Plant Biotechnology Journal最新文献

{"title":"A plant viral effector subverts FER‐RALF1 module‐mediated intracellular immunity","authors":"Penghuan Rui, Zhaoxing Jia, Xinxin Fang, Tianqi Yu, Wenqi Mao, Jiajia Lin, Hongying Zheng, Yuwen Lu, Feng Yu, Jianping Chen, Fei Yan, Guanwei Wu","doi":"10.1111/pbi.70099","DOIUrl":"https://doi.org/10.1111/pbi.70099","url":null,"abstract":"SummaryThe receptor‐like kinase FERONIA (FER) is a prominent member of the <jats:italic>Catharanthus roseus</jats:italic> RLK1 (CrRLK1L) family, functioning as a modulator of immune receptor kinase complex formation in response to rapid alkalinization factors (RALFs). Typically, FER recognizes mature extracellular RALFs to combat bacterial and fungal infections. However, any role of the FER‐RALF signalling cascade in plant viral infections remains unexplored. Here, we used turnip mosaic virus (TuMV), an important member of the genus <jats:italic>Potyvirus</jats:italic>, and the host <jats:italic>Nicotiana benthamiana</jats:italic> as a model system to explore the role of the FER‐RALF cascade in plant–virus interactions. RALF1 from <jats:italic>N. benthamiana</jats:italic> (NbRALF1) positively regulated host resistance to inhibit TuMV infection. Co‐expression studies showed that this process does not involve the conserved RRXL and YISY motifs typically associated with RALF function. Instead, NbRALF1 induced cell death and significantly inhibited TuMV infection in a manner that depends on the entire RALF1 sequence and also NbFER. These results suggest a novel mechanism where NbRALF1 may inhibit viral infection through intracellular interactions with NbFER, differing from the previously reported extracellular FER‐RALF interactions that induce resistance to fungi and bacteria. Furthermore, we discovered that TuMV 6K2 interacts with NbRALF1 and promotes its degradation through the 26S proteasome pathway, thereby counteracting the host resistance induced by the NbFER‐NbRALF1 cascade. Our findings imply the existence of an uncharacterized intracellular immunity signalling pathway mediated by the NbFER‐NbRALF1 cascade and reveal a mechanism by which plant viruses counteract RALF1‐FER module‐mediated immunity.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"125 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851009","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}

{"title":"Expression of mannanase and glucanases in lettuce chloroplasts and functional evaluation of enzyme cocktail against Candida albicans in oral cancer patient samples","authors":"Iqra Fatima, Geetanjali Wakade, Henry Daniell","doi":"10.1111/pbi.70046","DOIUrl":"https://doi.org/10.1111/pbi.70046","url":null,"abstract":"<i>Candida albicans</i> is a human pathogen responsible for several diseases. <i>C. albicans</i> cell wall contains chitin, glucan and mannan. Therefore, this study evaluated efficacy of enzyme cocktail containing lettuce-expressed chitinases, glucanases and mannanase against <i>C. albicans</i> in cell culture or cancer patient samples. Site-specific integration of the Man1, CelO, Cbh1, Cbh2 expression cassettes and removal of the selectable marker gene from lettuce transplastome was confirmed using three sets of PCR primers. Homoplasmy in transplastomic lines was confirmed in Southern blots by the absence of untransformed genomes. Unlike tobacco, lettuce transplastomic lines had no mosaic phenotype and yielded more biomass than untransformed plants. Maternal inheritance of transgenes was confirmed by lack of segregation when seedlings were germinated in the selection medium. Mannanase expressed in lettuce chloroplasts is thermostable, exhibiting the highest activity at 70 °C; expression increased up to 70 days of growth and is active in a broad range of pH (5–8). Endoglucanases and exoglucanases expressed in lettuce chloroplasts have a broad range of activities between 30 and 75 °C and pH 4–8. Based on observed biomass and mannanase expression level, up to 8640 million enzyme units could be harvested per acre/year. The enzyme cocktail effectively degraded the fungal cell wall, significantly reducing <i>C. albicans</i> viability in cultures and complete inhibition in oral cancer patient samples. Beyond biomedical applications of antifungal drugs, plant cell-based enzyme market is anticipated to double from $52 to &gt;$100 billion in 2028. Edible leaf-based enzyme production offers a new platform that is different from seed-based current technologies for various biotechnology applications.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"37 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849403","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}

{"title":"Identification of HSSP1 as a regulator of soybean protein content through QTL analysis and Soy-SPCC network","authors":"Huilin Tian, Yanbin Yin, Xin Li, Zhanguo Zhang, Shaowei Feng, Song Jin, Xue Han, Mingliang Yang, Chang Xu, Limin Hu, Chunyan Liu, Fanjiang Kong, Qingshan Chen, Zhaoming Qi","doi":"10.1111/pbi.70092","DOIUrl":"https://doi.org/10.1111/pbi.70092","url":null,"abstract":"Soybeans (<i>Glycine max</i> L. Merr.) are a major source of plant-based protein for human nutrition and livestock feed. Enhancing the protein content of soybean seeds is vital for meeting growing dietary needs and promoting sustainable agricultural practices. In this study, we first performed QTL (Quantitative Trait Loci) mapping analysis and constructed a Soybean Seed Protein Content Co-expression (Soy-SPCC) network to identify key genes associated with soybean seed protein accumulation. Next, we investigated the role of <i>High Seed Storage Protein1</i> (<i>HSSP1</i>) in regulating soybean seed protein content through a comprehensive analysis. Functional validation through overexpression and gene knockout experiments demonstrated that <i>HSSP1</i>, a key component of the Soy-SPCC network, significantly influences seed storage protein levels. Particularly, HSSP1 enhances the expression of <i>GmCG1</i> by binding directly to its cis-acting element, leading to increased protein content in soybean seeds. Furthermore, we performed a molecular module stacking breeding analysis of 120 candidate genes identified from the Soy-SPCC network, including <i>HSSP1</i>, to identify genetic variations associated with protein content. This study provides a novel perspective on soybean protein regulation. The identification of <i>HSSP1</i> as a critical regulator offers valuable insights for developing high-protein soybean varieties and advancing breeding strategies aimed at improving soybean seed quality.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"10 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849402","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}

{"title":"Resolving floral development dynamics using genome and single-cell temporal transcriptome of Dendrobium devonianum","authors":"Jing Wang, Ying Zhou, Manchang Zhang, Xinping Li, Tingxia Liu, Yinglin Liu, He Xie, Kaiying Wang, Peng Li, Zhichao Xu, Baozhong Duan","doi":"10.1111/pbi.70094","DOIUrl":"https://doi.org/10.1111/pbi.70094","url":null,"abstract":"<i>Dendrobium devonianum</i>, a species of the Orchidaceae family, is notable for its unique floral characteristics, which include two yellow spots and purple tips on its labellum, as well as fringed edges. However, the molecular mechanisms underlying flower pattern formation in <i>D. devonianum</i> remain poorly understood, hindering advancements in its breeding process. Here, a chromosome-scale genome of <i>D. devonianum</i> was presented for the first time, revealing two significant polyploidization events. Additionally, a high-resolution single-cell transcriptomic atlas was constructed, capturing 11 distinct cell clusters. Expression patterns of MADS-box genes were identified through temporal and spatial bulk RNA-Seq, revealing alignment with the ABCDE model of flower formation. Meanwhile, mass spectrometry imaging and scRNA analyses showed that the yellow spots were primarily associated with carotenoid biosynthesis gene expression, while the purple colour is predominantly linked to anthocyanin biosynthesis gene expression. These genes were mainly expressed in the epidermis and vascular cells. Developmental trajectory analyses of epidermal cells further uncovered a gene regulatory network and several transcription factors likely responsible for fringes formation along the labellum margin. This study provides valuable insights into the molecular mechanisms driving floral colour differentiation and structural traits in <i>D. devonianum</i>, contributing to a deeper understanding of orchid evolution, diversification and breeding.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"7 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837091","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}

{"title":"Identification and overexpression of RNA-decapping protein GhLSM1BS: Enhancing cotton somatic embryogenesis through up-regulating brassinosteroid biosynthesis","authors":"Zheng Yang, Jie He, Shuqian Yao, Xuxin Li, Chang Du, Juwu Gong, Haoliang Yan, Yanpeng Zhao, Yang Li, Youlu Yuan, Haihong Shang","doi":"10.1111/pbi.70090","DOIUrl":"https://doi.org/10.1111/pbi.70090","url":null,"abstract":"We identified two splicing variants of <i>GhLSM1B</i> (<i>GhLSM1BS</i> and <i>GhLSM1BL</i>) with distinct expression patterns and predicted 3D structures, despite sharing the same nuclear localization. Overexpression of <i>GhLSM1BS</i>, but not <i>GhLSM1BL</i>, accelerated cotton callus proliferation and altered cell morphology during somatic embryogenesis, accompanied by altered expression of <i>CYP450</i> family genes and elevated brassinosteroid levels.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"26 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831995","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}

{"title":"Modification of TAWAWA1-mediated panicle architecture by genome editing of a downstream conserved noncoding sequence in rice","authors":"Takeshi Kuroha, Fabien Lombardo, Watal M. Iwasaki, Svetlana Chechetka, Yoshihiro Kawahara, Akiko Yoshida, Takashi Makino, Hitoshi Yoshida","doi":"10.1111/pbi.70043","DOIUrl":"https://doi.org/10.1111/pbi.70043","url":null,"abstract":"&lt;p&gt;Genome editing has significantly advanced in recent years, with numerous attempts to integrate it into crop breeding (Gao, &lt;span&gt;2021&lt;/span&gt;). Many useful agronomic traits result from subtle changes in gene expression patterns conferred by natural variations (Olsen and Wendel, &lt;span&gt;2013&lt;/span&gt;). Therefore, the modification of regulatory sequences through genome editing presents a potential strategy to develop practical breeding resources. Promoters and &lt;i&gt;cis&lt;/i&gt;-regulatory elements (CREs) of several target genes have been extensively edited to alter their expression patterns in many crop species including tomato (Rodriguez-Leal &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;) and rice (Zhou &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;). However, such approaches require numerous genome edits across a wide range of promoter regions or rely on molecular genetic evidence for responsible CREs. Identifying optimal genome-editing target sites within large genome regions to improve desirable agronomic traits remains challenging. Here, we describe creation of quantitative trait variations in panicle branching by precise genome editing of a conserved noncoding sequence (CNS) (Freeling and Subramaniam, &lt;span&gt;2009&lt;/span&gt;) located downstream of the rice yield-related gene &lt;i&gt;TAWAWA1&lt;/i&gt; (&lt;i&gt;TAW1&lt;/i&gt;) (Yoshida &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2013&lt;/span&gt;) and demonstrate the potential of CNSs as targets for genome editing to fine-tune agronomic traits.&lt;/p&gt;\u0000&lt;p&gt;&lt;i&gt;TAW1&lt;/i&gt; is a member of the ALOG (&lt;i&gt;&lt;span style=\"text-decoration:underline\"&gt;A&lt;/span&gt;rabidopsis&lt;/i&gt; &lt;span style=\"text-decoration:underline\"&gt;L&lt;/span&gt;SH1 and &lt;i&gt;&lt;span style=\"text-decoration:underline\"&gt;O&lt;/span&gt;ryza&lt;/i&gt; &lt;span style=\"text-decoration:underline\"&gt;G&lt;/span&gt;1) gene family encoding putative transcriptional regulators. In grass species, ALOG family proteins are essential for specification of floral organ identity and the normal development of spikelet and inflorescence architecture (Jiang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;; Yoshida &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2013&lt;/span&gt;). In a screen of a transposon-mutagenized rice population, Yoshida &lt;i&gt;et al&lt;/i&gt;. (&lt;span&gt;2013&lt;/span&gt;) isolated two allelic mutants, &lt;i&gt;taw1&lt;/i&gt;-&lt;i&gt;D1&lt;/i&gt; and &lt;i&gt;taw1&lt;/i&gt;-&lt;i&gt;D2&lt;/i&gt; exhibiting elevated &lt;i&gt;TAW1&lt;/i&gt; expression and increased panicle branching. Both mutants carried &lt;i&gt;nDart1&lt;/i&gt;-&lt;i&gt;0&lt;/i&gt; transposons inserted approximately 0.9 kb downstream from the stop codon of &lt;i&gt;TAW1&lt;/i&gt; (Figure 1a) (Yoshida &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2013&lt;/span&gt;). Given the high conservation of genes governing inflorescence architecture across grass species, we hypothesized that conserved regulatory sequences would be located near the &lt;i&gt;taw1-D1&lt;/i&gt;/&lt;i&gt;-D2&lt;/i&gt; insertion sites in these species. We first identified &lt;i&gt;TAW1&lt;/i&gt; homologues in monocot species (Table S1; Figure S1), and then compared their genomic sequences (Figure 1a). We identified a CNS (hereafter, &lt;i&gt;TAW1&lt;/i&gt;-CNS) in grass species, including the BEP clade, within 50 bp downstream of the transposon insertion sites in &lt;i&gt;taw1-D1&lt;/i&gt;/-&lt;i","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"27 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827209","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}

{"title":"The IQ67‐domain protein IQD1 regulates fruit shape through complex multiprotein interactions in pepper (Capsicum annuum L.)","authors":"Lianzhen Mao, Yiyu Shen, Qingzhi Cui, Yu Huang, Xiang Zhang, Junheng Lv, Wujun Xing, Dan Zhang, Naying Fang, Daqing Chen, Zhuoxuan Wu, Peiru Li, Minghua Deng, Lijun Ou, Xuexiao Zou, Zhoubin Liu","doi":"10.1111/pbi.70078","DOIUrl":"https://doi.org/10.1111/pbi.70078","url":null,"abstract":"SummaryNatural genetic variation can be used to improve important crop agronomic traits, and understanding the genetic basis of natural variation in fruit shape can help breeders develop pepper varieties that meet market demand. In this study, we identified a QTL controlling fruit length–width ratio by conventional genetic mapping, encoding a previously uncharacterized gene <jats:italic>CaIQD1</jats:italic>. Reduced <jats:italic>CaIQD1 expression</jats:italic> resulted in short and wide fruits in pepper, whereas heterologous overexpression of <jats:italic>CaIQD1</jats:italic> resulted in narrower fruits in tomato. Further experiments suggested that <jats:italic>CaIQD1</jats:italic> regulates fruit shape in pepper by affecting cell proliferation, expansion and morphological changes. CaIQD1 also has a direct protein interaction with CaOFP20 in CaTRM‐like‐CaOFP20. Reduced <jats:italic>CaOFP20 expression</jats:italic> caused pepper fruits to become elongated and curved, whereas reduced <jats:italic>CaTRM‐like</jats:italic> expression led to the formation of rounder fruits. These gene expression changes had a significant effect on the expression of genes related to the cell cycle and cell expansion. The CaTRM‐like‐CaOFP20‐CaIQD1 module may thus represent a conserved regulatory pathway for controlling pepper fruit shape. CaIQD1 also showed direct interactions with the pepper calmodulin CaCaM7, the tubulin CaMAP70‐2 and the microtubule motor protein CaKLCR1, suggesting that the regulation of fruit shape by CaIQD1 is related to changes in microtubule dynamics mediated by Ca<jats:sup>2+</jats:sup>‐CaM. We also found that CaIQD1 interacts with several homologues of genes that typically regulate fruit shape in other plant species. In summary, our results show that CaIQD1 acts as a core hub in regulating pepper fruit shape through interactions with multiple proteins.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"42 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822719","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}

{"title":"Editing of an antiviral host factor boosts plant growth and yield of plant viral vector‐mediated heterologous protein expression","authors":"Zhu Fang, Xinru Zhao, Min Du, Xinyi Xu, Hui Zhou, Wei Guo, Xueping Zhou, Xiuling Yang","doi":"10.1111/pbi.70089","DOIUrl":"https://doi.org/10.1111/pbi.70089","url":null,"abstract":"","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"101 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822721","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}

{"title":"DinoSource: A comprehensive database of dinoflagellate genomic resources","authors":"Fuming Lai, Chongping Li, Yidong Zhang, Ying Li, Yuci Wang, Qiangwei Zhou, Yaping Fang, Hao Chen, Guoliang Li","doi":"10.1111/pbi.70054","DOIUrl":"https://doi.org/10.1111/pbi.70054","url":null,"abstract":"&lt;p&gt;Dinoflagellates are a taxonomically diverse and ecologically significant group of phytoplankton. They are also infamous for their involvement in harmful algal blooms, which have significant ecological and economic impacts. In recent years, substantial advances have been made in the analysis of dinoflagellate genomes, including sequencing, assembly and gene annotation, alongside the accumulation of extensive multi-omics data (González-Pech &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2021&lt;/span&gt;). Despite these developments, the large size and complexity of dinoflagellate genomes present ongoing challenges. Current resources, such as SAGER, primarily focus on genomic and transcriptomic data sets for &lt;i&gt;Symbiodiniaceae&lt;/i&gt; (Yu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;).&lt;/p&gt;\u0000&lt;p&gt;In this study, we have developed the first high-precision and comprehensive genome resource database for dinoflagellates, DinoSource (http://glab.hzau.edu.cn/dinosource), which provides 21 genome assemblies for all 20 currently sequenced dinoflagellate species (including two strains of &lt;i&gt;Polarella glacialis&lt;/i&gt;) (Table S1). Our database integrates 703 omics samples, which have been generated from our experiments as well as collected from public repositories such as GEO (Gene Expression Omnibus) and SRA (Sequence Read Archive) up to the present date (Figure 1a). The sources and species distribution of the data sets are detailed in the ‘Data’ page of DinoSource (Figures 1b and S1a).&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/eaf169d6-1eef-4e11-8aa4-58413c9db10c/pbi70054-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/eaf169d6-1eef-4e11-8aa4-58413c9db10c/pbi70054-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/abbf798d-6830-47f6-b49c-ebeb17ddbea9/pbi70054-fig-0001-m.png\" title=\"Details are in the caption following the image\"/&gt;&lt;/picture&gt;&lt;figcaption&gt;\u0000&lt;div&gt;&lt;strong&gt;Figure 1&lt;span style=\"font-weight:normal\"&gt;&lt;/span&gt;&lt;/strong&gt;&lt;div&gt;Open in figure viewer&lt;i aria-hidden=\"true\"&gt;&lt;/i&gt;&lt;span&gt;PowerPoint&lt;/span&gt;&lt;/div&gt;\u0000&lt;/div&gt;\u0000&lt;div&gt;Architecture and screenshots of the DinoSource database. (a) Data collection and sources. (b) Species distribution of omics data across different species. (c) DinoSource's web implementation includes three core modules: The boxplot displays expression profiles of a subset of genes associated with ko: K02634 across different treatments in &lt;i&gt;Breviolum minutum&lt;/i&gt;. (e) Gene differential expression analysis and functional enrichment analysis tools. (f) The stacked bar plot illustrates the proportion of three 5mC contexts at varying methylation levels across &lt;i&gt;B. minutum&lt;/i&gt;. (g) HiGlass visualizes the Hi-C interaction matrices for &lt;i&gt;Symbiodinium microadriaticum&lt;/i&gt; (GSM5023543) in the region chr19:800 K–10 MB. The blue triangular box highlights the identified TAD. (h) An example of using comparative genomics tools in DinoSource. The left panel shows a syntenic block located between &lt;i&gt;Fugacium kawagutii&lt;/i&gt; and &lt;i&gt;S. mic","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"39 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143819968","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}

{"title":"Natural allelic variation of basic helix–loop–helix transcription factor 25 regulates carotenoid biosynthesis in sweet potato","authors":"Zihao Wei, Meiqi Shang, Zhicheng Jiang, Hong Zhai, Shihan Xing, Zhen Wang, Shaozhen He, Shaopei Gao, Ning Zhao, Huan Zhang, Qingchang Liu","doi":"10.1111/pbi.70086","DOIUrl":"https://doi.org/10.1111/pbi.70086","url":null,"abstract":"Carotenoid-rich orange-fleshed sweet potato (OFSP) is an important staple diet and source of nutrition in developing countries, including Africa and Asia. However, the regulation of carotenoid biosynthesis remains to be better understood. A natural allelic variation closely linked to carotenoid biosynthesis was identified in the promoter region of the <i>IbbHLH25</i> gene that encodes a basic helix–loop–helix (bHLH) transcription factor, by transcriptome and haplotype analyses of different flesh colour sweet potato accessions. An 86-bp deletion reduced the transcription of the <i>IbbHLH25</i> promoter in white- and yellow-fleshed sweet potatoes; however, the deletion was absent in OFSP. <i>IbbHLH25</i> was highly expressed in the storage roots of carotenoid-rich sweet potato. The overexpression of <i>IbbHLH25</i> significantly increased the carotenoid contents (by 2.5-fold–6.0-fold) and proportions, especially β-carotene and β-cryptoxanthin; their contents increased by 21.2-fold–55.7-fold and 4.6-fold–9.5-fold, respectively, and their proportions increased by 48.5% and 13.0%, respectively, and the silencing of <i>IbbHLH25</i> had opposite effects. IbbHLH25 formed heterodimers with IbbHLH66 to directly and synergistically activate the transcription of carotenoid biosynthesis key genes <i>IbGGPPS</i>, <i>IbLCYB</i> and <i>IbBCH</i>. The overexpression of <i>IbbHLH66</i> significantly increased the carotenoid contents (by 2.3-fold–3.8-fold) and proportions, especially β-carotene and β-cryptoxanthin; their contents increased by 15.2-fold–25.6-fold and 3.1-fold–5.1-fold, respectively, and their proportions increased by 31.1% and 9.6%, respectively. These findings expand our understanding of bHLHs in regulating carotenoid biosynthesis and suggest additional roles in affecting carotenoid component proportions, providing candidate genes for nutritional biofortification of agricultural products.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"14 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143814132","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}