 unique miRNAs targeting ScCAMTA transcripts, highlighting potential post-transcriptional regulation. Additionally, protein-protein interaction networks indicated functional connections to stress signaling pathways. Finally, their expression patterns under drought stress were determined using RNA-seq data, which revealed that ScCAMTA7 is highly active under drought conditions, underscoring its potential role in drought response. This study furthers the insights into complex sugarcane genome and will assist in developing its drought-tolerant varieties.

随着高要求的复杂杂交甘蔗基因组最近（2023年）公开，它为在分子水平上进一步研究这一重要作物开辟了道路。我们对甘蔗多逆境响应转录因子家族——钙调素结合转录激活因子（Calmodulin-Binding transcription Activator， CAMTA）感兴趣。本文基于最新的甘蔗基因组序列信息，对ScCAMTA家族进行了全面的研究。在10 gb的基因组中，通过从高粱CAMTA共同结构域制备HMM模型，我们发现48个基因，其中46个基因携带所有CAMTA相关结构域，包括CG-1、TIG、IQ和Ank。系统发育分析将其归为7类。以高粱为参照，我们将它们命名为ScCAMTA1 - ScCAMTA7，而每个代表一类具有5-7个拷贝，如ScCAMTA1A - ScCAMTA1E，存在于杂交甘蔗的每个亚基因组（染色体）中。在确定它们的物理化学属性、miRNA靶点、蛋白质相互作用网络和基因组共线性的同时，我们观察到基因结构、蛋白质结构域和基序组织在系统发育分类中的进化守恒。启动子分析显示存在多种应激响应顺式调控元件，如MBS（干旱）和MYB（盐度），表明它们直接参与胁迫适应。MicroRNA靶标分析预测了20个独特的靶向ScCAMTA转录本的mirna，突出了潜在的转录后调控。此外，蛋白质相互作用网络表明了与应激信号通路的功能联系。最后，利用RNA-seq数据确定了它们在干旱胁迫下的表达模式，结果显示ScCAMTA7在干旱条件下高度活跃，强调了其在干旱响应中的潜在作用。这项研究将进一步深入了解复杂的甘蔗基因组，并将有助于开发其耐旱品种。

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引用次数: 0

Comprehensive genome-wide study of Glutaredoxin (GRX) gene family in the liverwort Marchantia polymorpha and exploring their roles in abiotic stress tolerance 多形地茅（Marchantia polymorpha） Glutaredoxin （GRX）基因家族的全基因组研究及其在非生物胁迫耐受中的作用

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-11 DOI: 10.1016/j.plgene.2025.100550

Shivani Singh , Garima Saxena , Prachi Mishra , Monica Kumari , Prasanna Dutta , Mehar Hasan Asif , Debasis Chakrabarty

Glutaredoxins (GRXs) are thiol-disulfide oxidoreductases that function as key regulators of redox homeostasis, development, and stress responses in plants. Despite their functional importance, little is known about the GRX gene family in early diverging land plants. In this study, we performed a comprehensive genome-wide identification of GRX genes in the liverwort Marchantia polymorpha and their role in abiotic stresses. A total of 17 MpGRX genes with 2 isoforms (19 MpGRX) containing the conserved Glutaredoxin domain (PF00462) were identified using BLAST, HMMER, and SMART approaches. Gene structure analysis revealed that six MpGRX genes contained a single intron, whereas the remaining genes exhibited more complex structures with three or more introns, suggesting gene expansion and functional diversification. Evolutionary analysis was conducted using non-synonymous (Ka) and synonymous (Ks) substitution rates between MpGRX genes and homologous genes from Physcomitrella patens, Ceratopteris richardii, Pinus taeda, Arabidopsis thaliana, and Oryza sativa. The results indicated generally low Ka values, except in one MpGRX–PtGRX pair with Ka = 1.59, suggesting potential functional divergence in gymnosperms. Ks-based divergence time estimates were consistent with known evolutionary separations. Selection pressure analysis based on Ka/Ks ratios revealed that most GRX gene pairs were under purifying selection, particularly those between M. polymorpha and mosses, ferns, and angiosperms.

This study provides novel insights into the structural diversity, evolutionary history, and selective constraints acting on the GRX gene family in M. polymorpha, offering a foundation for future functional and comparative studies in early land plant lineages.

Glutaredoxins （GRXs）是一种巯基二硫氧化还原酶，在植物氧化还原稳态、发育和胁迫反应中起关键调节作用。尽管GRX基因家族具有重要的功能，但对早期分化的陆生植物的GRX基因家族知之甚少。在这项研究中，我们对地茅（Marchantia polymorpha）的GRX基因进行了全面的全基因组鉴定及其在非生物胁迫中的作用。使用BLAST、HMMER和SMART方法共鉴定了17个MpGRX基因，其中2个同种异构体（19个MpGRX）含有保守的Glutaredoxin结构域（PF00462）。基因结构分析显示，6个MpGRX基因含有1个内含子，其余基因结构更为复杂，含有3个或更多内含子，表明基因扩增和功能多样化。采用非同义替换率（Ka）和同义替换率（Ks）对来自小立小立藓、richardii角羽蛾、taus taeda、拟南芥和Oryza sativa的MpGRX基因与同源基因进行了进化分析。结果表明，除了有一对MpGRX-PtGRX对Ka = 1.59外，其他裸子植物的Ka值普遍较低，提示裸子植物存在潜在的功能分化。基于ks的分化时间估计与已知的进化分离一致。基于Ka/Ks比的选择压力分析表明，大多数GRX基因对处于纯化选择状态，尤其是多形草与苔藓、蕨类和被子植物之间的选择。本研究对多形草GRX基因家族的结构多样性、进化历史和选择限制提供了新的见解，为未来早期陆地植物谱系的功能和比较研究提供了基础。

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引用次数: 0

Gene expression analysis of four Solanum tuberosum L. varieties in vitro induced with Alternaria alternata and Streptomyces werraensis extracts 互交菌和沃拉链霉菌提取物诱导4个龙葵品种的基因表达分析

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-09-08 DOI: 10.1016/j.plgene.2025.100546

Izdihar Ferhat , Wahiba Harrat , Emre Yörük , Boualem Harfi

Potato (Solanum tuberosum L.) is one of the major tuber food crops worldwide. However, its culture is threatened by several diseases like potato brown leaf spot which is related to Alternaria fungi. This study addresses the challenge of inducing resistance in four potato varieties against brown spot disease by in vitro culture. The approach relies on combining Streptomyces werraensis extracts, reported as potential biocontrol agents, and Alternaria alternata pathogen extracts in the potato culture medium. Initially, potato micropropagation and microtuberization media were optimized, followed by an acclimatization phase and a pathogenicity test on the four varieties (Arizona, Désirée, Spunta and Synergy). Subsequently, potato microtubers were produced in vitro, with microorganisms' extracts included in the culture medium. To assess for induced resistance, qRT-PCR analysis was conducted to evaluate gene expression levels, targeting the most relevant genes (ChtA1, ChtB3, PR1b, PRa1-like, WRKY31 and WRKY75-like). Gene expression analysis revealed significant differences between varieties, with Arizona variety showing the most vigorous response. These distinct varietal responses indicate genotype-specific reactions to the combined treatment of A. alternata and S. werraensis extracts. This research highlights the S. werraensis potential as a biocontrol agent to induce resistance in potatoes to A. alternata. The results support the integration of in vitro culture media supplemented with microorganism extracts for large-scale standardized potato production.

马铃薯（Solanum tuberosum L.）是世界主要的块茎粮食作物之一。但其栽培受到马铃薯褐叶斑病等病害的威胁。本研究解决了4个马铃薯品种在离体培养中诱导抗褐斑病的挑战。该方法依赖于在马铃薯培养基中结合报道为潜在生物防治剂的werraensis链霉菌提取物和交替稻瘟菌病原体提取物。首先，对4个马铃薯品种（Arizona、dsamsisame、Spunta和Synergy）进行了适化和致病性试验。随后，在培养基中加入微生物提取物，在体外生产马铃薯微块茎。为了评估诱导抗性，采用qRT-PCR分析评估基因表达水平，针对最相关的基因（ChtA1、ChtB3、PR1b、pra1 like、WRKY31和wrky75 like）。基因表达分析显示品种间差异显著，以亚利桑那品种表现出最强烈的反应。这些不同的品种反应表明，对互花荆芥和冬荆芥提取物联合处理有基因型特异性反应。本研究强调了稻角霉作为一种生物防治剂诱导马铃薯对稻角霉产生抗性的潜力。研究结果为马铃薯规模化标准化生产中微生物提取物和离体培养基的整合提供了依据。

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引用次数: 0

Identification and characterization of the CONSTANS-like gene family and its expression profiling under salt treatment in alfalfa (Medicago sativa L.) 紫花苜蓿（Medicago sativa L.） CONSTANS-like基因家族的鉴定、鉴定及其盐处理下的表达谱分析

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-29 DOI: 10.1016/j.plgene.2025.100544

Shuzhi Ma, Yiping Wei, Qinyan Bao, Zhaozhu Wen, Mengli Luo, Wenxuan Du

Alfalfa (Medicago sativa L.) is a globally cultivated, high-quality forage crop. The CONSTANS-LIKE (COL) genes play crucial roles in regulating flowering time and stress responses in plants. However, the functional characterization of COL genes in alfalfa remain largely unexplored. In this study, we conducted a genome-wide analysis of the Xinjiang Daye alfalfa genome and identified 36 MsCOL genes. Multiple sequence alignment confirmed that all MsCOL genes contain conserved B-box and CCT (CO, CO-like and TOC1) domains. Phylogenetic analysis and gene structure analyses classified the MsCOL genes into two subclades, exhibiting similar exon-intron organization and conserved motif distributions. Chromosomal mapping revealed that these genes are distributed across 22 chromosomes. Expression profiling under salt stress demonstrated that MsCOL genes exhibit expression patterns, indicating their potential involvement in abiotic stress responses. These findings enhance our understanding of MsCOL gene function in alfalfa and provide a theoretical basis for breeding salt-tolerant alfalfa cultivars.

苜蓿（Medicago sativa L.）是一种全球种植的优质饲料作物。CONSTANS-LIKE （COL）基因在调控植物开花时间和胁迫反应中起着至关重要的作用。然而，在苜蓿中COL基因的功能表征仍未得到充分的研究。在本研究中，我们对新疆大冶苜蓿基因组进行了全基因组分析，鉴定出36个MsCOL基因。多个序列比对证实，所有MsCOL基因都含有保守的B-box和CCT （CO、CO样和TOC1）结构域。系统发育分析和基因结构分析将MsCOL基因分为两个亚支系，具有相似的外显子-内含子组织和保守的基序分布。染色体图谱显示这些基因分布在22条染色体上。盐胁迫下的表达谱表明，MsCOL基因表现出表达模式，表明它们可能参与非生物胁迫反应。这些发现增加了我们对紫花苜蓿MsCOL基因功能的认识，为选育耐盐紫花苜蓿品种提供了理论依据。

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引用次数: 0

Induced genetic diversity through EMS mutagenesis in Davana (Artemisia pallens Bess.) and use of ISSR markers to underpin agronomical and chemical traits 通过EMS诱变诱导Davana （Artemisia pallens Bess.）的遗传多样性，并利用ISSR标记支持其农艺和化学性状

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-19 DOI: 10.1016/j.plgene.2025.100543

Arun J. Ganiger , Channayya Hiremath , K. Madhusudan , Manoj kumar Chandrasekaran , V.S. Pragadheesh

Davana (Artemisia pallens Bess.) is an annual aromatic herb that belongs to the Asteraceae family. The current research was attempted to identify elite high essential oil yielding davana mutants with high davanone content. To determine the LD₅₀ value of EMS, seeds of the local davana cultivar “Bangalore” were treated with the chemical mutagen ethyl methane sulphonate (EMS) at varying concentrations of 0.10 %, 0.2 %, 0.3 %, 0.40 %, and 0.50 % for 16 h. The LD₅₀ value was (0.40 % for 16 h) determined by probit analysis. In the M₁ generation, 3000 davana plants were evaluated and forwarded to M₂. Based on visual observation of 1500 M₂ plants, 250 mutants were chosen, and their essential oil and davanone content was assessed. In the M₂ generation, the quantitative traits evaluated and chemical constituents assessed had higher mean and moderate to high phenotypic co-efficient of variation, in comparison to the control. Essential oil yield had a strong and significantly positive correlation to the number of flowers per plant, flower head diameter, and fresh herb yield traits. Based on superiority over control and Mean + 1 SD of M₂ population, 22 and 14 mutants were identified for essential oil yield and davanone content, respectively. Molecular diversity analysis of 16 high essential oil yielding M₂ plants and two check cultivars using ISSR markers revealed an average 79 % polymorphism, with the primer UBC-845 having the highest polymorphic information content. We identified several superior mutants including DM2158 (essential oil content-0.5 %) and DM2103 (Davanone content-70.92 %), indicating that mutation breeding can be an effective strategy to develop novel davana cultivars with higher essential oil and davanone content.

Davana （Artemisia pallens Bess.）是一种一年生芳香草本植物，属于菊科。本研究旨在鉴定具有高davdavone含量的davdavone优质高精油突变体。为了确定EMS的LD50值，用不同浓度的化学诱变剂甲烷磺酸乙酯（EMS）处理本地达瓦纳品种“班加罗尔”的种子，分别为0.10%、0.2%、0.3%、0.40%和0.50%，处理16 h。通过probit分析，LD50值为0.40% （16 h）。在M1代中，对3000株达瓦纳草木进行了评价，并转发到M2上。在1500 M2植株目视观察的基础上，选择250个突变体，对其挥发油和达凡酮含量进行评价。在M2代中，所评价的数量性状和所评价的化学成分与对照相比，具有较高的平均变异和中高的表型变异系数。精油产量与单株花数、花头直径、鲜草产量性状呈极显著正相关。根据M2群体的对照优势和Mean + 1 SD，分别鉴定出22个和14个挥发油产量和davdavone含量的突变体。利用ISSR标记对16株精油高产植物M2和2个对照品种进行分子多样性分析，发现其多态性平均为79%，其中引物UBC-845多态性信息含量最高。本研究鉴定出DM2158（挥发油含量- 0.5%）和DM2103（达瓦酮含量- 70.92%）两个优良突变体，表明突变选育是培育高挥发油和达瓦酮含量达瓦纳新品种的有效策略。

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引用次数: 0

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