The number of tillers in rice directly determines the number of panicles, which is crucial for enhancing plant architecture and achieving high yields. Some important genes regulating rice tillering have been identified, but their underlying mechanisms remain unclear. FRIZZY PANICLE (FZP) encodes an AP2/ERF transcription factor. Beyond its well-established role in promoting spikelet formation during the reproductive phase, here we demonstrate that FZP also inhibits axillary buds outgrowth in the vegetative phase by suppressing the expression of a MADS-box gene (OsMADS57) that functions as a growth promoter. Consequently, genome editing of the FZP-bound cis-motif in the promoter of OsMADS57 releases its expression, leading to more tillers. Furthermore, domestication analysis shows that FZP has undergone strong selection in cultivated rice, while the downstream gene OsMADS57 has been differentiated between indica and japonica subspecies. Four functional SNPs in the promoter of OsMADS57 can increase rice tillering in most indica accessions by enhancing its expression. Our findings expose hidden pleiotropy of classic spikelet identity genes that are redeployed to control stem form, potentially enriching the gene resources for rice genetic improvement.
{"title":"FZP modulates tillering via OsMADS57 in rice","authors":"Hongwei Xing, Huan Wang, Yongyu Huang, Xin Ma, Sheng Wu, Yuanjie Li, Chuanqing Sun, Hongying Sun","doi":"10.1111/pbi.14578","DOIUrl":"https://doi.org/10.1111/pbi.14578","url":null,"abstract":"The number of tillers in rice directly determines the number of panicles, which is crucial for enhancing plant architecture and achieving high yields. Some important genes regulating rice tillering have been identified, but their underlying mechanisms remain unclear. <i>FRIZZY PANICLE</i> (<i>FZP</i>) encodes an AP2/ERF transcription factor. Beyond its well-established role in promoting spikelet formation during the reproductive phase, here we demonstrate that FZP also inhibits axillary buds outgrowth in the vegetative phase by suppressing the expression of a MADS-box gene (<i>OsMADS57</i>) that functions as a growth promoter. Consequently, genome editing of the FZP-bound cis-motif in the promoter of <i>OsMADS57</i> releases its expression, leading to more tillers. Furthermore, domestication analysis shows that <i>FZP</i> has undergone strong selection in cultivated rice, while the downstream gene <i>OsMADS57</i> has been differentiated between <i>indica</i> and <i>japonica</i> subspecies. Four functional SNPs in the promoter of <i>OsMADS57</i> can increase rice tillering in most <i>indica</i> accessions by enhancing its expression. Our findings expose hidden pleiotropy of classic spikelet identity genes that are redeployed to control stem form, potentially enriching the gene resources for rice genetic improvement.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"4 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385887","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}
Shujin Lin, Qian Zhang, Shiyan Bai, Liwen Yang, Guannan Qin, Liyuan Wang, Wenbin Wang, Cui Cheng, Da Zhang, Chunhua Lu, Jifeng Yuan, Jingying Li, Huanghao Yang, Xiaofeng Gu, Xiao Han
RNA interference (RNAi) has been widely used in agriculture. However, it is well accepted that common methods of plant RNAi are species-dependent and lack systematic efficiency. This study designed a thiolated siRNA nanoparticle, guanidinium (Gu+)-containing disulfide assembled siRNA (Gu+-siRNA), demonstrating remarkable species independence and efficient systemic gene silencing across different plant species. Our results indicate that this approach effectively utilizes the plant vascular system to deliver siRNA, enabling long-distance gene silencing across both monocot and dicot plants, such as rice and Arabidopsis. By applying this method, we successfully targeted and silenced key genes like STM, WER, MYB23, GD1, EIL1, and EIL2, which regulate plant development and enhance salt tolerance. This delivery system significantly expands the application of RNAi technology across different plants, serving as a valuable tool for advancing agricultural biotechnology, enhancing crop resistance, and improving agricultural productivity, while aligning with global goals for sustainable food production and crop improvement.
{"title":"Beyond species and spatial boundaries: Enabling long-distance gene silencing in plants via guanidinium-siRNA nanoparticles","authors":"Shujin Lin, Qian Zhang, Shiyan Bai, Liwen Yang, Guannan Qin, Liyuan Wang, Wenbin Wang, Cui Cheng, Da Zhang, Chunhua Lu, Jifeng Yuan, Jingying Li, Huanghao Yang, Xiaofeng Gu, Xiao Han","doi":"10.1111/pbi.14575","DOIUrl":"https://doi.org/10.1111/pbi.14575","url":null,"abstract":"RNA interference (RNAi) has been widely used in agriculture. However, it is well accepted that common methods of plant RNAi are species-dependent and lack systematic efficiency. This study designed a thiolated siRNA nanoparticle, guanidinium (Gu<sup>+</sup>)-containing disulfide assembled siRNA (Gu<sup>+</sup>-siRNA), demonstrating remarkable species independence and efficient systemic gene silencing across different plant species. Our results indicate that this approach effectively utilizes the plant vascular system to deliver siRNA, enabling long-distance gene silencing across both monocot and dicot plants, such as rice and Arabidopsis. By applying this method, we successfully targeted and silenced key genes like <i>STM</i>, <i>WER</i>, <i>MYB23</i>, <i>GD1</i>, <i>EIL1</i>, and <i>EIL2</i>, which regulate plant development and enhance salt tolerance. This delivery system significantly expands the application of RNAi technology across different plants, serving as a valuable tool for advancing agricultural biotechnology, enhancing crop resistance, and improving agricultural productivity, while aligning with global goals for sustainable food production and crop improvement.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"28 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258461","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}
Yang Liu, Ruchika Rajput, Md Torikul Islam, Ilenne Del Valle, Tao Yao, Rekha Agrawal, Brandon A. Boone, Carrie A. Eckert, Paul E. Abraham, Jin-Gui Chen, Gerald A. Tuskan, Xiaohan Yang
RNA plays a central role in plants, governing various cellular and physiological processes. Monitoring its dynamic abundance provides a discerning understanding of molecular mechanisms underlying plant responses to internal (developmental) and external (environmental) stimuli, paving the way for advances in plant biotechnology to engineer crops with improved resilience, quality and productivity. In general, traditional methods for analysis of RNA abundance in plants require destructive, labour-intensive and time-consuming assays. To overcome these limitations, we developed a transformative innovation for in vivo RNA imaging in plants. Specifically, we established a synthetic split ribozyme system that converts various RNA signals to orthogonal protein outputs, enabling in vivo visualisation of various RNA signals in plants. We demonstrated the utility of this system in transient expression experiments (i.e., leaf infiltration in Nicotiana benthamiana) to detect RNAs derived from transgenes and tobacco rattle virus, respectively. Also, we successfully engineered a split ribozyme-based biosensor in Arabidopsis thaliana for in vivo visualisation of endogenous gene expression at the cellular level, demonstrating the feasibility of multi-scale (e.g., cellular and tissue level) RNA imaging in plants. Furthermore, we developed a platform for easy incorporation of different protein outputs, allowing for flexible choice of reporters to optimise the detection of target RNAs.
{"title":"A split ribozyme system for in vivo plant RNA imaging and genetic engineering","authors":"Yang Liu, Ruchika Rajput, Md Torikul Islam, Ilenne Del Valle, Tao Yao, Rekha Agrawal, Brandon A. Boone, Carrie A. Eckert, Paul E. Abraham, Jin-Gui Chen, Gerald A. Tuskan, Xiaohan Yang","doi":"10.1111/pbi.14612","DOIUrl":"https://doi.org/10.1111/pbi.14612","url":null,"abstract":"RNA plays a central role in plants, governing various cellular and physiological processes. Monitoring its dynamic abundance provides a discerning understanding of molecular mechanisms underlying plant responses to internal (developmental) and external (environmental) stimuli, paving the way for advances in plant biotechnology to engineer crops with improved resilience, quality and productivity. In general, traditional methods for analysis of RNA abundance in plants require destructive, labour-intensive and time-consuming assays. To overcome these limitations, we developed a transformative innovation for <i>in vivo</i> RNA imaging in plants. Specifically, we established a synthetic split ribozyme system that converts various RNA signals to orthogonal protein outputs, enabling <i>in vivo</i> visualisation of various RNA signals in plants. We demonstrated the utility of this system in transient expression experiments (i.e., leaf infiltration in <i>Nicotiana benthamiana</i>) to detect RNAs derived from transgenes and tobacco rattle virus, respectively. Also, we successfully engineered a split ribozyme-based biosensor in <i>Arabidopsis thaliana</i> for <i>in vivo</i> visualisation of endogenous gene expression at the cellular level, demonstrating the feasibility of multi-scale (e.g., cellular and tissue level) RNA imaging in plants. Furthermore, we developed a platform for easy incorporation of different protein outputs, allowing for flexible choice of reporters to optimise the detection of target RNAs.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"141 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258378","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 functional difference of natural variations in conserved BR signalling genes and the genetic basis of rice indica–japonica differentiation are important yet unknown. Here, we discovered natural variations of the four key components (OsBRI1, OsBAK1, OsGSK3 and OsBZR1) in BR signalling pathway by GWAS using an indicator of indica–japonica differentiation in rice. Two major BR signalling haplotypes (BSHs), caused by co-selected variations of the four genetically unlinked genes, were identified to be highly differentiated between rice subspecies. The genetic contributions of BSHs to grain yield and quality were much higher than that of each component. Introducing alleles of japonica into indica employing substitution lines of OsBAK1, complementation lines of OsGSK3 and genetic populations of OsBRI1/OsBAK1/OsGSK3 confirmed their functional differences between two subspecies. The BSH differentiation led to weaker interaction between OsBRI1 and OsBAK1, stronger autophosphorylation and kinase activity of OsGSK3, less RNA/proteins and stronger phosphorylation of OsBZR1, and weaker BR sensitivity in indica than japonica rice, and regular expression trends of BR-response genes between subspecies, and then synergistically enhanced yield and superior quality of indica. Our results demonstrate that BSHs contribute to rice inter-subspecies diversity, and will provide proof-of-concept breeding strategy and useful targets in crops.
{"title":"BR signalling haplotypes contribute to indica–japonica differentiation for grain yield and quality in rice","authors":"Xinyi Yang, Juncheng Zhang, Lusheng Wang, Chunyu Zhang, Pengkun Xu, Yanhua Li, Sibin Yu, Yibo Li","doi":"10.1111/pbi.14610","DOIUrl":"https://doi.org/10.1111/pbi.14610","url":null,"abstract":"The functional difference of natural variations in conserved BR signalling genes and the genetic basis of rice <i>indica</i>–<i>japonica</i> differentiation are important yet unknown. Here, we discovered natural variations of the four key components (<i>OsBRI1</i>, <i>OsBAK1</i>, <i>OsGSK3</i> and <i>OsBZR1</i>) in BR signalling pathway by GWAS using an indicator of <i>indica</i>–<i>japonica</i> differentiation in rice. Two major BR signalling haplotypes (BSHs), caused by co-selected variations of the four genetically unlinked genes, were identified to be highly differentiated between rice subspecies. The genetic contributions of BSHs to grain yield and quality were much higher than that of each component. Introducing alleles of <i>japonica</i> into <i>indica</i> employing substitution lines of <i>OsBAK1</i>, complementation lines of <i>OsGSK3</i> and genetic populations of <i>OsBRI1</i>/<i>OsBAK1</i>/<i>OsGSK3</i> confirmed their functional differences between two subspecies. The BSH differentiation led to weaker interaction between OsBRI1 and OsBAK1, stronger autophosphorylation and kinase activity of OsGSK3, less RNA/proteins and stronger phosphorylation of OsBZR1, and weaker BR sensitivity in <i>indica</i> than <i>japonica</i> rice, and regular expression trends of BR-response genes between subspecies, and then synergistically enhanced yield and superior quality of <i>indica</i>. Our results demonstrate that BSHs contribute to rice inter-subspecies diversity, and will provide proof-of-concept breeding strategy and useful targets in crops.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"44 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258377","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}
Lignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defence. Here, we identified an ethyl methanesulfonate (EMS)-derived Aegilops tauschii mutant named brown glume and internode 1 (bgi1), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identified AET6Gv20438400 (BGI1) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon in BGI1. We validated the function of BGI1 using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues. BGI1 knockout mutants exhibited reduced lignin content and shearing force relative to wild type, while BGI1 overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot and Fusarium crown rot. We confirmed that BGI1 exhibits CAD activity both in vitro and in vivo, playing an important role in lignin biosynthesis. BGI1 was highly expressed in the stem and spike, with its localisation observed in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated with BGI1. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signalling pathway. The identification and functional characterisation of BGI1 significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defence against pathogen infection in wheat.
{"title":"Manipulation of the brown glume and internode 1 gene leads to alterations in the colouration of lignified tissues, lignin content and pathogen resistance in wheat","authors":"Lei Hua, Rui Song, Xiaohua Hao, Jing Zhang, Yanna Liu, Jing Luo, Xiaopeng Ren, Hongna Li, Guiping Wang, Shams ur Rehman, Jiajie Wu, Daolin Fu, Yuxiu Dong, Xiaodong Wang, Chaozhong Zhang, Shisheng Chen","doi":"10.1111/pbi.14604","DOIUrl":"https://doi.org/10.1111/pbi.14604","url":null,"abstract":"Lignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defence. Here, we identified an ethyl methanesulfonate (EMS)-derived <i>Aegilops tauschii</i> mutant named <i>brown glume and internode 1</i> (<i>bgi1</i>), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identified <i>AET6Gv20438400</i> (<i>BGI1</i>) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon in <i>BGI1</i>. We validated the function of <i>BGI1</i> using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues. <i>BGI1</i> knockout mutants exhibited reduced lignin content and shearing force relative to wild type, while <i>BGI1</i> overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot and <i>Fusarium</i> crown rot. We confirmed that BGI1 exhibits CAD activity both <i>in vitro</i> and <i>in vivo</i>, playing an important role in lignin biosynthesis. <i>BGI1</i> was highly expressed in the stem and spike, with its localisation observed in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated with <i>BGI1</i>. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signalling pathway. The identification and functional characterisation of <i>BGI1</i> significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defence against pathogen infection in wheat.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"50 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124897","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}
Furong Wang, Lieqiong Kuang, Zelin Xiao, Ze Tian, Xinfa Wang, Hanzhong Wang, Xiaoling Dun
Vitamin E (VE) is essential for plants and animals. Rapeseed oil is rich in α-tocopherol (α-T), which is the most bioactive form of VE in human body. This study demonstrated that VE in rapeseed seeds was mainly controlled by embryo genotype through incomplete diallel hybridization. By genome-wide association study, the QTL-qVE.C02 associated with VE and α-T contents was detected in a Brassica napus association population, and the phenotypic contribution rate was up to 18.71%. BnaC02.VTE4, encoding gama-tocopherol methyltransferase, was proved as the target gene of qVE.C02 by genetic complementation. Two BnaC02.VTE4 haplotypes were identified in the population. Compared with BnaC02.VTE4HapH, a point mutation from A to G at the 3′ splicing site of the second intron were found in BnaC02.VTE4HapL, resulting in alternative splicing and early termination of translation. HapL1052(G-A), the site-directed mutagenesis fragment of BnaC02.VTE4HapL, was introduced into Arabidopsis vte4 mutant and 8S088 (a BnaC02.VTE4HapL accession), and the contents of VE and α-T in atvte4-4 and 8S088 seeds were increased by 90.10% to 307.29%. These demonstrated the point mutation as the causal for the difference in VE biosynthesis in rapeseed. Further, this variation also led to the significant difference in glucosinolate content between BnaC02.VTE4HapH and BnaC02.VTE4HapL accessions. Multi-omics analysis suggested that the expression of some genes and the accumulation of several metabolites related to the glucosinolate biosynthesis pathway were significantly increased in BnaC02.VTE4HapL group. Moreover, by functional marker identification, the BnaC02.VTE4HapH was found to be selected during domestication. Our findings offered promising opportunities for enhancing rapeseed quality traits.
{"title":"An alternative splicing caused by a natural variation in BnaC02.VTE4 gene affects vitamin E and glucosinolate content in rapeseed (Brassica napus L.)","authors":"Furong Wang, Lieqiong Kuang, Zelin Xiao, Ze Tian, Xinfa Wang, Hanzhong Wang, Xiaoling Dun","doi":"10.1111/pbi.14603","DOIUrl":"https://doi.org/10.1111/pbi.14603","url":null,"abstract":"Vitamin E (VE) is essential for plants and animals. Rapeseed oil is rich in α-tocopherol (α-T), which is the most bioactive form of VE in human body. This study demonstrated that VE in rapeseed seeds was mainly controlled by embryo genotype through incomplete diallel hybridization. By genome-wide association study, the QTL-qVE.C02 associated with VE and α-T contents was detected in a <i>Brassica napus</i> association population, and the phenotypic contribution rate was up to 18.71%. <i>BnaC02.VTE4</i>, encoding gama-tocopherol methyltransferase, was proved as the target gene of qVE.C02 by genetic complementation. Two <i>BnaC02.VTE4</i> haplotypes were identified in the population. Compared with <i>BnaC02.VTE4</i><sup>HapH</sup>, a point mutation from A to G at the 3′ splicing site of the second intron were found in <i>BnaC02.VTE4</i><sup>HapL</sup>, resulting in alternative splicing and early termination of translation. HapL<sup>1052(G-A)</sup>, the site-directed mutagenesis fragment of <i>BnaC02.VTE4</i><sup>HapL</sup>, was introduced into <i>Arabidopsis vte4</i> mutant and 8S088 (a <i>BnaC02.VTE4</i><sup>HapL</sup> accession), and the contents of VE and α-T in <i>atvte4-4</i> and 8S088 seeds were increased by 90.10% to 307.29%. These demonstrated the point mutation as the causal for the difference in VE biosynthesis in rapeseed. Further, this variation also led to the significant difference in glucosinolate content between <i>BnaC02.VTE4</i><sup>HapH</sup> and <i>BnaC02.VTE4</i><sup>HapL</sup> accessions. Multi-omics analysis suggested that the expression of some genes and the accumulation of several metabolites related to the glucosinolate biosynthesis pathway were significantly increased in <i>BnaC02.VTE4</i><sup>HapL</sup> group. Moreover, by functional marker identification, the <i>BnaC02.VTE4</i><sup>HapH</sup> was found to be selected during domestication. Our findings offered promising opportunities for enhancing rapeseed quality traits.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"63 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084145","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}
Prunus mume, an important ornamental woody plant in the Rosaceae family, contains many interspecific hybridizations. Purple colour is a breeding trait of aesthetic value for P. mume, but little is known about the origin and genetic architecture of this trait. Here we address these issues by producing a haplotype-resolved genome from an interspecific hybrid cultivar of P. mume (M) and P. cerasifera ‘Pissardii’ (C), named P. mume ‘Meiren’, followed by a detailed molecular characterization. The final length of the diploid genome is 499.47 Mb, with 250.66 Mb of haplotype M (HM) and 248.79 Mb of haplotype C (HC). Approximately 95.42% (476.61 Mb) of the phased assembly is further anchored to 16 homologous chromosomes. Based on the genomic variation, we identify a 1.8 Mb large-fragmented inversion (INV) on chromosome 1b of HC, which co-segregates with purple colour traits of ‘Meiren’ inherited from its purple C parent ‘Pissardii’. We find that a MYB transcription factor, PmmMYB10.5b, resides at the distal breakpoint of the INV, which displays consistent allele-specific expression (ASE). By directly binding to the promoter of anthocyanin synthetic alleles, PmmMYB10.5b serves as a co-activator to promote anthocyanin accumulation in ‘Meiren’ organs. Notably, the INV identified in ‘Meiren’ is generated from ‘Pissardii’ rather than P. cerasifera, which alters the promoter sequence of PmmMYB10.5b, activates its expression and results in the purple colour trait. Results from this study shed light on the evolutionary origin of purple colour in ‘Meiren’ and could potentially provide guidance on the genetic improvement of colour traits in ornamental woody plants.
{"title":"Haplotype-resolved genome assembly provides new insights into the genomic origin of purple colour in Prunus mume","authors":"Juan Meng, Ziwei Li, Haoning Wang, Runtian Miao, Xu Liu, Dapeng Miao, Chunxu Zhao, Guijia Wang, Tangren Cheng, Qixiang Zhang, Lidan Sun","doi":"10.1111/pbi.14595","DOIUrl":"https://doi.org/10.1111/pbi.14595","url":null,"abstract":"<i>Prunus mume</i>, an important ornamental woody plant in the Rosaceae family, contains many interspecific hybridizations. Purple colour is a breeding trait of aesthetic value for <i>P. mume</i>, but little is known about the origin and genetic architecture of this trait. Here we address these issues by producing a haplotype-resolved genome from an interspecific hybrid cultivar of <i>P. mume</i> (M) and <i>P. cerasifera</i> ‘Pissardii’ (C), named <i>P. mume</i> ‘Meiren’, followed by a detailed molecular characterization. The final length of the diploid genome is 499.47 Mb, with 250.66 Mb of haplotype M (HM) and 248.79 Mb of haplotype C (HC). Approximately 95.42% (476.61 Mb) of the phased assembly is further anchored to 16 homologous chromosomes. Based on the genomic variation, we identify a 1.8 Mb large-fragmented inversion (INV) on chromosome 1b of HC, which co-segregates with purple colour traits of ‘Meiren’ inherited from its purple C parent ‘Pissardii’. We find that a MYB transcription factor, <i>PmmMYB10.5b</i>, resides at the distal breakpoint of the INV, which displays consistent allele-specific expression (ASE). By directly binding to the promoter of anthocyanin synthetic alleles, <i>PmmMYB10.5b</i> serves as a co-activator to promote anthocyanin accumulation in ‘Meiren’ organs. Notably, the INV identified in ‘Meiren’ is generated from ‘Pissardii’ rather than <i>P. cerasifera</i>, which alters the promoter sequence of <i>PmmMYB10.5b</i>, activates its expression and results in the purple colour trait. Results from this study shed light on the evolutionary origin of purple colour in ‘Meiren’ and could potentially provide guidance on the genetic improvement of colour traits in ornamental woody plants.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"22 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084149","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}
Huan Chen, Tiange Zhou, Xianxin Wu, Vikranth Kumar, Xingguo Lan, Yuan Hu Xuan
SummaryLight signalling regulates plant growth and stress resistance, whereas its mechanism in controlling saline‐alkaline tolerance (SAT) remains largely unknown. This study identified that light signalling, primarily mediated by Phytochrome B (PhyB), inhibited ammonium transporter 1 (AMT1) to negatively regulate SAT. Our previous findings have shown that PhyB can impede the transcription factors indeterminate domain 10 (IDD10) and brassinazole resistant 1 (BZR1) to reduce NH4+ uptake, thereby modulating SAT and sheath blight (ShB) resistance in rice. However, inhibition of IDD10 and BZR1 in the phyB background did not fully suppress NH4+ uptake, suggesting that other signalling pathways regulated AMT1 downstream of PhyB. Further analysis revealed that PhyB interacted with Calcineurin B‐like protein‐interacting protein kinase 31 (CIPK31), which positively regulated AMT1 expression. CIPK31 also interacted with Teosinte Branched1/Cycloidea/PCF19 (TCP19), a key regulator of nitrogen use efficiency (NUE). However, PhyB neither degraded CIPK31 nor directly interacted with TCP19. Instead, PhyB inhibited the CIPK31‐TCP19 interaction, releasing TCP19, which repressed AMT1;2 directly and AMT1;1 and AMT1;3 indirectly, thereby inhibiting NH4+ uptake and SAT while reducing ShB resistance. Additionally, Phytochrome Interacting Factor‐Like 15 (PIL15) interacted with TCP19. Different from TCP19, PIL15 directly activated AMT1;2 to promote SAT, suggesting a balancing mechanism for NH4+ uptake downstream of PhyB. Furthermore, PIL15 interacted with IDD10 and BZR1 to form a transcriptional complex that collaboratively activated AMT1;2 expression. Overall, this study provides novel insights into how PhyB signalling regulates NH4+ uptake and coordinates SAT and ShB resistance in rice.
{"title":"Phytochrome B‐mediated light signalling enhances rice resistance to saline‐alkaline and sheath blight by regulating multiple downstream transcription factors","authors":"Huan Chen, Tiange Zhou, Xianxin Wu, Vikranth Kumar, Xingguo Lan, Yuan Hu Xuan","doi":"10.1111/pbi.14599","DOIUrl":"https://doi.org/10.1111/pbi.14599","url":null,"abstract":"SummaryLight signalling regulates plant growth and stress resistance, whereas its mechanism in controlling saline‐alkaline tolerance (SAT) remains largely unknown. This study identified that light signalling, primarily mediated by Phytochrome B (PhyB), inhibited <jats:italic>ammonium transporter 1</jats:italic> (<jats:italic>AMT1</jats:italic>) to negatively regulate SAT. Our previous findings have shown that PhyB can impede the transcription factors indeterminate domain 10 (IDD10) and brassinazole resistant 1 (BZR1) to reduce NH<jats:sub>4</jats:sub><jats:sup>+</jats:sup> uptake, thereby modulating SAT and sheath blight (ShB) resistance in rice. However, inhibition of IDD10 and BZR1 in the <jats:italic>phyB</jats:italic> background did not fully suppress NH<jats:sub>4</jats:sub><jats:sup>+</jats:sup> uptake, suggesting that other signalling pathways regulated <jats:italic>AMT1</jats:italic> downstream of PhyB. Further analysis revealed that PhyB interacted with Calcineurin B‐like protein‐interacting protein kinase 31 (CIPK31), which positively regulated <jats:italic>AMT1</jats:italic> expression. CIPK31 also interacted with Teosinte Branched1/Cycloidea/PCF19 (TCP19), a key regulator of nitrogen use efficiency (NUE). However, PhyB neither degraded CIPK31 nor directly interacted with TCP19. Instead, PhyB inhibited the CIPK31‐TCP19 interaction, releasing TCP19, which repressed <jats:italic>AMT1;2</jats:italic> directly and <jats:italic>AMT1;1</jats:italic> and <jats:italic>AMT1;3</jats:italic> indirectly, thereby inhibiting NH<jats:sub>4</jats:sub><jats:sup>+</jats:sup> uptake and SAT while reducing ShB resistance. Additionally, Phytochrome Interacting Factor‐Like 15 (PIL15) interacted with TCP19. Different from TCP19, PIL15 directly activated <jats:italic>AMT1;2</jats:italic> to promote SAT, suggesting a balancing mechanism for NH<jats:sub>4</jats:sub><jats:sup>+</jats:sup> uptake downstream of PhyB. Furthermore, PIL15 interacted with IDD10 and BZR1 to form a transcriptional complex that collaboratively activated <jats:italic>AMT1;2</jats:italic> expression. Overall, this study provides novel insights into how PhyB signalling regulates NH<jats:sub>4</jats:sub><jats:sup>+</jats:sup> uptake and coordinates SAT and ShB resistance in rice.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"128 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072416","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}
Cytosine methylation (mCG) is an important heritable epigenetic modification, yet its functions remain to be fully defined in important crops. This study investigates mCG in soybean following the loss-of-function mutation of two GmMET1 genes. We generated knockout mutants of GmMET1s by CRISPR-Cas9 and conducted comprehensive methylome and transcriptome analyses. Our findings unravel the functional redundancy of the two GmMET1s, with GmMET1b being more critically involved in maintaining mCG levels, and complete knockout of both copies is lethal. We establish that genome-wide mCG levels scale with aggregated expression of GmMET1s. We identify a set of mCG-regulated genes whose expression levels were quantitatively modulated by upstream, body, or downstream mCG. Moreover, we find genes that were negatively regulated by upstream or body mCG are enriched in specific biological processes such as that of jasmonic acid metabolism. Notably, >80% of the differentially methylated genes (DMGs) in the mutants also exist as DMGs in natural soybean populations. Phenotypically, mutants that are heterozygous for GmMET1a and homozygous for GmMET1b knockouts (GmMET1a+/-GmMET1b-/-) exhibited early flowering, which was inherited by their selfed progeny (GmMET1a+/+GmMET1b-/-) with otherwise normal growth and development. Moreover, mutation of either GmMET1s, with slight reduction of mCG levels and similar phenotypes compared to the wild type under normal conditions, showed enhanced tolerance to cold and drought stresses. Together, our results underscore highly orchestrated regulatory effects of mCG on gene expression in soybean, which dictates growth, development and stress responses, implicating its utility in the improvement of soybean for better adaptability and higher yield.
{"title":"A modulatory role of CG methylation on gene expression in soybean implicates its potential utility in breeding.","authors":"Ying Wang, Hongwei Xun, Jiameng Lv, Wanting Ju, Yuhui Jiang, Meng Wang, Ruihong Guo, Mengru Zhang, Xiaoyang Ding, Bao Liu, Chunming Xu","doi":"10.1111/pbi.14606","DOIUrl":"https://doi.org/10.1111/pbi.14606","url":null,"abstract":"<p><p>Cytosine methylation (mCG) is an important heritable epigenetic modification, yet its functions remain to be fully defined in important crops. This study investigates mCG in soybean following the loss-of-function mutation of two GmMET1 genes. We generated knockout mutants of GmMET1s by CRISPR-Cas9 and conducted comprehensive methylome and transcriptome analyses. Our findings unravel the functional redundancy of the two GmMET1s, with GmMET1b being more critically involved in maintaining mCG levels, and complete knockout of both copies is lethal. We establish that genome-wide mCG levels scale with aggregated expression of GmMET1s. We identify a set of mCG-regulated genes whose expression levels were quantitatively modulated by upstream, body, or downstream mCG. Moreover, we find genes that were negatively regulated by upstream or body mCG are enriched in specific biological processes such as that of jasmonic acid metabolism. Notably, >80% of the differentially methylated genes (DMGs) in the mutants also exist as DMGs in natural soybean populations. Phenotypically, mutants that are heterozygous for GmMET1a and homozygous for GmMET1b knockouts (GmMET1a<sup>+/-</sup>GmMET1b<sup>-/-</sup>) exhibited early flowering, which was inherited by their selfed progeny (GmMET1a<sup>+/+</sup>GmMET1b<sup>-/-</sup>) with otherwise normal growth and development. Moreover, mutation of either GmMET1s, with slight reduction of mCG levels and similar phenotypes compared to the wild type under normal conditions, showed enhanced tolerance to cold and drought stresses. Together, our results underscore highly orchestrated regulatory effects of mCG on gene expression in soybean, which dictates growth, development and stress responses, implicating its utility in the improvement of soybean for better adaptability and higher yield.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062170","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}
Hui Du, Zefeng Zhai, Jin Pu, Jun Liang, Rongyan Wang, Zhong Zhang, Pei Wang, Yanhui Zhu, Lian Huang, Dawei Li, Kaiyuan Chen, Guangtao Zhu, Chunzhi Zhang
Anthocyanin biosynthesis and accumulation determines the colour of tuber flesh in potato (Solanum tuberosum) and influences nutritional quality. However, the regulatory mechanism behind anthocyanin biosynthesis in potato tuber flesh remains unclear. In this study, we identified the Pigmented tuber flesh (Pf) locus through a genome-wide association study using 135 diploid potato landraces. Genome editing of two tandem R2R3 MYB transcription factor genes, StMYB200 and StMYB210, within the Pf locus demonstrated that both genes are involved in anthocyanin biosynthesis in tuber flesh. Molecular and biochemical assays revealed that StMYB200 promotes StMYB210 transcription by directly binding to a 1.7-kb insertion present in the StMYB210 promoter, while StMYB210 also regulates its own expression. Furthermore, StMYB200 and StMYB210 both activated the expression of the basic helix–loop–helix transcription factor gene StbHLH1 and interacted with StbHLH1 to regulate anthocyanin biosynthesis. An analysis of the StMYB210 promoter in different diploid potato accessions showed that the 1.7-kb insertion is associated with flesh colour in potato. These findings reveal the genetic and molecular mechanism by which the Pf locus regulates anthocyanin accumulation in tuber flesh and provide an important reference for breeding new potato varieties with colourful flesh.
{"title":"Two tandem R2R3 MYB transcription factor genes cooperatively regulate anthocyanin accumulation in potato tuber flesh","authors":"Hui Du, Zefeng Zhai, Jin Pu, Jun Liang, Rongyan Wang, Zhong Zhang, Pei Wang, Yanhui Zhu, Lian Huang, Dawei Li, Kaiyuan Chen, Guangtao Zhu, Chunzhi Zhang","doi":"10.1111/pbi.14602","DOIUrl":"https://doi.org/10.1111/pbi.14602","url":null,"abstract":"Anthocyanin biosynthesis and accumulation determines the colour of tuber flesh in potato (<i>Solanum tuberosum</i>) and influences nutritional quality. However, the regulatory mechanism behind anthocyanin biosynthesis in potato tuber flesh remains unclear. In this study, we identified the <i>Pigmented tuber flesh</i> (<i>Pf</i>) locus through a genome-wide association study using 135 diploid potato landraces. Genome editing of two tandem R2R3 MYB transcription factor genes, <i>StMYB200</i> and <i>StMYB210</i>, within the <i>Pf</i> locus demonstrated that both genes are involved in anthocyanin biosynthesis in tuber flesh. Molecular and biochemical assays revealed that StMYB200 promotes <i>StMYB210</i> transcription by directly binding to a 1.7-kb insertion present in the <i>StMYB210</i> promoter, while StMYB210 also regulates its own expression. Furthermore, StMYB200 and StMYB210 both activated the expression of the basic helix–loop–helix transcription factor gene <i>StbHLH1</i> and interacted with StbHLH1 to regulate anthocyanin biosynthesis. An analysis of the <i>StMYB210</i> promoter in different diploid potato accessions showed that the 1.7-kb insertion is associated with flesh colour in potato. These findings reveal the genetic and molecular mechanism by which the <i>Pf</i> locus regulates anthocyanin accumulation in tuber flesh and provide an important reference for breeding new potato varieties with colourful flesh.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"40 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057028","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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