Genomic selection (GS) is a new breeding strategy. Generally, traditional methods are used for predicting traits based on the whole genome. However, the prediction accuracy of these models remains limited because they cannot fully reflect the intricate nonlinear interactions between genotypes and traits. Here, a novel single nucleotide polymorphism (SNP) feature extraction technique based on the Pearson-Collinearity Selection (PCS) is firstly presented and improves prediction accuracy across several known models. Furthermore, gene network prediction model (NetGP) is a novel deep learning approach designed for phenotypic prediction. It utilizes transcriptomic dataset (Trans), genomic dataset (SNP) and multi-omics dataset (Trans + SNP). The NetGP model demonstrated better performance compared to other models in genomic predictions, transcriptomic predictions and multi-omics predictions. NetGP multi-omics model performed better than independent genomic or transcriptomic prediction models. Prediction performance evaluations using several other plants' data showed good generalizability for NetGP. Taken together, our study not only offers a novel and effective tool for plant genomic selection but also points to new avenues for future plant breeding research.
{"title":"Genomic prediction with NetGP based on gene network and multi-omics data in plants.","authors":"Longyang Zhao, Ping Tang, Jinjing Luo, Jianxiang Liu, Xin Peng, Mengyuan Shen, Chengrui Wang, Junliang Zhao, Degui Zhou, Zhilan Fan, Yibo Chen, Runfeng Wang, Xiaoyan Tang, Zhi Xu, Qi Liu","doi":"10.1111/pbi.14577","DOIUrl":"https://doi.org/10.1111/pbi.14577","url":null,"abstract":"<p><p>Genomic selection (GS) is a new breeding strategy. Generally, traditional methods are used for predicting traits based on the whole genome. However, the prediction accuracy of these models remains limited because they cannot fully reflect the intricate nonlinear interactions between genotypes and traits. Here, a novel single nucleotide polymorphism (SNP) feature extraction technique based on the Pearson-Collinearity Selection (PCS) is firstly presented and improves prediction accuracy across several known models. Furthermore, gene network prediction model (NetGP) is a novel deep learning approach designed for phenotypic prediction. It utilizes transcriptomic dataset (Trans), genomic dataset (SNP) and multi-omics dataset (Trans + SNP). The NetGP model demonstrated better performance compared to other models in genomic predictions, transcriptomic predictions and multi-omics predictions. NetGP multi-omics model performed better than independent genomic or transcriptomic prediction models. Prediction performance evaluations using several other plants' data showed good generalizability for NetGP. Taken together, our study not only offers a novel and effective tool for plant genomic selection but also points to new avenues for future plant breeding research.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412627","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}
Danyel Fernandes Contiliani, Simon Sretenovic, Micah Dailey, Man Zhou, Yanhao Cheng, Silvana Creste, Shunyuan Xiao, Yiping Qi
CRISPR-Cas-based cytosine base editors (CBEs) are prominent tools that perform site-specific and precise C-to-T conversions catalysed by cytidine deaminases. However, their use is often constrained by stringent editing preferences for genomic contexts, off-target effects and restricted editing windows. To expand the repertoire of CBEs, we systematically screened 66 novel cytidine deaminases sourced from various organisms, predominantly from the animal kingdom and benchmarked them in rice protoplasts using the nCas9-BE3 configuration. After selecting candidates in rice protoplasts and further validation in transgenic rice lines, we unveiled a few cytidine deaminases exhibiting high editing efficiencies and wide editing windows. CBEs based on these cytidine deaminases also displayed minimal frequencies of indels and C-to-R (R = A/G) conversions, suggesting high purity in C-to-T base editing. Furthermore, we highlight the highly efficient cytidine deaminase OoA3GX2 derived from Orca (killer whale) for its comparable activity across GC/CC/TC/AC sites, thus broadening the targeting scope of CBEs for robust multiplexed base editing. Finally, the whole-genome sequencing analyses revealed very few sgRNA-dependent and -independent off-target effects in independent T0 lines. This study expands the cytosine base-editing toolkit with many cytidine deaminases sourced from mammals, providing better-performing CBEs that can be further leveraged for sophisticated genome engineering strategies in rice and likely in other plant species.
基于 CRISPR-Cas 的胞嘧啶碱基编辑器（CBEs）是由胞苷脱氨酶催化进行位点特异性和精确的 C-T 转换的重要工具。然而，它们的使用往往受到基因组上下文严格的编辑偏好、脱靶效应和编辑窗口限制的制约。为了扩大细胞苷脱氨酶的范围，我们系统地筛选了 66 种新型细胞苷脱氨酶，它们主要来自动物界的各种生物，并使用 nCas9-BE3 配置在水稻原生质体中对它们进行了基准测试。在水稻原生质体中筛选出候选者并在转基因水稻品系中进一步验证后，我们发现了一些具有高编辑效率和宽编辑窗口的胞苷脱氨酶。基于这些胞苷脱氨酶的 CBE 还显示出极少的嵌合和 C 到 R（R = A/G）转换频率，表明 C 到 T 碱基编辑的纯度很高。此外，我们还重点介绍了源自虎鲸（Orca）的高效胞苷脱氨酶 OoA3GX2，它在 GC/CC/TC/AC 位点上具有可比的活性，从而扩大了 CBE 的靶向范围，实现了稳健的多重碱基编辑。最后，全基因组测序分析表明，在独立的 T0 株系中，依赖和不依赖 sgRNA 的脱靶效应非常少。这项研究扩展了胞嘧啶碱基编辑工具包，增加了许多来自哺乳动物的胞苷脱氨酶，提供了性能更好的 CBEs，可进一步用于水稻和其他植物物种的复杂基因组工程策略。
{"title":"Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice.","authors":"Danyel Fernandes Contiliani, Simon Sretenovic, Micah Dailey, Man Zhou, Yanhao Cheng, Silvana Creste, Shunyuan Xiao, Yiping Qi","doi":"10.1111/pbi.70000","DOIUrl":"https://doi.org/10.1111/pbi.70000","url":null,"abstract":"<p><p>CRISPR-Cas-based cytosine base editors (CBEs) are prominent tools that perform site-specific and precise C-to-T conversions catalysed by cytidine deaminases. However, their use is often constrained by stringent editing preferences for genomic contexts, off-target effects and restricted editing windows. To expand the repertoire of CBEs, we systematically screened 66 novel cytidine deaminases sourced from various organisms, predominantly from the animal kingdom and benchmarked them in rice protoplasts using the nCas9-BE3 configuration. After selecting candidates in rice protoplasts and further validation in transgenic rice lines, we unveiled a few cytidine deaminases exhibiting high editing efficiencies and wide editing windows. CBEs based on these cytidine deaminases also displayed minimal frequencies of indels and C-to-R (R = A/G) conversions, suggesting high purity in C-to-T base editing. Furthermore, we highlight the highly efficient cytidine deaminase OoA3GX2 derived from Orca (killer whale) for its comparable activity across GC/CC/TC/AC sites, thus broadening the targeting scope of CBEs for robust multiplexed base editing. Finally, the whole-genome sequencing analyses revealed very few sgRNA-dependent and -independent off-target effects in independent T<sub>0</sub> lines. This study expands the cytosine base-editing toolkit with many cytidine deaminases sourced from mammals, providing better-performing CBEs that can be further leveraged for sophisticated genome engineering strategies in rice and likely in other plant species.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412628","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}
Salvia plebeia is an important traditional Chinese medicinal herb, with flavonoids and phenolic acids as its primary bioactive components. However, the absence of a reference genome hinders our understanding of genetic basis underlying the synthesis of these components. Here, we present a high-quality, chromosome-scale genome assembly of S. plebeia, spanning 1.22 Gb, with a contig N50 of 91.72 Mb and 36 861 annotated protein-coding genes. Leveraging the genome data, we identified four catalytic enzymes—one rosmarinic acid synthase (RAS) and three cytochrome P450 monooxygenases (CYP450s) —in S. plebeia, which are involved in rosmarinic acid biosynthesis. We demonstrate that SpRAS catalyses the conjugation of various acyl donors and acceptors, resulting in the formation of rosmarinic acid and its precursor compounds. SpCYP98A75, SpCYP98A77 and SpCYP98A78 catalyse the formation of rosmarinic acid from its precursors at either the C-3 or the C-3′ position. Notably, SpCYP98A75 exhibited a stronger hydroxylation capacity at the C-3′ position, whereas SpCYP98A77 and SpCYP98A78 demonstrate greater hydroxylation efficiency at the C-3 position. Furthermore, SpCYP98A75 hydroxylated both the C-3 and C-3′ positions simultaneously, promoting the conversion of 4-coumaroyl-4′-hydroxyphenyllactic acid to rosmarinic acid. Next, using a hairy root genetic transformation system for S. plebeia, we identified a basic helix–loop–helix protein type transcription factor, SpbHLH54, which positively regulates the biosynthesis of rosmarinic acid and homoplantaginin in S. plebeia. These findings provide a valuable genomic resource for elucidating the mechanisms of rosmarinic acid biosynthesis and its regulation and improve the understanding of evolutionary patterns within the Lamiaceae family.
{"title":"The chromosome-scale assembly of the Salvia plebeia genome provides insight into the biosynthesis and regulation of rosmarinic acid","authors":"Yiqun Dai, Mengqian He, Hui Liu, Huihui Zeng, Kaixuan Wang, Rui Wang, Xiaojing Ma, Yan Zhu, Guoyong Xie, Yucheng Zhao, Minjian Qin","doi":"10.1111/pbi.14601","DOIUrl":"https://doi.org/10.1111/pbi.14601","url":null,"abstract":"<i>Salvia plebeia</i> is an important traditional Chinese medicinal herb, with flavonoids and phenolic acids as its primary bioactive components. However, the absence of a reference genome hinders our understanding of genetic basis underlying the synthesis of these components. Here, we present a high-quality, chromosome-scale genome assembly of <i>S. plebeia</i>, spanning 1.22 Gb, with a contig N50 of 91.72 Mb and 36 861 annotated protein-coding genes. Leveraging the genome data, we identified four catalytic enzymes—one rosmarinic acid synthase (RAS) and three cytochrome P450 monooxygenases (CYP450s) —in <i>S. plebeia</i>, which are involved in rosmarinic acid biosynthesis. We demonstrate that SpRAS catalyses the conjugation of various acyl donors and acceptors, resulting in the formation of rosmarinic acid and its precursor compounds. SpCYP98A75, SpCYP98A77 and SpCYP98A78 catalyse the formation of rosmarinic acid from its precursors at either the C-3 or the C-3′ position. Notably, SpCYP98A75 exhibited a stronger hydroxylation capacity at the C-3′ position, whereas SpCYP98A77 and SpCYP98A78 demonstrate greater hydroxylation efficiency at the C-3 position. Furthermore, SpCYP98A75 hydroxylated both the C-3 and C-3′ positions simultaneously, promoting the conversion of 4-coumaroyl-4′-hydroxyphenyllactic acid to rosmarinic acid. Next, using a hairy root genetic transformation system for <i>S. plebeia</i>, we identified a basic helix–loop–helix protein type transcription factor, <i>SpbHLH54</i>, which positively regulates the biosynthesis of rosmarinic acid and homoplantaginin in <i>S. plebeia</i>. These findings provide a valuable genomic resource for elucidating the mechanisms of rosmarinic acid biosynthesis and its regulation and improve the understanding of evolutionary patterns within the Lamiaceae family.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"519 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401613","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}
Jinjing Wang, Xiaoyan Yang, Lijun Fan, Haojie Ye, Gefei Hao, Peiyi Wang
SummaryAbiotic stress severely hinders plant growth and development, resulting in a considerable reduction in crop yields. Salicylic acid (SA) serves as a central signal mediating abiotic stress responses in plants. Real‐time fluorescence tracking using specific probes can enhance our understanding of the SA‐triggered modulation underlying these events. However, in complicated living plant microenvironments, selective recognition and bioimaging of SA is a great challenge for scientists due to the severe background interference and SA analogues. Herein, an efficient fluorescence probing technology employing a highly selective rhodamine probe—phoxrodam was developed, which realizes the precise bioimaging of SA in salt‐stressed plant seedlings. Experimental findings reveal that phoxrodam demonstrates exceptional selectivity (fluorescence intensity: IPhoxrodam+SA/IPhoxrodam+SA analogues > 4.29‐fold), high sensitivity (limit of detection = 6.42 nM, fluorescence quantum yield: ΦPhoxrodam+SA = 0.36) and good anti‐interference properties. Furthermore, we confirmed that phoxrodam accurately detects SA in the roots of salt‐stressed wheat seedlings, the low‐temperature resistance of Nicotiana benthamiana and the heavy metal resistance of pea seeds, using in vivo confocal imaging. This study provides a feasible strategy for efficiently tracking plant signalling molecules and promotes the in‐depth research of SA‐mediated physiological mechanisms, laying a key foundation for the future development of new immune activation inducers.
{"title":"The rational design of a Rhodamine fluorescent probe enables the selective detection and bioimaging of salicylic acid in plants under abiotic stress","authors":"Jinjing Wang, Xiaoyan Yang, Lijun Fan, Haojie Ye, Gefei Hao, Peiyi Wang","doi":"10.1111/pbi.70003","DOIUrl":"https://doi.org/10.1111/pbi.70003","url":null,"abstract":"SummaryAbiotic stress severely hinders plant growth and development, resulting in a considerable reduction in crop yields. Salicylic acid (SA) serves as a central signal mediating abiotic stress responses in plants. Real‐time fluorescence tracking using specific probes can enhance our understanding of the SA‐triggered modulation underlying these events. However, in complicated living plant microenvironments, selective recognition and bioimaging of SA is a great challenge for scientists due to the severe background interference and SA analogues. Herein, an efficient fluorescence probing technology employing a highly selective rhodamine probe—phoxrodam was developed, which realizes the precise bioimaging of SA in salt‐stressed plant seedlings. Experimental findings reveal that phoxrodam demonstrates exceptional selectivity (fluorescence intensity: <jats:italic>I</jats:italic><jats:sub>Phoxrodam+SA</jats:sub>/<jats:italic>I</jats:italic><jats:sub>Phoxrodam+SA analogues</jats:sub> > 4.29‐fold), high sensitivity (limit of detection = 6.42 nM, fluorescence quantum yield: Φ<jats:sub>Phoxrodam+SA</jats:sub> = 0.36) and good anti‐interference properties. Furthermore, we confirmed that phoxrodam accurately detects SA in the roots of salt‐stressed wheat seedlings, the low‐temperature resistance of <jats:italic>Nicotiana benthamiana</jats:italic> and the heavy metal resistance of pea seeds, using <jats:italic>in vivo</jats:italic> confocal imaging. This study provides a feasible strategy for efficiently tracking plant signalling molecules and promotes the in‐depth research of SA‐mediated physiological mechanisms, laying a key foundation for the future development of new immune activation inducers.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"13 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401574","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 integration of haploid induction and genome editing, termed HI-Edit/IMGE, is a promising tool for generating targeted mutations for crop breeding. However, the technical components and stacking suitable for the maize seed industry have yet to be fully characterised and tested. Here, we developed and assessed three HI-Edit/IMGE maize lines: EditWx, EditSh, and EditWx&Sh, using the haploid inducer CHOI3 and lines engineered using the CRISPR-Cas9 system targeting the Waxy1 (Wx1) and Shrunken2 (Sh2) genes. We meticulously characterised the HI-Edit/IMGE systems, focusing on copy numbers and the mutant alleles mtl and dmp, which facilitate haploid induction. Using B73 and six other parental lines of major commercial varieties as recipients, HI-Edit/IMGE demonstrated maternal haploid induction efficiencies ranging from 8.55% to 20.89% and targeted mutation rates between 0.38% and 1.46%. Comprehensive assessment verified the haploid identification, target gene editing accuracy, genome background integrity, and related agronomic traits. Notably, EditWx&Sh successfully combined distinct CRISPR-Cas9 systems to induce multiple desired mutations, highlighting the potential of HI-Edit/IMGE in accelerating the integration of edited traits into commercial maize varieties. Our findings underscore the importance of meticulous Cas9 copy number characterisation and highlight potential challenges related to somatic chimerism. We also validated the performance of single-cross haploids derived using the HI-Edit/IMGE process. Our results confirm the industrial applicability of generating targeted mutations through pollination and provide critical insights for further optimising this technology.
{"title":"Harnessing haploid-inducer mediated genome editing for accelerated maize variety development","authors":"Lina Li, Xiao Fu, Xiantao Qi, Bing Xiao, Changling Liu, Qingyu Wu, Jinjie Zhu, Chuanxiao Xie","doi":"10.1111/pbi.14608","DOIUrl":"https://doi.org/10.1111/pbi.14608","url":null,"abstract":"The integration of haploid induction and genome editing, termed HI-Edit/IMGE, is a promising tool for generating targeted mutations for crop breeding. However, the technical components and stacking suitable for the maize seed industry have yet to be fully characterised and tested. Here, we developed and assessed three HI-Edit/IMGE maize lines: Edit<sup><i>Wx</i></sup>, Edit<sup><i>Sh</i></sup>, and Edit<sup><i>Wx</i>&<i>Sh</i></sup>, using the haploid inducer CHOI3 and lines engineered using the CRISPR-Cas9 system targeting the <i>Waxy1</i> (<i>Wx1</i>) and <i>Shrunken2</i> (<i>Sh2</i>) genes. We meticulously characterised the HI-Edit/IMGE systems, focusing on copy numbers and the mutant alleles <i>mtl</i> and <i>dmp</i>, which facilitate haploid induction. Using B73 and six other parental lines of major commercial varieties as recipients, HI-Edit/IMGE demonstrated maternal haploid induction efficiencies ranging from 8.55% to 20.89% and targeted mutation rates between 0.38% and 1.46%. Comprehensive assessment verified the haploid identification, target gene editing accuracy, genome background integrity, and related agronomic traits. Notably, Edit<sup><i>Wx</i>&<i>Sh</i></sup> successfully combined distinct CRISPR-Cas9 systems to induce multiple desired mutations, highlighting the potential of HI-Edit/IMGE in accelerating the integration of edited traits into commercial maize varieties. Our findings underscore the importance of meticulous <i>Cas9</i> copy number characterisation and highlight potential challenges related to somatic chimerism. We also validated the performance of single-cross haploids derived using the HI-Edit/IMGE process. Our results confirm the industrial applicability of generating targeted mutations through pollination and provide critical insights for further optimising this technology.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"65 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393422","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}
Adenosine 5′-triphosphate (ATP) is the energy currency of living organisms and the primary form of organic phosphate (Po) involved in cellular metabolism. In plants, some ATP is released into the extracellular matrix (ECM) in response to various stimuli, where it functions as extracellular ATP (eATP), a key signalling molecule. Recent advances have shed light on the mechanisms of eATP signalling in plants. This review consolidates these findings, beginning with the role of eATP in regulating plant growth, development and responses to biotic and abiotic stresses. It further summarizes the pathways of eATP accumulation and degradation in the ECM and introduces the cellular signalling pathways mediating eATP responses, as reported in key studies. Finally, perspectives on future research directions in this field are presented.
{"title":"Extracellular ATP: an emerging multifaceted regulator of plant fitness","authors":"De Peng Yuan, Daewon Kim, Yuan Hu Xuan","doi":"10.1111/pbi.70006","DOIUrl":"https://doi.org/10.1111/pbi.70006","url":null,"abstract":"Adenosine 5′-triphosphate (ATP) is the energy currency of living organisms and the primary form of organic phosphate (Po) involved in cellular metabolism. In plants, some ATP is released into the extracellular matrix (ECM) in response to various stimuli, where it functions as extracellular ATP (eATP), a key signalling molecule. Recent advances have shed light on the mechanisms of eATP signalling in plants. This review consolidates these findings, beginning with the role of eATP in regulating plant growth, development and responses to biotic and abiotic stresses. It further summarizes the pathways of eATP accumulation and degradation in the ECM and introduces the cellular signalling pathways mediating eATP responses, as reported in key studies. Finally, perspectives on future research directions in this field are presented.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"129 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393424","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}
Linalool not only is one of characteristic flavour volatiles of tea, contributing to floral aroma, but also a kind of defensive compounds, playing essential roles in resistance against biotic/abiotic stresses. Although the linalool synthases have been identified, much is unknown about the regulation mechanism in tea plants. We identified two pairs of MYB paralogs as linalool biosynthesis activators, in which one pair (CsMYB148/CsMYB193) specifically expressed in flowers, and another (CsMYB68/CsMYB147) highly expressed in flowers, leaves, fruits and roots. These activators interacted with CsMYC2 to form MYC2-MYB complexes to regulate linalool synthase. While Jasmonate ZIM-domain (JAZ) proteins served as the linalool biosynthesis repressors by interfering MYC2-MYB complex. Further, we found that the transcripts of CsMYB68/CsMYB147 were significantly upregulated by jasmonic acid (JA) to improve linalool products during tea processing and that linalool pathway may as one of the downstream pathways of JA signalling and DNA methylation processes to participate in cold resistance. Under cold stress, JA signalling was activated to elevate the abundance of MYC-MYB complexes; meanwhile, DNA demethylation was also activated, leading to declining methylation levels and increasing transcripts of CsMYB68/CsMYB147. Our study provides a new insight into synergistically improving tea quality and tea plant resistance.
{"title":"Divergent MYB paralogs determine spatial distribution of linalool mediated by JA and DNA demethylation participating in aroma formation and cold tolerance of tea plants","authors":"Rui Yue, Yaling Li, Yujia Qi, Xiaoyu Liang, Ziqing Zheng, Zhili Ye, Wei Tong, Xiongyuan Si, Yanrui Zhang, Enhua Xia, Penghui Li","doi":"10.1111/pbi.14598","DOIUrl":"https://doi.org/10.1111/pbi.14598","url":null,"abstract":"Linalool not only is one of characteristic flavour volatiles of tea, contributing to floral aroma, but also a kind of defensive compounds, playing essential roles in resistance against biotic/abiotic stresses. Although the <i>linalool synthases</i> have been identified, much is unknown about the regulation mechanism in tea plants. We identified two pairs of MYB paralogs as linalool biosynthesis activators, in which one pair (CsMYB148/CsMYB193) specifically expressed in flowers, and another (CsMYB68/CsMYB147) highly expressed in flowers, leaves, fruits and roots. These activators interacted with CsMYC2 to form MYC2-MYB complexes to regulate <i>linalool synthase</i>. While Jasmonate ZIM-domain (JAZ) proteins served as the linalool biosynthesis repressors by interfering MYC2-MYB complex. Further, we found that the transcripts of <i>CsMYB68</i>/<i>CsMYB147</i> were significantly upregulated by jasmonic acid (JA) to improve linalool products during tea processing and that linalool pathway may as one of the downstream pathways of JA signalling and DNA methylation processes to participate in cold resistance. Under cold stress, JA signalling was activated to elevate the abundance of MYC-MYB complexes; meanwhile, DNA demethylation was also activated, leading to declining methylation levels and increasing transcripts of <i>CsMYB68</i>/<i>CsMYB147</i>. Our study provides a new insight into synergistically improving tea quality and tea plant resistance.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"41 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385834","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}
Haoyu Chen, Yetong Qi, Yong Wang, Jie Liu, Ruirui Lu, Xinhui Zhao, Ruiyu Chen, Yueji Wang, Lei Zhu, Shouru Sun, Jianbin Hu, Luming Yang, Guanghui An
Lettuce is one of the most important vegetables worldwide. Bolting time is an important agronomic trait in lettuce production. Premature bolting reduces crop quality and marketability. Here, we genetically clone the LsBLH2 gene controlling bolting time in lettuce. LsBLH2 encodes a BEL1-like homeodomain protein. In the late bolting parent, the LsBLH2 had a 1-bp deletion in exon 1 which leads to a premature stop codon. CRISPR/cas9 knocking out and complementary tests showed that the loss-of-function of LsBLH2 delays bolting in lettuce. ChIP-seq, gene expression and phytohormone analysis showed that LsBLH2 regulates the gibberellin (GA) biosynthesis and metabolism. LsBLH2 binds to the promoter of the LsGA20ox1 and LsGA2ox8 and regulates their expression, leading to the bioactive GA accumulation during the vegetative-to-reproductive phase transition. Both LsOFP6 and LsKNAT3 interact with LsBLH2 and regulate bolting in a LsBLH2-dependent manner. LsOFP6 promotes, while LsKNAT3 suppresses the effects of LsBLH2 on GA biosynthesis during the transition and rosette stage in lettuce, respectively. In summary, the LsBLH2–LsOFP6–LsKANT3 module orchestrates bioactive GA accumulation to regulate bolting in lettuce, which provides insight into the bolting development process and offers new approaches for lettuce breeding to prevent premature bolting.
{"title":"LsBLH2–LsOFP6–LsKANT3 module regulates bolting by orchestrating the gibberellin biosynthesis and metabolism in lettuce","authors":"Haoyu Chen, Yetong Qi, Yong Wang, Jie Liu, Ruirui Lu, Xinhui Zhao, Ruiyu Chen, Yueji Wang, Lei Zhu, Shouru Sun, Jianbin Hu, Luming Yang, Guanghui An","doi":"10.1111/pbi.14614","DOIUrl":"https://doi.org/10.1111/pbi.14614","url":null,"abstract":"Lettuce is one of the most important vegetables worldwide. Bolting time is an important agronomic trait in lettuce production. Premature bolting reduces crop quality and marketability. Here, we genetically clone the <i>LsBLH2</i> gene controlling bolting time in lettuce. <i>LsBLH2</i> encodes a BEL1-like homeodomain protein. In the late bolting parent, the <i>LsBLH2</i> had a 1-bp deletion in exon 1 which leads to a premature stop codon. CRISPR/cas9 knocking out and complementary tests showed that the loss-of-function of <i>LsBLH2</i> delays bolting in lettuce. ChIP-seq, gene expression and phytohormone analysis showed that <i>LsBLH2</i> regulates the gibberellin (GA) biosynthesis and metabolism. LsBLH2 binds to the promoter of the <i>LsGA20ox1</i> and <i>LsGA2ox8</i> and regulates their expression, leading to the bioactive GA accumulation during the vegetative-to-reproductive phase transition. Both LsOFP6 and LsKNAT3 interact with LsBLH2 and regulate bolting in a LsBLH2-dependent manner. LsOFP6 promotes, while LsKNAT3 suppresses the effects of LsBLH2 on GA biosynthesis during the transition and rosette stage in lettuce, respectively. In summary, the LsBLH2–LsOFP6–LsKANT3 module orchestrates bioactive GA accumulation to regulate bolting in lettuce, which provides insight into the bolting development process and offers new approaches for lettuce breeding to prevent premature bolting.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"160 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385835","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}
Yan Yao, Fangfang Chen, Chaoyan Wu, Xiaosa Chang, Weijia Cheng, Qiuxia Wang, Zixin Deng, Tiangang Liu, Li Lu
Glycosylation plays an important role in the structural diversification of plant natural products. The identification of efficient glycosyltransferases is also a crucial step for the biosynthesis of valuable glycoside products. However, functional characterization of glycosyltransferases (GTs) from an extensive plant gene list is labour-intensive and challenging. Salidroside is a bioactive component derived from plants, widely utilized in the fields of food and medicine. Here, through transcriptome analysis and structure-based virtual screening, we identified two GTs that participated in the biosynthesis of salidroside from a rarely studied herbaceous plant, Astilbe chinensis. Ach15909 was found to possess high catalytic activity as evidenced by the determination of its catalytic parameters. The key residues that determine its catalytic activity were further determined. Additionally, Ach15909 shows a preference for substrates with a volume of <150 Å3, and replacing the interdomain linker region located between the N- and C-terminal domains of Ach15909 allows it to accept substrates that were previously not catalyzable. Overall, the structure-based virtual screening approach showed high efficiency and cost-effectiveness; the successful identification of GTs in salidroside glycosylation sheds light on uncovering additional plant biosynthesis enzymes in the forthcoming research.
{"title":"Structure-based virtual screening aids the identification of glycosyltransferases in the biosynthesis of salidroside","authors":"Yan Yao, Fangfang Chen, Chaoyan Wu, Xiaosa Chang, Weijia Cheng, Qiuxia Wang, Zixin Deng, Tiangang Liu, Li Lu","doi":"10.1111/pbi.70002","DOIUrl":"https://doi.org/10.1111/pbi.70002","url":null,"abstract":"Glycosylation plays an important role in the structural diversification of plant natural products. The identification of efficient glycosyltransferases is also a crucial step for the biosynthesis of valuable glycoside products. However, functional characterization of glycosyltransferases (GTs) from an extensive plant gene list is labour-intensive and challenging. Salidroside is a bioactive component derived from plants, widely utilized in the fields of food and medicine. Here, through transcriptome analysis and structure-based virtual screening, we identified two GTs that participated in the biosynthesis of salidroside from a rarely studied herbaceous plant, <i>Astilbe chinensis</i>. Ach15909 was found to possess high catalytic activity as evidenced by the determination of its catalytic parameters. The key residues that determine its catalytic activity were further determined. Additionally, Ach15909 shows a preference for substrates with a volume of <150 Å<sup>3</sup>, and replacing the interdomain linker region located between the N- and C-terminal domains of Ach15909 allows it to accept substrates that were previously not catalyzable. Overall, the structure-based virtual screening approach showed high efficiency and cost-effectiveness; the successful identification of GTs in salidroside glycosylation sheds light on uncovering additional plant biosynthesis enzymes in the forthcoming research.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"10 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385833","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}
Transgene-free genome editing is important for crop improvement as it reduces unanticipated genomic changes. While mRNA delivery systems offer a powerful method for achieving transgene-free genome editing, they remain inefficient and challenging in plants. Here we describe an efficient mRNA delivery system for plants with substantially improved editing efficiency. By optimizing the 5′ untranslated regions (5′UTRs) and poly(A) tails of in vitro-transcribed (IVT) mRNAs and coating the mRNA with protamine during particle bombardment, we have developed an optimized mRNA delivery system termed v2_TMV/DEN2. This system enhanced the efficiencies of knock-out, A-to-G and C-to-T base editing by an average 4.7-, 3.4- and 2.5-fold at various endogenous sites compared with plasmid-based transient delivery system via particle bombardment in rice suspension cells and wheat immature embryos 48 h post-transformation. Furthermore, we obtained edited plants with efficiencies of 5.0–180.8% and 26.1–26.2% using v2_TMV/DEN2 in rice and wheat, respectively, compared with 0.0–43.2% and 4.7–10.4% using plasmids. Our study provides a convenient and efficient mRNA delivery system for transgene-free genome editing in plants.
{"title":"An efficient mRNA delivery system for genome editing in plants","authors":"Fengti Qiu, Chenxiao Xue, Jinxing Liu, Boshu Li, Qiang Gao, Ronghong Liang, Kunling Chen, Caixia Gao","doi":"10.1111/pbi.14591","DOIUrl":"https://doi.org/10.1111/pbi.14591","url":null,"abstract":"Transgene-free genome editing is important for crop improvement as it reduces unanticipated genomic changes. While mRNA delivery systems offer a powerful method for achieving transgene-free genome editing, they remain inefficient and challenging in plants. Here we describe an efficient mRNA delivery system for plants with substantially improved editing efficiency. By optimizing the 5′ untranslated regions (5′UTRs) and poly(A) tails of <i>in vitro</i>-transcribed (IVT) mRNAs and coating the mRNA with protamine during particle bombardment, we have developed an optimized mRNA delivery system termed v2_TMV/DEN2. This system enhanced the efficiencies of knock-out, A-to-G and C-to-T base editing by an average 4.7-, 3.4- and 2.5-fold at various endogenous sites compared with plasmid-based transient delivery system via particle bombardment in rice suspension cells and wheat immature embryos 48 h post-transformation. Furthermore, we obtained edited plants with efficiencies of 5.0–180.8% and 26.1–26.2% using v2_TMV/DEN2 in rice and wheat, respectively, compared with 0.0–43.2% and 4.7–10.4% using plasmids. Our study provides a convenient and efficient mRNA delivery system for transgene-free genome editing in plants.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"15 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375471","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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