Zhifeng Wang, Peigang Liu, Chengzhi Jiao, Yazhou Zhang, Zilong Xu, Tianbao Lin, Yan Zhu, Xin Jing, Yuan Huang, Nan Chao, Mengjie Zhao, Yan Liu, Huizi Liu, Bo Sun, Fen Zhang, Quanzi Li, Zhiqiang Lv, Xuepeng Sun, Ying‐Chung Jimmy Lin, Jia Wei
Mulberry is a representative economic tree species valued for both poverty alleviation and medicinal use. To advance the understanding of mulberry genomics and demography, we assembled high‐quality haploid genomes of two widely cultivated mulberry varieties NS14 and QS1, and analysed 376 accessions from 12 countries, including 39 ancient trees to investigate their origin and spreading. Population genetic analyses revealed that mulberry originated in the Yunnan‐Guizhou Plateau (YGP) and subsequently spread northward from South China to North China. This migration resulted in significant genetic differentiation between northern and southern populations, with the southern populations exhibiting higher genetic diversity. A total of 37 traits related to development and immunity were analysed in 203 accessions, and a genome‐wide association study (GWAS) was used to identify 204 associated loci. Five causal gene haplotypes were pinpointed for key production traits of mulberry trees, including branch pitch, branch length, budburst timing, leaf thickness, and leaf size (leaf area, leaf width, and leaf length). To further explore loci related to disease resistance, we examined the resistance of 538 F 1 hybrids derived from NS14 (resistant) and QS1 (susceptible). Through bulked segregant analysis and GWAS, we identified a G‐type RLK (receptor‐like kinase) tandem gene cluster. Transcriptomic analyses revealed opposite expression trends of these RLK genes in NS14 and QS1, further supporting their role in mulberry blight resistance. Our findings provide valuable genomic and demographic insights for future multi‐purpose breeding efforts in mulberry.
{"title":"Haplotype‐Resolved Genome Assembly and Population Genomics Reveal Evolutionary History and Agronomic Traits of Mulberry","authors":"Zhifeng Wang, Peigang Liu, Chengzhi Jiao, Yazhou Zhang, Zilong Xu, Tianbao Lin, Yan Zhu, Xin Jing, Yuan Huang, Nan Chao, Mengjie Zhao, Yan Liu, Huizi Liu, Bo Sun, Fen Zhang, Quanzi Li, Zhiqiang Lv, Xuepeng Sun, Ying‐Chung Jimmy Lin, Jia Wei","doi":"10.1111/pbi.70473","DOIUrl":"https://doi.org/10.1111/pbi.70473","url":null,"abstract":"Mulberry is a representative economic tree species valued for both poverty alleviation and medicinal use. To advance the understanding of mulberry genomics and demography, we assembled high‐quality haploid genomes of two widely cultivated mulberry varieties NS14 and QS1, and analysed 376 accessions from 12 countries, including 39 ancient trees to investigate their origin and spreading. Population genetic analyses revealed that mulberry originated in the Yunnan‐Guizhou Plateau (YGP) and subsequently spread northward from South China to North China. This migration resulted in significant genetic differentiation between northern and southern populations, with the southern populations exhibiting higher genetic diversity. A total of 37 traits related to development and immunity were analysed in 203 accessions, and a genome‐wide association study (GWAS) was used to identify 204 associated loci. Five causal gene haplotypes were pinpointed for key production traits of mulberry trees, including branch pitch, branch length, budburst timing, leaf thickness, and leaf size (leaf area, leaf width, and leaf length). To further explore loci related to disease resistance, we examined the resistance of 538 F <jats:sub>1</jats:sub> hybrids derived from NS14 (resistant) and QS1 (susceptible). Through bulked segregant analysis and GWAS, we identified a G‐type RLK (receptor‐like kinase) tandem gene cluster. Transcriptomic analyses revealed opposite expression trends of these RLK genes in NS14 and QS1, further supporting their role in mulberry blight resistance. Our findings provide valuable genomic and demographic insights for future multi‐purpose breeding efforts in mulberry.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"19 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145599015","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}
Heading date is a critical determinant of regional adaptation and yield potential. Here, we identify an E286K substitution in TaSG‐D1, encoding an STKc_GSK3 kinase, which delays heading date in wheat. Mechanistically, this substitution strengthens the physical interaction between TaSG‐D1 and TaWRKY53 and enhances the phosphorylation of TaWRKY53. Interestingly, the phosphorylation confers increased transcriptional activation of TaWRKY53 to the downstream gene VRN2 . We further show that TaWRKY53 has been under artificial selection during Chinese wheat breeding. Modern cultivars frequently carry a premature stop codon in TaWRKY53, resulting in a 34 amino acid truncation relative to local landraces. This truncation eliminates phosphorylation of TaWRKY53 and impairs its transcriptional activity, which reduces VRN2 expression and ultimately accelerates heading. Our findings unveil a TaSG‐D1–TaWRKY53 regulatory module controlling heading date and identify key genetic variants underlying wheat adaptation to the double‐cropping system in China.
{"title":"Natural Variation of TaSG‐D1‐TaWRKY53 Module Regulates Heading Date in Wheat","authors":"Xingyuan Xi, Tong Zhu, Guangxian Cui, Yan Zhou, Baoyue Zhang, Haoran Qi, Hongjiao Jiang, Zhen Qin, Yumei Zhang, Huiru Peng, Yingyin Yao, Zhaorong Hu, Zhongfu Ni, Ive De Smet, Qixin Sun, Mingming Xin","doi":"10.1111/pbi.70469","DOIUrl":"https://doi.org/10.1111/pbi.70469","url":null,"abstract":"Heading date is a critical determinant of regional adaptation and yield potential. Here, we identify an E286K substitution in TaSG‐D1, encoding an STKc_GSK3 kinase, which delays heading date in wheat. Mechanistically, this substitution strengthens the physical interaction between TaSG‐D1 and TaWRKY53 and enhances the phosphorylation of TaWRKY53. Interestingly, the phosphorylation confers increased transcriptional activation of TaWRKY53 to the downstream gene <jats:italic>VRN2</jats:italic> . We further show that TaWRKY53 has been under artificial selection during Chinese wheat breeding. Modern cultivars frequently carry a premature stop codon in TaWRKY53, resulting in a 34 amino acid truncation relative to local landraces. This truncation eliminates phosphorylation of TaWRKY53 and impairs its transcriptional activity, which reduces <jats:italic>VRN2</jats:italic> expression and ultimately accelerates heading. Our findings unveil a <jats:italic>TaSG‐D1–TaWRKY53</jats:italic> regulatory module controlling heading date and identify key genetic variants underlying wheat adaptation to the double‐cropping system in China.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"29 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583028","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}
Meilian Xu, Lang Yan, Min Zhu, Zhitian Zhan, Hong Chen, Dantong Wang, Zhenping Zheng, Yujie Zhang, Lizhong Xiong, Yubing He
The CRISPR/Cas9 gene‐editing technology has been widely used in defining gene functions and crop improvement. However, some genes are essential for plant growth and development. Loss‐of‐function homozygous mutations in essential genes lead to plant death or sterility. Mutations in essential genes need to be maintained and propagated in heterozygous plants. CRISPR/Cas9 technology is highly efficient in generating homozygous or bi‐allelic mutations at T0 generation in rice, making it difficult to generate useful genetic materials for essential genes using traditional gene editing technology. In this study, we designed Transgene‐Killer CRISPR (TKC)‐mediated mismatch‐spacer targeting (TKC‐M) to efficiently generate heritable heterozygous mutations in essential genes in rice. Leveraging our earlier transgenic offspring self‐elimination TKC platform, TKC‐M relied on timely self‐elimination of Cas9 and engineered gRNA‐target mismatches to enrich heritable heterozygous or mosaic incomplete‐edited T0 mutants and heterozygous progeny. We found that the sensitivity of targets to spacer mismatch(es) varies. A single‐base mismatch at gRNA positions 11 or 17 yielded abundant heritable heterozygotes in sensitive targets. For insensitive targets, dual mismatches at positions 8 and 15 maximised heritable heterozygotes. Co‐transformation of rice with TKC vectors carrying gRNA without mismatches (G1), gRNA with a mismatch at position 11 (M11) and M8 + M15 spacers, termed TKC‐M Cocktail (TKC‐MC) significantly increased the incomplete‐edited mutant ratio compared with using G1 alone. This work establishes a technical foundation for generating mutant libraries that cover every single gene in a plant genome and for in‐depth research on essential genes.
{"title":"TKC ‐ MC : An Effective Strategy for Generating Heritable Heterozygous Mutations in Essential Genes in Rice","authors":"Meilian Xu, Lang Yan, Min Zhu, Zhitian Zhan, Hong Chen, Dantong Wang, Zhenping Zheng, Yujie Zhang, Lizhong Xiong, Yubing He","doi":"10.1111/pbi.70472","DOIUrl":"https://doi.org/10.1111/pbi.70472","url":null,"abstract":"The CRISPR/Cas9 gene‐editing technology has been widely used in defining gene functions and crop improvement. However, some genes are essential for plant growth and development. Loss‐of‐function homozygous mutations in essential genes lead to plant death or sterility. Mutations in essential genes need to be maintained and propagated in heterozygous plants. CRISPR/Cas9 technology is highly efficient in generating homozygous or bi‐allelic mutations at T0 generation in rice, making it difficult to generate useful genetic materials for essential genes using traditional gene editing technology. In this study, we designed Transgene‐Killer CRISPR (TKC)‐mediated mismatch‐spacer targeting (TKC‐M) to efficiently generate heritable heterozygous mutations in essential genes in rice. Leveraging our earlier transgenic offspring self‐elimination TKC platform, TKC‐M relied on timely self‐elimination of Cas9 and engineered gRNA‐target mismatches to enrich heritable heterozygous or mosaic incomplete‐edited T0 mutants and heterozygous progeny. We found that the sensitivity of targets to spacer mismatch(es) varies. A single‐base mismatch at gRNA positions 11 or 17 yielded abundant heritable heterozygotes in sensitive targets. For insensitive targets, dual mismatches at positions 8 and 15 maximised heritable heterozygotes. Co‐transformation of rice with <jats:italic>TKC</jats:italic> vectors carrying gRNA without mismatches (G1), gRNA with a mismatch at position 11 (M11) and M8 + M15 spacers, termed TKC‐M Cocktail (TKC‐MC) significantly increased the incomplete‐edited mutant ratio compared with using G1 alone. This work establishes a technical foundation for generating mutant libraries that cover every single gene in a plant genome and for in‐depth research on essential genes.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"359 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583029","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>Fluxes of intracellular metabolic reactions are an integrated output of multiple cellular processes, from transcription to post-translational modifications that shape cell physiology (Koley et al. <span>2024</span>) and can be used to raise targets for improving different metabolic traits (Treves et al. <span>2022</span>). Intracellular metabolic fluxes are not measured, but are estimated using approaches from Metabolic Flux Analysis (MFA) (Wiechert <span>2001</span>) that integrate data on (time-resolved) label enrichment of metabolites, obtained from stable isotope labelling experiments, into a mathematical model of a reaction network with underlying atom transitions. Yet, their estimation at genome scale from time-resolved isotope labelling data remains unresolved. We present NeuralFlux, a deep learning–based approach that enables the systematic exploration of the design space of stable isotope labelling experiments supporting the planning of informative experiments for genome-scale flux estimation.</p> <p>The label enrichments for individual metabolites in a given reaction network can be calculated using a system of coupled ordinary differential equations (ODEs) that describe the change in labelling of a metabolite's pool as a function of steady-state reaction fluxes, steady-state (compartmentalised) metabolite concentrations and label enrichments. The inverse problem is that of estimating a steady-state flux distribution and (compartmentalised) metabolite concentrations for which the simulated label enrichments, using the system of ODEs, minimise a distance measure to the measured label enrichments. Elementary metabolic units (EMUs) (Antoniewicz et al. <span>2007</span>) reduce the number of variables in simulating label enrichment, and have facilitated genome-scale flux estimation with data from isotopic stationary states.</p> <p>By contrast, in experiments with nutrients for which the input labelled atoms cannot be differentiated (e.g., carbon in CO<sub>2</sub> or nitrogen in NO<sub>3</sub><sup>−</sup>), data from an isotopic stationary state are not informative as all atoms will be labelled; therefore, in this case, time-resolved labelling patterns from the transient phase must be used for flux estimation. This has resulted in the development of Isotopically non-stationary MFA (INST-MFA) approaches, particularly in photosynthetic organisms (Koley et al. <span>2024</span>). Despite these advances, flux estimation at a genome scale with INST-MFA approaches remains challenging (Koley et al. <span>2024</span>), since existing solutions are applicable to networks of a few reactions (e.g., INCA; Young <span>2014</span>) or are computationally demanding, affecting reproducibility (Gopalakrishnan et al. <span>2018</span>).</p> <p>Given a reaction network together with a set of sampled steady-state flux distributions and (compartmentalised) metabolite concentrations, our approach, termed NeuralFlux, makes use of the corresponding system of ODEs
细胞内代谢反应的通量是多个细胞过程的综合输出，从转录到塑造细胞生理的翻译后修饰（Koley et al. 2024），可用于提高改善不同代谢性状的靶标（Treves et al. 2022）。细胞内代谢通量不进行测量，而是使用代谢通量分析（MFA） （Wiechert 2001）的方法进行估计，该方法将从稳定同位素标记实验获得的代谢物（时间分辨率）标记富集数据整合到具有潜在原子跃迁的反应网络的数学模型中。然而，他们从时间分辨同位素标记数据在基因组尺度上的估计仍然没有解决。我们提出了NeuralFlux，这是一种基于深度学习的方法，可以系统地探索稳定同位素标记实验的设计空间，支持基因组尺度通量估计的信息性实验规划。给定反应网络中单个代谢物的标记富集可以使用耦合常微分方程（ode）系统来计算，该系统将代谢物池的标记变化描述为稳态反应通量、稳态（分区）代谢物浓度和标记富集的函数。相反的问题是估计稳态通量分布和（划分的）代谢物浓度，其中模拟的标签富集，使用ode系统，最小化距离测量到测量的标签富集。基本代谢单位（emu） （Antoniewicz et al. 2007）减少了模拟标签富集的变量数量，并促进了利用同位素稳态数据进行基因组尺度通量估计。相比之下，在不能区分输入标记原子的营养物实验中（例如，CO2中的碳或NO3−中的氮），来自同位素定态的数据不能提供信息，因为所有原子都将被标记；因此，在这种情况下，必须使用瞬态相位的时间分辨标记模式进行通量估计。这导致了同位素非固定MFA （INST-MFA）方法的发展，特别是在光合生物中（Koley et al. 2024）。尽管取得了这些进展，但使用INST-MFA方法在基因组尺度上进行通量估计仍然具有挑战性（Koley等人，2024），因为现有的解决方案适用于少数反应网络（例如，INCA; Young 2014），或者计算要求高，影响了可重复性（Gopalakrishnan等人，2018）。给定一个反应网络以及一组采样的稳态通量分布和（划分的）代谢物浓度，我们的方法，称为NeuralFlux，利用相应的ode系统来模拟标签富集，以质量同位素分布（mid）的形式，为emu在与实验测量相对应的时间点（图1c）。然后，NeuralFlux使用稳态通量分布以及（划分的）代谢物浓度作为完全连接的神经网络的输入，该神经网络具有三个隐藏层，分别为216、36和6个节点，用于在给定时间点预测一个EMU的MID。考虑到模拟MID的平均标准差低于典型MID测量的标准差（图1g），在通量估计中使用这些神经网络代替数值求解ode系统。NeuralFlux的解空间由训练神经网络所用的采样值定义，其边界需要使用文献中的信息。这种方法可以将计算工作量减少两到三个数量级（图1）。图1在图查看器中打开powerpointneuralflux的工作流程，评估估计的通量，以及它们与大型拟沙菌模型中氨基酸标记数据的置信区间。(a)代谢物a - d的反应网络玩具模型，三个反应，包括原子跃迁，用箭头表示。(b) N样品稳态通量分布和代谢物浓度分布。(c)通过数值求解常微分方程系统得到的时间分辨质量同位素分布。(d)训练使用生成的数据样本和相应的模拟MIDs来预测MIDs的神经网络。(e)特定时间点MIDs的实验测量值。(f)估计代谢物浓度和稳态通量，使预测值和实测值之间的卡方统计量L减小到最小。(g)大多数MID/time-point对的模拟MID值与代理神经网络推断的MID值之间的标准差；中位数用红色标记。(h) 100次运行模拟MID值和通过替代神经网络推断值所需的计算时间比。
{"title":"NeuralFlux: Estimation of Reaction Fluxes at a Genome-Scale Level From Time-Resolved Isotope Labelling Patterns Using Deep Learning","authors":"Sebastian Huß, Zoran Nikoloski","doi":"10.1111/pbi.70470","DOIUrl":"https://doi.org/10.1111/pbi.70470","url":null,"abstract":"<p>Fluxes of intracellular metabolic reactions are an integrated output of multiple cellular processes, from transcription to post-translational modifications that shape cell physiology (Koley et al. <span>2024</span>) and can be used to raise targets for improving different metabolic traits (Treves et al. <span>2022</span>). Intracellular metabolic fluxes are not measured, but are estimated using approaches from Metabolic Flux Analysis (MFA) (Wiechert <span>2001</span>) that integrate data on (time-resolved) label enrichment of metabolites, obtained from stable isotope labelling experiments, into a mathematical model of a reaction network with underlying atom transitions. Yet, their estimation at genome scale from time-resolved isotope labelling data remains unresolved. We present NeuralFlux, a deep learning–based approach that enables the systematic exploration of the design space of stable isotope labelling experiments supporting the planning of informative experiments for genome-scale flux estimation.</p>\u0000<p>The label enrichments for individual metabolites in a given reaction network can be calculated using a system of coupled ordinary differential equations (ODEs) that describe the change in labelling of a metabolite's pool as a function of steady-state reaction fluxes, steady-state (compartmentalised) metabolite concentrations and label enrichments. The inverse problem is that of estimating a steady-state flux distribution and (compartmentalised) metabolite concentrations for which the simulated label enrichments, using the system of ODEs, minimise a distance measure to the measured label enrichments. Elementary metabolic units (EMUs) (Antoniewicz et al. <span>2007</span>) reduce the number of variables in simulating label enrichment, and have facilitated genome-scale flux estimation with data from isotopic stationary states.</p>\u0000<p>By contrast, in experiments with nutrients for which the input labelled atoms cannot be differentiated (e.g., carbon in CO<sub>2</sub> or nitrogen in NO<sub>3</sub><sup>−</sup>), data from an isotopic stationary state are not informative as all atoms will be labelled; therefore, in this case, time-resolved labelling patterns from the transient phase must be used for flux estimation. This has resulted in the development of Isotopically non-stationary MFA (INST-MFA) approaches, particularly in photosynthetic organisms (Koley et al. <span>2024</span>). Despite these advances, flux estimation at a genome scale with INST-MFA approaches remains challenging (Koley et al. <span>2024</span>), since existing solutions are applicable to networks of a few reactions (e.g., INCA; Young <span>2014</span>) or are computationally demanding, affecting reproducibility (Gopalakrishnan et al. <span>2018</span>).</p>\u0000<p>Given a reaction network together with a set of sampled steady-state flux distributions and (compartmentalised) metabolite concentrations, our approach, termed NeuralFlux, makes use of the corresponding system of ODEs","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"40 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554829","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}
Li Li,Fu Shi,Yaqiong Wang,Yanbin Guan,Ya'nan Wu,Ling Chen,Junli Chang,Mingjie Chen,Jun Xiao,Guangxiao Yang,Yuesheng Wang,Guangyuan He,Yin Li
Floret fertility is a key determinant of grain number per spike and an important factor in cereal crop yield. However, the mechanisms by which phytohormone signalling and transcription factors coordinately regulate floret fertility and spikelet development are not well understood, especially in wheat. In this study, we identified the role of jasmonic acid (JA) in the regulation of floret fertility in wheat. TaSPL13-2B, a JA-responsive regulator, directly represses the gene expression of the key JA signalling factor TaJAZ1 to improve floret fertility and increase the number of florets and grains per spikelet. The TaSPL13-2B-regulated JA signalling module (TaJAZ1-TaMYC2) contributes to floret fertility by inducing the expression of TaMADS1, an E-class gene critical for floral organ identity and floret meristem activity, and increasing the content of jasmonoyl-isoleucine (JA-Ile) by upregulating the expression of genes involved in JA biosynthesis. We further demonstrated that TaSPL13-2B is a potential target for yield improvement through field trials. Our work provides mechanistic insights into floret fertility and demonstrates that improving floret fertility could be a promising strategy to increase yield.
{"title":"Wheat TaSPL13-2B Improves Floret Fertility and Enhances Grain Number per Spikelet Through Jasmonic Acid Signalling Pathway.","authors":"Li Li,Fu Shi,Yaqiong Wang,Yanbin Guan,Ya'nan Wu,Ling Chen,Junli Chang,Mingjie Chen,Jun Xiao,Guangxiao Yang,Yuesheng Wang,Guangyuan He,Yin Li","doi":"10.1111/pbi.70463","DOIUrl":"https://doi.org/10.1111/pbi.70463","url":null,"abstract":"Floret fertility is a key determinant of grain number per spike and an important factor in cereal crop yield. However, the mechanisms by which phytohormone signalling and transcription factors coordinately regulate floret fertility and spikelet development are not well understood, especially in wheat. In this study, we identified the role of jasmonic acid (JA) in the regulation of floret fertility in wheat. TaSPL13-2B, a JA-responsive regulator, directly represses the gene expression of the key JA signalling factor TaJAZ1 to improve floret fertility and increase the number of florets and grains per spikelet. The TaSPL13-2B-regulated JA signalling module (TaJAZ1-TaMYC2) contributes to floret fertility by inducing the expression of TaMADS1, an E-class gene critical for floral organ identity and floret meristem activity, and increasing the content of jasmonoyl-isoleucine (JA-Ile) by upregulating the expression of genes involved in JA biosynthesis. We further demonstrated that TaSPL13-2B is a potential target for yield improvement through field trials. Our work provides mechanistic insights into floret fertility and demonstrates that improving floret fertility could be a promising strategy to increase yield.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"101 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545043","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}
Cold stress adversely affects plant growth and development, significantly limiting fruit yield and quality in citrus. Ichang papeda ( Citrus ichangensis ), a cold‐tolerant citrus species, serves as a valuable genetic resource for studying cold adaptation, yet the key genes and their modes of action underlying the cold stress response remain largely unexplored. In this study, we identified CiWRKY27 as a critical positive regulator of cold tolerance in Ichang papeda. Through DNA affinity purification sequencing (DAP‐seq) and RNA‐sequencing analyses we uncovered 717 potential target genes of CiWRKY27, many of which are associated with stress adaptation. Further investigation revealed that CiWRKY27 directly activated CiCAD7 and CiGSTF6 by binding to W‐box elements in their promoters, thereby enhancing lignin biosynthesis and reactive oxygen species (ROS) detoxification to confer cold tolerance. Functional assays confirmed that both CiCAD7 and CiGSTF6 contributed positively to cold tolerance. Additionally, CiRAP2.7, an RAP2 (AP2/ERF) transcription factor, physically interacted with CiWRKY27 to synergistically amplify the activation of CiCAD7 . Intriguingly, CiRAP2.7 was itself regulated by CiWRKY27 and functioned as a transcriptional activator of CiCAD7 for rendering cold tolerance. Taken together, our findings demonstrate that CiWRKY27 works, alone or together with CiRAP2.7, to modulate cold tolerance by regulating CiCAD7 ‐mediated lignin biosynthesis and CiGSTF6‐ dependent ROS scavenging. This study gains valuable insights into the molecular regulation of lignin biosynthesis and ROS homeostasis under cold stress, and offers a promising molecular module for improving cold tolerance in citrus and other crops.
{"title":"WRKY27‐RAP2.7 Regulatory Module Promotes Cold Tolerance via Modulation of Lignin Biosynthesis and Redox Homeostasis by Regulating Cinnamyl Alcohol Dehydrogenase 7 and Glutathione S‐Transferase F6","authors":"Jing Qu, Peng Xiao, Yilei Wang, Tian Fang, Haowei Chen, Chunlong Li, Ji‐Hong Liu","doi":"10.1111/pbi.70439","DOIUrl":"https://doi.org/10.1111/pbi.70439","url":null,"abstract":"Cold stress adversely affects plant growth and development, significantly limiting fruit yield and quality in citrus. Ichang papeda ( <jats:italic>Citrus ichangensis</jats:italic> ), a cold‐tolerant citrus species, serves as a valuable genetic resource for studying cold adaptation, yet the key genes and their modes of action underlying the cold stress response remain largely unexplored. In this study, we identified CiWRKY27 as a critical positive regulator of cold tolerance in Ichang papeda. Through DNA affinity purification sequencing (DAP‐seq) and RNA‐sequencing analyses we uncovered 717 potential target genes of CiWRKY27, many of which are associated with stress adaptation. Further investigation revealed that CiWRKY27 directly activated <jats:italic>CiCAD7</jats:italic> and <jats:italic>CiGSTF6</jats:italic> by binding to W‐box elements in their promoters, thereby enhancing lignin biosynthesis and reactive oxygen species (ROS) detoxification to confer cold tolerance. Functional assays confirmed that both <jats:italic>CiCAD7</jats:italic> and <jats:italic>CiGSTF6</jats:italic> contributed positively to cold tolerance. Additionally, CiRAP2.7, an RAP2 (AP2/ERF) transcription factor, physically interacted with CiWRKY27 to synergistically amplify the activation of <jats:italic>CiCAD7</jats:italic> . Intriguingly, CiRAP2.7 was itself regulated by CiWRKY27 and functioned as a transcriptional activator of <jats:italic>CiCAD7</jats:italic> for rendering cold tolerance. Taken together, our findings demonstrate that CiWRKY27 works, alone or together with CiRAP2.7, to modulate cold tolerance by regulating <jats:italic>CiCAD7</jats:italic> ‐mediated lignin biosynthesis and <jats:italic>CiGSTF6‐</jats:italic> dependent ROS scavenging. This study gains valuable insights into the molecular regulation of lignin biosynthesis and ROS homeostasis under cold stress, and offers a promising molecular module for improving cold tolerance in citrus and other crops.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"93 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535860","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}
Seed oil content is a key trait in soybean, yet its genetic basis remains largely unresolved. Here, we identify GmABHD6, an α/β-hydrolase domain-containing gene, as the causal gene underlying a major quantitative trait locus (QTL) for seed oil content on chromosome 16. Through fine-mapping in a chromosome segment substitution population derived from Glycine max (SN14) and wild Glycine soja (ZYD00006), we fine-mapped the QTL to a 150-kb interval. Functional analyses reveal that overexpression of GmABHD6 significantly reduces seed oil content, whereas gene editing to truncate GmABHD6 led to increased oil accumulation. These modifications also alter seed protein levels, seed size and 100-seed weight, indicating pleiotropic effects on seed composition and yield traits. Integrated transcriptomic and metabolomic profiling of transgenic lines highlighted widespread changes in lipid metabolism and energy pathways associated with GmABHD6 activity. Further functional characterisation indicates that the ERF transcription factor GmERF physically binds to the GmABHD6 promoter region to regulate its expression. Population genetic analyses show strong signatures of selection at the GmABHD6 locus, suggesting that favourable alleles are enriched during soybean domestication and improvement. Our findings establish GmABHD6 as a domestication-related gene that negatively regulates seed oil content and provide new insights into the genetic mechanisms driving soybean seed composition and evolution.
{"title":"An α/β-Hydrolase GmABHD6 Controls Seed Oil Content and Yield in Soybean","authors":"Kaixin Yu, Limin Hu, Bo Sun, Zehao Chen, Xu Li, Shiyu Zhang, Huilin Tian, Wenjing Zhang, Shimin Ren, Xue Han, Chang Xu, Siming Wei, Mingliang Yang, Fanjiang Kong, Qingshan Chen, Zhaoming Qi","doi":"10.1111/pbi.70466","DOIUrl":"https://doi.org/10.1111/pbi.70466","url":null,"abstract":"Seed oil content is a key trait in soybean, yet its genetic basis remains largely unresolved. Here, we identify <i>GmABHD6</i>, an α/β-hydrolase domain-containing gene, as the causal gene underlying a major quantitative trait locus (QTL) for seed oil content on chromosome 16. Through fine-mapping in a chromosome segment substitution population derived from <i>Glycine max</i> (SN14) and wild <i>Glycine soja</i> (ZYD00006), we fine-mapped the QTL to a 150-kb interval. Functional analyses reveal that overexpression of <i>GmABHD6</i> significantly reduces seed oil content, whereas gene editing to truncate <i>GmABHD6</i> led to increased oil accumulation. These modifications also alter seed protein levels, seed size and 100-seed weight, indicating pleiotropic effects on seed composition and yield traits. Integrated transcriptomic and metabolomic profiling of transgenic lines highlighted widespread changes in lipid metabolism and energy pathways associated with <i>GmABHD6</i> activity. Further functional characterisation indicates that the ERF transcription factor GmERF physically binds to the <i>GmABHD6</i> promoter region to regulate its expression. Population genetic analyses show strong signatures of selection at the <i>GmABHD6</i> locus, suggesting that favourable alleles are enriched during soybean domestication and improvement. Our findings establish <i>GmABHD6</i> as a domestication-related gene that negatively regulates seed oil content and provide new insights into the genetic mechanisms driving soybean seed composition and evolution.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"7 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145532044","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}
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