<p>Alfalfa (<i>Medicago sativa</i> L.) is a perennial leguminous forage extensively planted around the world (Annicchiarico <i>et al</i>., <span>2015</span>). As a result, improving alfalfa forage yield and quality is a crucial agricultural goal (Kumar, <span>2011</span>). Branching traits has a significant impact on the yield of alfalfa (Gou <i>et al</i>., <span>2018</span>). The previous report showed that <i>HEADLESS</i> (<i>HDL</i>), the orthologue of <i>WUSCHEL</i> (<i>WUS</i>) in <i>M. truncatula</i>, is required for axillary meristem maintenance (Wang <i>et al</i>., <span>2019</span>), implying <i>HDL</i> has the potential to regulate the number of branches. To test this hypothesis, 35S promoter-driven <i>HDL</i> transgene was introduced into alfalfa. Ten transgenic plants (OX-1, OX-3 and OX-5) with high expression were selected for phenotypic investigation (Figure S1a). Compared with the wild-type, the <i>HDL-OX</i> plants display more branches (Figure 1a–c). Furthermore, overexpressing <i>HDL</i> increases plant height and produces larger, dark green leaves (Figures 1d,e, S1b–f), suggesting that increased <i>HDL</i> activity affects not only branching but also leaf development in alfalfa.</p> <figure><picture> <source media="(min-width: 1650px)" srcset="/cms/asset/568e93da-4021-431b-a271-b21b7e0bffa2/pbi14569-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/568e93da-4021-431b-a271-b21b7e0bffa2/pbi14569-fig-0001-m.jpg" loading="lazy" src="/cms/asset/b048812f-4047-4b7e-be75-5b9bf97a45fe/pbi14569-fig-0001-m.png" title="Details are in the caption following the image"/></picture><figcaption> <div><strong>Figure 1<span style="font-weight:normal"></span></strong><div>Open in figure viewer<i aria-hidden="true"></i><span>PowerPoint</span></div> </div> <div><i>HDL-OX</i> improves forage biomass and quality of alfalfa. (a–c) Primary and secondary branch phenotype (a, b) and number (c) of the wild-type and <i>HDL-OX</i> plants. Bars = 4 cm. (d, e) Plant height (d) and internode (IN) length (e). (f) <i>HDL</i> binding to the CNNGCNA motif (upper panel); Interaction of <i>HDL</i> with the CNNGCNA and its substituted sequences in LUC assays (lower panel). (g) Expression of branch regulation genes. (h) LUC assay showing repression of <i>MsMAX3</i> by <i>HDL</i> in <i>Arabidopsis</i> protoplasts. (i) Location of the fragments (P1–P3) used for ChIP-qPCR assays in the <i>MsMAX3</i> promoter. (j, k) ChIP-qPCR and EMSA assays showing that <i>HDL</i> binds to the P2 fragment of the <i>MsMAX3</i> promoter. (l) Flowering phenotype. Bars = 4 cm. (m) Days of the first flower flowering. (n) Expression of <i>MsFTa1</i>. (o) LUC assay showing repression of <i>MsFTa1</i> by <i>HDL</i>. (p) Location of the fragments (P1–P5) used for ChIP-qPCR assays in the <i>MsFTa1</i> promoter. (q, r) ChIP-qPCR and EMSA assays showing that <i>HDL</i> binds to the P3 fragment of the <i>MsFTa1</i> promoter in vivo. (s–u) The <i>HDL-OX<
苜蓿（Medicago sativa L.）是世界上广泛种植的多年生豆科牧草（Annicchiarico et al., 2015）。因此，提高苜蓿饲料产量和质量是一个至关重要的农业目标（Kumar, 2011）。分支性状对苜蓿产量有显著影响（Gou et al., 2018）。先前的报道显示，在M. truncatula中，HEADLESS （HDL）是WUSCHEL （WUS）的同源物，是腋窝分生组织维持所必需的（Wang et al., 2019），这意味着HDL具有调节分支数量的潜力。为了验证这一假设，将35S启动子驱动的HDL转基因引入苜蓿。选择10株高表达转基因植株（OX-1、OX-3和OX-5）进行表型研究（图S1a）。与野生型相比，HDL-OX植株显示出更多的分枝（图1a-c）。此外，过表达HDL会增加植株高度，产生更大的深绿色叶片（图1d，e, S1b-f），这表明HDL活性的增加不仅会影响苜蓿的分枝，还会影响叶片发育。图1在图视图中打开powerpoint dl - ox提高了苜蓿的饲料生物量和品质。（a - c）野生型和HDL-OX植株的一次和次枝表型（a, b）和数量(c)。条= 4厘米。（d, e）株高(d)和节间（IN）长度(e)。(f) HDL与CNNGCNA基序的结合（上图）；LUC检测中HDL与CNNGCNA及其取代序列的相互作用（下图）。(g)分支调控基因的表达。(h) LUC分析显示拟南芥原生质体中高密度脂蛋白抑制MsMAX3。(i)用于MsMAX3启动子ChIP-qPCR检测的片段（P1-P3）的位置。（j, k） ChIP-qPCR和EMSA分析显示HDL与MsMAX3启动子的P2片段结合。(l)开花表型。条= 4厘米。(m)第一朵花开花的日子。(n) MsFTa1的表达。(o) LUC分析显示高密度脂蛋白抑制MsFTa1。(p)用于MsFTa1启动子ChIP-qPCR检测的片段（P1-P5）的位置。（q, r） ChIP-qPCR和EMSA分析显示HDL在体内与MsFTa1启动子的P3片段结合。（s - u） HDL-OX植株生物量(s)、粗蛋白质(t)和粗脂肪(u)含量均增加。值代表平均值±SD；所有统计学显著性采用学生t检验（*P < 0.05, **P < 0.01, ***P < 0.001）。(v) HDL在饲料改良中的工作模型。为了研究HDL的调节机制，我们进行了染色质免疫沉淀测序（ChIP-Seq）。与保守的wus结合基序TAAT相反，我们发现了一个7 bp的新型HDL结合序列CNNGCNA（图1f）。进一步分析表明HDL与MsTPL/MsTPRs相互作用形成复合物并作为转录抑制因子（图1f和S2）。点突变分析表明，核心碱基对HDL的DNA结合至关重要（图1f）。然后，我们分析了与分支形成相关的几个已知关键基因的表达，发现在HDL-OX植物中，MsMAX3的表达显著降低（图1g）。MsMAX3参与独脚金内酯（SLs）的生物合成，定位于细胞核和细胞质中（图S3a，c）。MAX3同源突变体的功能丧失表现为枝分枝增加（Umehara et al., 2008）。此外，苜蓿中独角甾内酯受体MsD14的下调也会导致茎分枝增加（Ma et al., 2022）。瞬时表达表明HDL抑制MsMAX3的表达（图1）。ChIP-qPCR和EMSA结果显示HDL可以直接结合到MsMAX3启动子的P2片段上（图1i-k）。此外，通过RNA干扰下调MsMAX3导致分支增加（图S4），遗传学上表明HDL通过抑制MsMAX3促进分支形成。开花使牧草质量降低到相对饲料价值的45%左右（Casler和Vogel， 1999）。HDL-OX植株表现出晚花表型，与野生型相比，第一朵花在更晚的节点上开花(图11，图11；S5)。MsFTa1定位于细胞核和细胞质中（图S3b）， MsFTa1突变延迟开花并改善饲料质量(Lorenzo et al., 2020；Wolabu et al., 2023)。RT-qPCR分析显示，在HDL-OX植株中，MsFTa1显著降低（图1n）。此外，瞬时表达表明HDL抑制MsFTa1的表达（图10）。ChIP-qPCR和EMSA分析显示HDL可以直接与MsFTa1启动子结合（图1p-r），表明HDL下调MsFTa1是转基因苜蓿开花晚表型的原因。”此外，HDL-OX植株不仅叶片/茎比显著增加，而且鲜、干生物量也显著增加（图15和图6）。 饲料质量测定表明，HDL-OX植株的粗蛋白质、粗脂肪、水溶性糖、微量元素、中性和酸性洗涤纤维含量显著增加（图11、图6、图6）；表S1)。此外，转录组学分析显示，在HDL-OX植物中有5474个基因差异表达，其中3117个基因上调，2357个基因下调(图S7a；表S2)。在被归类为生物过程的18种氧化石墨烯差异术语中，生物调节、细胞过程和代谢过程最为显著，因为它们与HDL-OX性状相关，如分支增加、开花时间延迟和微量元素含量改变(图S7b；表S3)。此外，KEGG分析显示，这些基因富集于脂肪酸生物合成、淀粉和蔗糖代谢相关途径以及各种氨基酸合成途径中(图S8-S11；表S4-S7)，支持HDL-OX植株饲料质量的提高。尽管许多生长素相关基因，如AUX/IAA、ARF和SAUR的表达发生了变化，但HDL-OX植物的生长素含量没有显著变化(图S12；表S8)。总的来说，我们的研究提供了证据，支持使用HDL作为改善饲料质量的分子工具（图1v）。
{"title":"Manipulation of WUSCHEL orthologue expression improves the forage yield and quality in Medicago","authors":"Hongfeng Wang, Yiteng Xu, Yan Wang, Zhiqun Gu, Feng Yuan, Lu Han, Shupeng Liu, Shuwei Liu, Zhichao Lu, Ying'e Chen, Qiaolan Liang, Chunxiang Fu, Ruicai Long, Qingchuan Yang, Zeng-Yu Wang, Chuanen Zhou","doi":"10.1111/pbi.14569","DOIUrl":"https://doi.org/10.1111/pbi.14569","url":null,"abstract":"<p>Alfalfa (<i>Medicago sativa</i> L.) is a perennial leguminous forage extensively planted around the world (Annicchiarico <i>et al</i>., <span>2015</span>). As a result, improving alfalfa forage yield and quality is a crucial agricultural goal (Kumar, <span>2011</span>). Branching traits has a significant impact on the yield of alfalfa (Gou <i>et al</i>., <span>2018</span>). The previous report showed that <i>HEADLESS</i> (<i>HDL</i>), the orthologue of <i>WUSCHEL</i> (<i>WUS</i>) in <i>M. truncatula</i>, is required for axillary meristem maintenance (Wang <i>et al</i>., <span>2019</span>), implying <i>HDL</i> has the potential to regulate the number of branches. To test this hypothesis, 35S promoter-driven <i>HDL</i> transgene was introduced into alfalfa. Ten transgenic plants (OX-1, OX-3 and OX-5) with high expression were selected for phenotypic investigation (Figure S1a). Compared with the wild-type, the <i>HDL-OX</i> plants display more branches (Figure 1a–c). Furthermore, overexpressing <i>HDL</i> increases plant height and produces larger, dark green leaves (Figures 1d,e, S1b–f), suggesting that increased <i>HDL</i> activity affects not only branching but also leaf development in alfalfa.</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/568e93da-4021-431b-a271-b21b7e0bffa2/pbi14569-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/568e93da-4021-431b-a271-b21b7e0bffa2/pbi14569-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/b048812f-4047-4b7e-be75-5b9bf97a45fe/pbi14569-fig-0001-m.png\" title=\"Details are in the caption following the image\"/></picture><figcaption>\u0000<div><strong>Figure 1<span style=\"font-weight:normal\"></span></strong><div>Open in figure viewer<i aria-hidden=\"true\"></i><span>PowerPoint</span></div>\u0000</div>\u0000<div><i>HDL-OX</i> improves forage biomass and quality of alfalfa. (a–c) Primary and secondary branch phenotype (a, b) and number (c) of the wild-type and <i>HDL-OX</i> plants. Bars = 4 cm. (d, e) Plant height (d) and internode (IN) length (e). (f) <i>HDL</i> binding to the CNNGCNA motif (upper panel); Interaction of <i>HDL</i> with the CNNGCNA and its substituted sequences in LUC assays (lower panel). (g) Expression of branch regulation genes. (h) LUC assay showing repression of <i>MsMAX3</i> by <i>HDL</i> in <i>Arabidopsis</i> protoplasts. (i) Location of the fragments (P1–P3) used for ChIP-qPCR assays in the <i>MsMAX3</i> promoter. (j, k) ChIP-qPCR and EMSA assays showing that <i>HDL</i> binds to the P2 fragment of the <i>MsMAX3</i> promoter. (l) Flowering phenotype. Bars = 4 cm. (m) Days of the first flower flowering. (n) Expression of <i>MsFTa1</i>. (o) LUC assay showing repression of <i>MsFTa1</i> by <i>HDL</i>. (p) Location of the fragments (P1–P5) used for ChIP-qPCR assays in the <i>MsFTa1</i> promoter. (q, r) ChIP-qPCR and EMSA assays showing that <i>HDL</i> binds to the P3 fragment of the <i>MsFTa1</i> promoter in vivo. (s–u) The <i>HDL-OX<","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"68 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Cas12j-8 nuclease, derived from the type V CRISPR system, is approximately half the size of Cas9 and recognizes a 5′-TTN-3′ protospacer adjacent motif sequence, thus potentially having broad application in genome editing for crop improvement. However, its editing efficiency remains low in plants. In this study, we rationally engineered both the crRNA and the Cas12j-8 nuclease. The engineered crRNA and Cas12j-8 markedly improved genome editing efficiency in plants. When combined, they exhibited robust editing activity in soybean and rice, enabling the editing of target sites that were previously uneditable. Notably, for certain target sequences, the editing activity was comparable to that of SpCas9 when targeting identical sequences, and it outperformed the Cas12j-2 variant, nCas12j-2, across all tested targets. Additionally, we developed cytosine base editors based on the engineered crRNA and Cas12j-8, demonstrating an average increase of 5.36- to 6.85-fold in base-editing efficiency (C to T) compared with the unengineered system in plants, with no insertions or deletions (indels) observed. Collectively, these findings indicate that the engineered hypercompact CRISPR/Cas12j-8 system serves as an efficient tool for genome editing mediated by both nuclease cleavage and base editing in plants.
{"title":"Engineering an optimized hypercompact CRISPR/Cas12j-8 system for efficient genome editing in plants","authors":"Shasha Bai, Xingyu Cao, Lizhe Hu, Danling Hu, Dongming Li, Yongwei Sun","doi":"10.1111/pbi.14574","DOIUrl":"https://doi.org/10.1111/pbi.14574","url":null,"abstract":"The Cas12j-8 nuclease, derived from the type V CRISPR system, is approximately half the size of Cas9 and recognizes a 5′-TTN-3′ protospacer adjacent motif sequence, thus potentially having broad application in genome editing for crop improvement. However, its editing efficiency remains low in plants. In this study, we rationally engineered both the crRNA and the Cas12j-8 nuclease. The engineered crRNA and Cas12j-8 markedly improved genome editing efficiency in plants. When combined, they exhibited robust editing activity in soybean and rice, enabling the editing of target sites that were previously uneditable. Notably, for certain target sequences, the editing activity was comparable to that of SpCas9 when targeting identical sequences, and it outperformed the Cas12j-2 variant, nCas12j-2, across all tested targets. Additionally, we developed cytosine base editors based on the engineered crRNA and Cas12j-8, demonstrating an average increase of 5.36- to 6.85-fold in base-editing efficiency (C to T) compared with the unengineered system in plants, with no insertions or deletions (indels) observed. Collectively, these findings indicate that the engineered hypercompact CRISPR/Cas12j-8 system serves as an efficient tool for genome editing mediated by both nuclease cleavage and base editing in plants.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"4 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dong Jiang, Guoqun Yang, Li-Jun Huang, Xia Peng, Chuantong Cui, Yakov Kuzyakov, Ning Li
Liquid crystal monomers (LCMs), the integral components in the manufacture of digital displays, have engendered environmental concerns due to extensive utilization and intensive emission. Despite their prevalence and ecotoxicity, the LCM impacts on plant growth and agricultural yield remain inadequately understood. In this study, we investigated the specific response mechanisms of tobacco, a pivotal agricultural crop and model plant, to four representative LCMs (2OdF3B, 5CB, 4PiMeOP, 2BzoCP) through integrative molecular and physiological approaches. The findings reveal specific impacts, with 4PiMeOP exerting the most pronounced effects, followed by 2BzoCP, 5CB, and 2OdF3B. LCM exposure disrupts the photosynthetic apparatus, exacerbating reactive oxygen species (ROS) levels in leaves, which in turn triggers the upregulation of antioxidative enzymes and the synthesis of antioxidant substances. Additionally, LCMs strongly stimulate the expression of genes involved in abscisic acid (ABA) biosynthesis and signalling pathways. The AI-assisted meta-analysis implicates ABA as a critical regulator in the tobacco response to LCMs. Notably, exogenous application of ABA alleviates LCM-induced toxicities, highlighting the pivotal role of ABA in stress amelioration. Our study provides novel insights into the toxicity and tolerance mechanisms of LCMs in plants, shedding light on both their harmful effects on the ecosystems and potential adaptation responses. This is crucial to develop sustainable agricultural systems by reducing the negative environmental impacts caused by emerging organic pollutants.
{"title":"Integrative molecular and physiological insights into the phytotoxic impact of liquid crystal monomer exposure and the protective strategy in plants","authors":"Dong Jiang, Guoqun Yang, Li-Jun Huang, Xia Peng, Chuantong Cui, Yakov Kuzyakov, Ning Li","doi":"10.1111/pbi.14526","DOIUrl":"10.1111/pbi.14526","url":null,"abstract":"<p>Liquid crystal monomers (LCMs), the integral components in the manufacture of digital displays, have engendered environmental concerns due to extensive utilization and intensive emission. Despite their prevalence and ecotoxicity, the LCM impacts on plant growth and agricultural yield remain inadequately understood. In this study, we investigated the specific response mechanisms of tobacco, a pivotal agricultural crop and model plant, to four representative LCMs (2OdF3B, 5CB, 4PiMeOP, 2BzoCP) through integrative molecular and physiological approaches. The findings reveal specific impacts, with 4PiMeOP exerting the most pronounced effects, followed by 2BzoCP, 5CB, and 2OdF3B. LCM exposure disrupts the photosynthetic apparatus, exacerbating reactive oxygen species (ROS) levels in leaves, which in turn triggers the upregulation of antioxidative enzymes and the synthesis of antioxidant substances. Additionally, LCMs strongly stimulate the expression of genes involved in abscisic acid (ABA) biosynthesis and signalling pathways. The AI-assisted meta-analysis implicates ABA as a critical regulator in the tobacco response to LCMs. Notably, exogenous application of ABA alleviates LCM-induced toxicities, highlighting the pivotal role of ABA in stress amelioration. Our study provides novel insights into the toxicity and tolerance mechanisms of LCMs in plants, shedding light on both their harmful effects on the ecosystems and potential adaptation responses. This is crucial to develop sustainable agricultural systems by reducing the negative environmental impacts caused by emerging organic pollutants.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"23 2","pages":"644-659"},"PeriodicalIF":10.1,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.14526","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chaopu Zhang, Qiqi Liang, Yuye Yu, Shaojuan Jin, Jinmei Huang, Zhongping Xu, Erbao Liu, Wensheng Wang, Fan Zhang, Fangzhou Liu, Yingyao Shi, Fenge Li, Zhikang Li, Shuangxia Jin, Min Li
<p>Genome-wide selection (GS) represents a contemporary methodology that harnesses a comprehensive array of molecular markers across the entire genome. However, challenges such as lack of informative molecular markers and selection of appropriate and efficient GS model(s) have confined most GS-based breeding efforts to the realm of laboratory simulations (Wang <i>et al</i>., <span>2023</span>). Compared to the conventional prediction models, the machine learning (ML) algorithm provides new insights for solving challenges such as big data analysis and high-performance parallel computing. GS using ML also has some limitations at the current stage such as limitations in model selection.</p> <p>Here, the MFMGP software is a fusion model that is based on a variety of ML training methods. The normalization fusion method with exponential decay weights involves assigning weights to the prediction results of each model and applying the exponential decay to these weights, so that more recent and/or more relevant model predictions have higher weights. Then, a weighted average of the model's prediction results is calculated to obtain the final fusion prediction by normalizing these weights (Figure 1a). The software of MFMGP for interactive GS analyses was made available at website: http://www.biohuaxing.com/#/MFMGP. To verify the prediction accuracy of the MFMGP model, we compared MFMGP with seven commonly used GS models. These included the classical GS model (GBLUP), four ML-based models (LightGBM, SVR, XGBoost and HGBoost) and two DL-based (DNNGP and DeepCCR) models.</p> <figure><picture> <source media="(min-width: 1650px)" srcset="/cms/asset/96b5e04f-412c-4447-a23e-77f24ecd952c/pbi14532-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/96b5e04f-412c-4447-a23e-77f24ecd952c/pbi14532-fig-0001-m.jpg" loading="lazy" src="/cms/asset/cde0d7f6-73bd-41fa-819c-73433ebc1c88/pbi14532-fig-0001-m.png" title="Details are in the caption following the image"/></picture><figcaption> <div><strong>Figure 1<span style="font-weight:normal"></span></strong><div>Open in figure viewer<i aria-hidden="true"></i><span>PowerPoint</span></div> </div> <div>Prediction accuracy of eight methods based on three crop datasets. (a) The design and algorithmic framework for Multiple Machine Learning Fusion Model for Genomics Prediction (MFMGP). (b) Phenotypic variation of the agronomic traits in rice. (c) Performance of eight methods in predicting 13 traits using rice 3KRP (<i>n</i> = 2110). The red arrow and text box indicate the proportion by which the MFMGP model can improve accuracy compared to the other seven models. (d) Performance of eight methods in predicting six traits using wheat dataset (<i>n</i> = 2000). (e) Performance of eight methods in predicting four traits using cotton dataset (<i>n</i> = 1245). Prediction accuracy of eight methods based on maize (<i>n</i> = 6210) (f) and pig datasets (<i>n</i> = 1490) (g). (h) The relationshi
{"title":"MFMGP: an integrated machine learning fusion model for genomic prediction","authors":"Chaopu Zhang, Qiqi Liang, Yuye Yu, Shaojuan Jin, Jinmei Huang, Zhongping Xu, Erbao Liu, Wensheng Wang, Fan Zhang, Fangzhou Liu, Yingyao Shi, Fenge Li, Zhikang Li, Shuangxia Jin, Min Li","doi":"10.1111/pbi.14532","DOIUrl":"https://doi.org/10.1111/pbi.14532","url":null,"abstract":"<p>Genome-wide selection (GS) represents a contemporary methodology that harnesses a comprehensive array of molecular markers across the entire genome. However, challenges such as lack of informative molecular markers and selection of appropriate and efficient GS model(s) have confined most GS-based breeding efforts to the realm of laboratory simulations (Wang <i>et al</i>., <span>2023</span>). Compared to the conventional prediction models, the machine learning (ML) algorithm provides new insights for solving challenges such as big data analysis and high-performance parallel computing. GS using ML also has some limitations at the current stage such as limitations in model selection.</p>\u0000<p>Here, the MFMGP software is a fusion model that is based on a variety of ML training methods. The normalization fusion method with exponential decay weights involves assigning weights to the prediction results of each model and applying the exponential decay to these weights, so that more recent and/or more relevant model predictions have higher weights. Then, a weighted average of the model's prediction results is calculated to obtain the final fusion prediction by normalizing these weights (Figure 1a). The software of MFMGP for interactive GS analyses was made available at website: http://www.biohuaxing.com/#/MFMGP. To verify the prediction accuracy of the MFMGP model, we compared MFMGP with seven commonly used GS models. These included the classical GS model (GBLUP), four ML-based models (LightGBM, SVR, XGBoost and HGBoost) and two DL-based (DNNGP and DeepCCR) models.</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/96b5e04f-412c-4447-a23e-77f24ecd952c/pbi14532-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/96b5e04f-412c-4447-a23e-77f24ecd952c/pbi14532-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/cde0d7f6-73bd-41fa-819c-73433ebc1c88/pbi14532-fig-0001-m.png\" title=\"Details are in the caption following the image\"/></picture><figcaption>\u0000<div><strong>Figure 1<span style=\"font-weight:normal\"></span></strong><div>Open in figure viewer<i aria-hidden=\"true\"></i><span>PowerPoint</span></div>\u0000</div>\u0000<div>Prediction accuracy of eight methods based on three crop datasets. (a) The design and algorithmic framework for Multiple Machine Learning Fusion Model for Genomics Prediction (MFMGP). (b) Phenotypic variation of the agronomic traits in rice. (c) Performance of eight methods in predicting 13 traits using rice 3KRP (<i>n</i> = 2110). The red arrow and text box indicate the proportion by which the MFMGP model can improve accuracy compared to the other seven models. (d) Performance of eight methods in predicting six traits using wheat dataset (<i>n</i> = 2000). (e) Performance of eight methods in predicting four traits using cotton dataset (<i>n</i> = 1245). Prediction accuracy of eight methods based on maize (<i>n</i> = 6210) (f) and pig datasets (<i>n</i> = 1490) (g). (h) The relationshi","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"39 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within and among species, as well as the roles of host genes and non-coding RNAs in the transposition process, remain elusive. With advancements in large-scale pan-genome sequencing and the development of open data sharing, large-scale comparative genomics studies have become feasible. Here, we performed complete de novo TE annotations and identified active TEs in 310 plant genome assemblies across 119 species and seven crop populations. Using 811 high-quality genomes, we detected 13 844 553 TE-induced structural variants (TE-SVs), providing unprecedented resolution in delineating recent TE activities. Our integrative analysis revealed a mutual evolutionary relationship between TEs and host genomes. On one hand, host genes and ncRNAs are involved in the transposition process, as evidenced by their colocalization and coactivation with TEs, and may play a role in chromatin regulation. On the other hand, TEs drive genetic innovation by promoting the duplication of host genes and inserting into regulatory regions. Moreover, genes influenced by active TEs are linked to plant growth, nutrient absorption, storage metabolism and environmental adaptation, aiding in crop domestication and adaptation. This TE dynamics atlas not only reveals evolutionary and functional features linked to transposition activity but also highlights the role of TEs in crop domestication and adaptation, paving the way for future exploration of TE-mediated genome evolution and crop improvement strategies.
{"title":"Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies","authors":"Yan Huang, Sunil Kumar Sahu, Xin Liu","doi":"10.1111/pbi.14570","DOIUrl":"https://doi.org/10.1111/pbi.14570","url":null,"abstract":"Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within and among species, as well as the roles of host genes and non-coding RNAs in the transposition process, remain elusive. With advancements in large-scale pan-genome sequencing and the development of open data sharing, large-scale comparative genomics studies have become feasible. Here, we performed complete <i>de novo</i> TE annotations and identified active TEs in 310 plant genome assemblies across 119 species and seven crop populations. Using 811 high-quality genomes, we detected 13 844 553 TE-induced structural variants (TE-SVs), providing unprecedented resolution in delineating recent TE activities. Our integrative analysis revealed a mutual evolutionary relationship between TEs and host genomes. On one hand, host genes and ncRNAs are involved in the transposition process, as evidenced by their colocalization and coactivation with TEs, and may play a role in chromatin regulation. On the other hand, TEs drive genetic innovation by promoting the duplication of host genes and inserting into regulatory regions. Moreover, genes influenced by active TEs are linked to plant growth, nutrient absorption, storage metabolism and environmental adaptation, aiding in crop domestication and adaptation. This TE dynamics atlas not only reveals evolutionary and functional features linked to transposition activity but also highlights the role of TEs in crop domestication and adaptation, paving the way for future exploration of TE-mediated genome evolution and crop improvement strategies.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"130 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142940439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jie Hao, Yan Yan, Yao Zhang, Yiyang Zhang, Yune Cao, Longguo Wu
Superoxide dismutase (SOD) plays an important role to respond in the defence against damage when tomato leaves are under different types of adversity stresses. This work employed microhyperspectral imaging (MHSI) and visible near-infrared (Vis–NIR) hyperspectral imaging (HSI) technologies to predict tomato leaf SOD activity. The macroscopic model of SOD activity in tomato leaves was constructed using the convolutional neural network in conjunction with the long and short-term temporal memory (CNN-LSTM) technique. Using heterogeneous two-dimensional correlation spectra (H2D-COS), the sensitive macroscopic and microscopic absorption peaks connected to tomato leaves' SOD activity were made clear. The combination of CNN-LSTM algorithm and H2D-COS analysis was used to research transfer learning between microscopic and macroscopic models based on sensitive wavelengths. The results demonstrated that the CNN-LSTM model, which was based on the FD preprocessed spectra, had the best performance for the microscopic model, with RC and RP reaching 0.9311 and 0.9075, and RMSEC and RMSEP reaching 0.0109 U/mg and 0.0127 U/mg respectively. There were 10 macroscopic and 10 microscopic significant sensitivity peaks found. The transfer learning was carried out using sensitive wavelengths, and the model performed well with an RP value of 0.7549 and an RMSEP of 0.0725 U/mg. The combined CNN algorithm and H2D-COS analysis demonstrated the viability of transfer learning across microscopic and macroscopic models for quantitative tomato leaf SOD prediction.
{"title":"A cross-scale transfer learning framework: prediction of SOD activity from leaf microstructure to macroscopic hyperspectral imaging","authors":"Jie Hao, Yan Yan, Yao Zhang, Yiyang Zhang, Yune Cao, Longguo Wu","doi":"10.1111/pbi.14566","DOIUrl":"https://doi.org/10.1111/pbi.14566","url":null,"abstract":"Superoxide dismutase (SOD) plays an important role to respond in the defence against damage when tomato leaves are under different types of adversity stresses. This work employed microhyperspectral imaging (MHSI) and visible near-infrared (Vis–NIR) hyperspectral imaging (HSI) technologies to predict tomato leaf SOD activity. The macroscopic model of SOD activity in tomato leaves was constructed using the convolutional neural network in conjunction with the long and short-term temporal memory (CNN-LSTM) technique. Using heterogeneous two-dimensional correlation spectra (H2D-COS), the sensitive macroscopic and microscopic absorption peaks connected to tomato leaves' SOD activity were made clear. The combination of CNN-LSTM algorithm and H2D-COS analysis was used to research transfer learning between microscopic and macroscopic models based on sensitive wavelengths. The results demonstrated that the CNN-LSTM model, which was based on the FD preprocessed spectra, had the best performance for the microscopic model, with R<sub>C</sub> and R<sub>P</sub> reaching 0.9311 and 0.9075, and RMSEC and RMSEP reaching 0.0109 U/mg and 0.0127 U/mg respectively. There were 10 macroscopic and 10 microscopic significant sensitivity peaks found. The transfer learning was carried out using sensitive wavelengths, and the model performed well with an R<sub>P</sub> value of 0.7549 and an RMSEP of 0.0725 U/mg. The combined CNN algorithm and H2D-COS analysis demonstrated the viability of transfer learning across microscopic and macroscopic models for quantitative tomato leaf SOD prediction.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"24 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142937721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>Germplasm resources with rich genetic diversities are indispensable, but often fail short to need the demand for crop breeding (Snowdon <i>et al</i>., <span>2015</span>). Genomic introgression in hybrids of closely related species is considered to be an important source for genetic diversity enhancement, which is mainly through homoeologous exchanges (HEs) among homoeologous chromosomes (Zhou <i>et al</i>., <span>2021</span>). However, the technical bottleneck in terms of the low introgression frequency of genome segments in interspecific hybrid offspring (Quezada-Martinez <i>et al</i>., <span>2021</span>), has not been solved, even though the cross between diploid <i>B. rapa</i> (A<sub>r</sub>A<sub>r</sub>) and <i>B. napus</i> (A<sub>n</sub>A<sub>n</sub>C<sub>n</sub>C<sub>n</sub>) was reported to increase the recombination frequency between A<sub>n</sub> and A<sub>r</sub> (Boideau <i>et al</i>., <span>2021</span>). On the other hand, how to elevate homoeologous chromosome recombination and genome introgression between two different species remains to be studied. Here we report an allotriploid-involved genetic system that can tremendously increase introgression frequency between two closely related species and thereby generate rich phenotypic variations, and a pipeline for genome-wide identification of introgressed segments.</p> <p>The chromosomes of a diploid <i>Brassica rapa</i> L. ssp. <i>pekinensis</i> (Chinese cabbage) NDCCBr (AA, 2n = 20) were doubled by the colchicine treatment to create a tetraploid <i>B. rapa</i> 9403Br (AAAA, 2n = 40) that was then hybridized with a diploid <i>B. oleracea</i> L. var. <i>capitata</i> (cabbage) 9501Bo (CC, 2n = 18) to produce allotriploid hybrids (AAC, 2n = 29) via ovary and ovule culture. Three allotriploids were subsequently backcrossed with another genotype diploid <i>B. rapa</i> 01-4-11Br, then 12 resultant offsprings were randomly selected and selfed for two successive generations. Finally, microspores were isolated from these selfed progenies and cultured to generate homozygous <i>B. rapa</i>–<i>B. oleracea</i> introgression lines (Boideau <i>et al.,</i> <span>2021</span>) (Figure 1a). The introgression lines were diploid, showing normal meiotic behaviour (Figure S1a–h). The presence of <i>B. oleracea</i> introgressed segments was confirmed by <i>B. oleracea</i> genome-specific InDel markers compared to <i>B. rapa</i> (Figures S1i and S2).</p> <figure><picture> <source media="(min-width: 1650px)" srcset="/cms/asset/cc899ee0-9798-4a19-8105-9dd37553abbd/pbi14564-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/cc899ee0-9798-4a19-8105-9dd37553abbd/pbi14564-fig-0001-m.jpg" loading="lazy" src="/cms/asset/e00ea885-55aa-4767-8a95-10f8795d01e8/pbi14564-fig-0001-m.png" title="Details are in the caption following the image"/></picture><figcaption> <div><strong>Figure 1<span style="font-weight:normal"></span></strong><div>Open in figure viewer<i aria-hidden=
{"title":"An efficient allotriploid-mediated system of generating genomic introgression from Brassica oleracea to B. rapa","authors":"Aixia Gu, Xiaomin Li, Zengfeng Wang, Yanhua Wang, Shuxin Xuan, Wei Ma, Yiguo Hong, Yalei Zhao, Xueping Chen, Shuangxia Luo, Yuanming Liu, Shengyi Liu, Yuanyuan Zhang, Jianjun Zhao, Shuxing Shen","doi":"10.1111/pbi.14564","DOIUrl":"https://doi.org/10.1111/pbi.14564","url":null,"abstract":"<p>Germplasm resources with rich genetic diversities are indispensable, but often fail short to need the demand for crop breeding (Snowdon <i>et al</i>., <span>2015</span>). Genomic introgression in hybrids of closely related species is considered to be an important source for genetic diversity enhancement, which is mainly through homoeologous exchanges (HEs) among homoeologous chromosomes (Zhou <i>et al</i>., <span>2021</span>). However, the technical bottleneck in terms of the low introgression frequency of genome segments in interspecific hybrid offspring (Quezada-Martinez <i>et al</i>., <span>2021</span>), has not been solved, even though the cross between diploid <i>B. rapa</i> (A<sub>r</sub>A<sub>r</sub>) and <i>B. napus</i> (A<sub>n</sub>A<sub>n</sub>C<sub>n</sub>C<sub>n</sub>) was reported to increase the recombination frequency between A<sub>n</sub> and A<sub>r</sub> (Boideau <i>et al</i>., <span>2021</span>). On the other hand, how to elevate homoeologous chromosome recombination and genome introgression between two different species remains to be studied. Here we report an allotriploid-involved genetic system that can tremendously increase introgression frequency between two closely related species and thereby generate rich phenotypic variations, and a pipeline for genome-wide identification of introgressed segments.</p>\u0000<p>The chromosomes of a diploid <i>Brassica rapa</i> L. ssp. <i>pekinensis</i> (Chinese cabbage) NDCCBr (AA, 2n = 20) were doubled by the colchicine treatment to create a tetraploid <i>B. rapa</i> 9403Br (AAAA, 2n = 40) that was then hybridized with a diploid <i>B. oleracea</i> L. var. <i>capitata</i> (cabbage) 9501Bo (CC, 2n = 18) to produce allotriploid hybrids (AAC, 2n = 29) via ovary and ovule culture. Three allotriploids were subsequently backcrossed with another genotype diploid <i>B. rapa</i> 01-4-11Br, then 12 resultant offsprings were randomly selected and selfed for two successive generations. Finally, microspores were isolated from these selfed progenies and cultured to generate homozygous <i>B. rapa</i>–<i>B. oleracea</i> introgression lines (Boideau <i>et al.,</i> <span>2021</span>) (Figure 1a). The introgression lines were diploid, showing normal meiotic behaviour (Figure S1a–h). The presence of <i>B. oleracea</i> introgressed segments was confirmed by <i>B. oleracea</i> genome-specific InDel markers compared to <i>B. rapa</i> (Figures S1i and S2).</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/cc899ee0-9798-4a19-8105-9dd37553abbd/pbi14564-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/cc899ee0-9798-4a19-8105-9dd37553abbd/pbi14564-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/e00ea885-55aa-4767-8a95-10f8795d01e8/pbi14564-fig-0001-m.png\" title=\"Details are in the caption following the image\"/></picture><figcaption>\u0000<div><strong>Figure 1<span style=\"font-weight:normal\"></span></strong><div>Open in figure viewer<i aria-hidden=","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"82 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142937773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Here, we evaluated the role of ethylene in regulating the NaHCO3 stress tolerance of grapevines and clarified the mechanism by which VvERF1B regulates the response to NaHCO3 stress. The exogenous application of ACC and VvACS3 overexpression in grapevines and grape calli revealed that ethylene increased NaHCO3 stress tolerance, and this was accompanied by increased plasma membrane H+-ATPase (PMA) activity. The expression of VvERF1B was strongly induced by ACC, and overexpression of this gene in grapevines conferred increased NaHCO3 stress tolerance and enhanced PMA activity and H+ and oxalate secretion. Additionally, the function of VvERF1B was also verified using mutant transgenic grape calli and overexpression in Arabidopsis plants. The expression of VvPMA10 was strongly induced following the overexpression of VvERF1B in grapevine roots, and VvPMA10 was shown to regulate PMA activity, oxalate and H+ secretion, and NaHCO3 stress tolerance via its overexpression and mutation in grapevine roots, calli, and/or Arabidopsis. However, VvPMA10 was not a direct target gene of VvERF1B but was directly transactivated by VvMYC2. The function of VvMYC2 was shown to be similar to that of VvPMA10 via its overexpression and mutation in grape calli. Additional experiments revealed that the interaction of VvERF1B with VvMYC2 increased its ability to activate VvPMA10 expression and that VvMYC2 played a role in the VvERF1B-mediated pathway. Overall, the VvERF1B-VvMYC2-VvPMA pathway played a role in regulating ethylene-induced NaHCO3 stress tolerance in grapevines, and this process contributed to increases in PMA activity and H+ and oxalate secretion.
{"title":"Ethylene increases the NaHCO3 stress tolerance of grapevines partially via the VvERF1B-VvMYC2-VvPMA10 pathway","authors":"Guangqing Xiang, Zongbao Fan, Shuxia Lan, Dezheng Wei, Yazhe Gao, Hui Kang, Yuxin Yao","doi":"10.1111/pbi.14565","DOIUrl":"https://doi.org/10.1111/pbi.14565","url":null,"abstract":"Here, we evaluated the role of ethylene in regulating the NaHCO<sub>3</sub> stress tolerance of grapevines and clarified the mechanism by which <i>VvERF1B</i> regulates the response to NaHCO<sub>3</sub> stress. The exogenous application of ACC and <i>VvACS3</i> overexpression in grapevines and grape calli revealed that ethylene increased NaHCO<sub>3</sub> stress tolerance, and this was accompanied by increased plasma membrane H<sup>+</sup>-ATPase (PMA) activity. The expression of <i>VvERF1B</i> was strongly induced by ACC, and overexpression of this gene in grapevines conferred increased NaHCO<sub>3</sub> stress tolerance and enhanced PMA activity and H<sup>+</sup> and oxalate secretion. Additionally, the function of <i>VvERF1B</i> was also verified using mutant transgenic grape calli and overexpression in <i>Arabidopsis</i> plants. The expression of <i>VvPMA10</i> was strongly induced following the overexpression of <i>VvERF1B</i> in grapevine roots, and <i>VvPMA10</i> was shown to regulate PMA activity, oxalate and H<sup>+</sup> secretion, and NaHCO<sub>3</sub> stress tolerance via its overexpression and mutation in grapevine roots, calli, and/or <i>Arabidopsis</i>. However, <i>VvPMA10</i> was not a direct target gene of VvERF1B but was directly transactivated by VvMYC2. The function of <i>VvMYC2</i> was shown to be similar to that of <i>VvPMA10</i> via its overexpression and mutation in grape calli. Additional experiments revealed that the interaction of VvERF1B with VvMYC2 increased its ability to activate <i>VvPMA10</i> expression and that VvMYC2 played a role in the VvERF1B-mediated pathway. Overall, the VvERF1B-VvMYC2-VvPMA pathway played a role in regulating ethylene-induced NaHCO<sub>3</sub> stress tolerance in grapevines, and this process contributed to increases in PMA activity and H<sup>+</sup> and oxalate secretion.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"79 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142936543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mehmet Tahir Husunet, Rumeysa Mese, Esra Sunduz Yigittekin, Hasan Basri Ila
The genus Euphorbia, belonging to the family Euphorbiaceae, represents a significant ethnobotanical heritage due to the diverse bioactive properties exhibited. In this study, the phytochemical composition and biological activities of latex and aerial parts of the water extract of Euphorbia gaillardotii were investigated. Phytochemical analyses were performed using gas chromatography-mass spectrometry and high-performance liquid chromatography techniques and total antioxidants, phenolics, sugars, organic acids, and aroma components were quantitatively determined. The effects of the test compounds on physicochemical parameters in aqueous media were evaluated by electrical conductivity, dissolved oxygen concentration, and pH measurements. Antimicrobial activity was evaluated on Gram-positive and Gram-negative bacteria and yeast strains using the disk diffusion method. The cytotoxic activity on the MCF-7 human breast cancer cell line was measured spectrophotometrically using the Cell Counting Kit-8 proliferation/apoptosis detection kit. The results showed that E. gaillardotii latex and aerial parts water extract significantly affected the physicochemical parameters of aqueous media, especially at high concentrations. The test substances displayed antimicrobial activity, with the latex-impregnated disks demonstrating larger inhibition zones than the aerial parts extract. The results showed that both the latex and extract treatments exhibited concentration-dependent effects on MCF-7 cell viability (P < 0.001). Furthermore, in silico docking analyses revealed a robust binding affinity of succinic acid, the most prevalent bioactive compound in the extract, towards the B-cell lymphoma 2 (Bcl-2) molecule, with a binding energy of −6.16 kcal/mol. This may be associated with the observed cytotoxicity. These results suggest that E. gaillardotii may be a valuable source for potential pharmacological applications.
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