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}
Zhongze Li, Minjae Kim, Jose Roberto da Silva Nascimento, Bertrand Legeret, Gabriel Lemes Jorge, Marie Bertrand, Fred Beisson, Jay J. Thelen, Yonghua Li-Beisson
The first step in chloroplast de novo fatty acid synthesis is catalysed by acetyl-CoA carboxylase (ACCase). As the rate-limiting step for this pathway, ACCase is subject to both positive and negative regulation. In this study, we identify a Chlamydomonas homologue of the plant carboxyltransferase interactor 1 (CrCTI1) and show that this protein interacts with the Chlamydomonas α-carboxyltransferase (Crα-CT) subunit of the ACCase by yeast two-hybrid protein–protein interaction assay. Three independent CRISPR-Cas9 mediated knockout mutants for CrCTI1 each produced an ‘enhanced oil’ phenotype, accumulating 25% more total fatty acids and storing up to fivefold more triacylglycerols (TAGs) in lipid droplets. The TAG phenotype of the crcti1 mutants was not influenced by light but was affected by trophic growth conditions. By growing cells under heterotrophic conditions, we observed a crucial function of CrCTI1 in balancing lipid accumulation and cell growth. Mutating a previously mapped in vivo phosphorylation site (CrCTI1 Ser108 to either Ala or to Asp), did not affect the interaction with Crα-CT. However, mutating all six predicted phosphorylation sites within Crα-CT to create a phosphomimetic mutant reduced this pairwise interaction significantly. Comparative proteomic analyses of the crcti1 mutants and WT suggested a role for CrCTI1 in regulating carbon flux by coordinating carbon metabolism, antioxidant and fatty acid β-oxidation pathways, to enable cells to adapt to carbon availability. Taken together, this study identifies CrCTI1 as a negative regulator of fatty acid synthesis in algae and provides a new molecular brick for the genetic engineering of microalgae for biotechnology purposes.
{"title":"Knocking out the carboxyltransferase interactor 1 (CTI1) in Chlamydomonas boosted oil content by fivefold without affecting cell growth","authors":"Zhongze Li, Minjae Kim, Jose Roberto da Silva Nascimento, Bertrand Legeret, Gabriel Lemes Jorge, Marie Bertrand, Fred Beisson, Jay J. Thelen, Yonghua Li-Beisson","doi":"10.1111/pbi.14581","DOIUrl":"https://doi.org/10.1111/pbi.14581","url":null,"abstract":"The first step in chloroplast <i>de novo</i> fatty acid synthesis is catalysed by acetyl-CoA carboxylase (ACCase). As the rate-limiting step for this pathway, ACCase is subject to both positive and negative regulation. In this study, we identify a Chlamydomonas homologue of the plant carboxyltransferase interactor 1 (CrCTI1) and show that this protein interacts with the Chlamydomonas α-carboxyltransferase (Crα-CT) subunit of the ACCase by yeast two-hybrid protein–protein interaction assay. Three independent CRISPR-Cas9 mediated knockout mutants for CrCTI1 each produced an ‘enhanced oil’ phenotype, accumulating 25% more total fatty acids and storing up to fivefold more triacylglycerols (TAGs) in lipid droplets. The TAG phenotype of the <i>crcti1</i> mutants was not influenced by light but was affected by trophic growth conditions. By growing cells under heterotrophic conditions, we observed a crucial function of CrCTI1 in balancing lipid accumulation and cell growth. Mutating a previously mapped <i>in vivo</i> phosphorylation site (CrCTI1 Ser108 to either Ala or to Asp), did not affect the interaction with Crα-CT. However, mutating all six predicted phosphorylation sites within Crα-CT to create a phosphomimetic mutant reduced this pairwise interaction significantly. Comparative proteomic analyses of the <i>crcti1</i> mutants and WT suggested a role for CrCTI1 in regulating carbon flux by coordinating carbon metabolism, antioxidant and fatty acid β-oxidation pathways, to enable cells to adapt to carbon availability. Taken together, this study identifies CrCTI1 as a negative regulator of fatty acid synthesis in algae and provides a new molecular brick for the genetic engineering of microalgae for biotechnology purposes.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"207 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057033","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}
Jingfang Dong, Shaohong Zhang, Haifei Hu, Jian Wang, Risheng Li, Jing Wu, Jiansong Chen, Lian Zhou, Yamei Ma, Wenhui Li, Shuai Nie, Shaokui Wang, Guiquan Zhang, Bin Liu, Junliang Zhao, Tifeng Yang
Improving cold tolerance at the flowering stage (CTF) in rice is crucial for minimising yield loss, making the identification and application of cold-tolerant genes and QTLs imperative for effective molecular breeding. The long lead time, dependence on cold treatment conditions, and the inherent complexity of the trait make studying the genetic basis of CTF in rice challenging. To date, the fine-mapping or cloning of QTLs specific to CTF has not yet been achieved. In this study, single segment substitution lines (SSSLs) were constructed using HJX74 as the recipient and IR58025B, known for good CTF, as the donor. This approach led to the identification of two cold tolerance QTLs, qCTF3 and qCTF6, in rice. qCTF6 has promising breeding potential. Further, we identified the causal gene CTF1 underlying qCTF6 through map-based cloning. CTF1 which encodes a conserved putative protein, has two SNPs within its coding sequence that influence CTF in rice. Additionally, genetic variations in the promoter of CTF1 also contributes to CTF. Thirteen variant sites of CTF1 in the four cold tolerance SSSLs are consistent with the IR58025B. Moreover, we analysed 307 accessions to characterise haplotypes based on the 13 variation sites, identifying five distinct haplotypes. The selection and evolutionary analysis indicate that the cold-tolerant haplotype of CTF1 is a newly generated mutation that has undergone selection in japonica during domestication. This study not only provides a novel favourable gene for molecular breeding of CTF but also highlights the potential of CTF1 in advancing rice breeding.
{"title":"Natural variation in CTF1 conferring cold tolerance at the flowering stage in rice","authors":"Jingfang Dong, Shaohong Zhang, Haifei Hu, Jian Wang, Risheng Li, Jing Wu, Jiansong Chen, Lian Zhou, Yamei Ma, Wenhui Li, Shuai Nie, Shaokui Wang, Guiquan Zhang, Bin Liu, Junliang Zhao, Tifeng Yang","doi":"10.1111/pbi.14600","DOIUrl":"https://doi.org/10.1111/pbi.14600","url":null,"abstract":"Improving cold tolerance at the flowering stage (CTF) in rice is crucial for minimising yield loss, making the identification and application of cold-tolerant genes and QTLs imperative for effective molecular breeding. The long lead time, dependence on cold treatment conditions, and the inherent complexity of the trait make studying the genetic basis of CTF in rice challenging. To date, the fine-mapping or cloning of QTLs specific to CTF has not yet been achieved. In this study, single segment substitution lines (SSSLs) were constructed using HJX74 as the recipient and IR58025B, known for good CTF, as the donor. This approach led to the identification of two cold tolerance QTLs, <i>qCTF3</i> and <i>qCTF6</i>, in rice. <i>qCTF6</i> has promising breeding potential. Further, we identified the causal gene <i>CTF1</i> underlying <i>qCTF6</i> through map-based cloning<i>. CTF1</i> which encodes a conserved putative protein, has two SNPs within its coding sequence that influence CTF in rice. Additionally, genetic variations in the promoter of <i>CTF1</i> also contributes to CTF. Thirteen variant sites of <i>CTF1</i> in the four cold tolerance SSSLs are consistent with the IR58025B. Moreover, we analysed 307 accessions to characterise haplotypes based on the 13 variation sites, identifying five distinct haplotypes. The selection and evolutionary analysis indicate that the cold-tolerant haplotype of <i>CTF1</i> is a newly generated mutation that has undergone selection in <i>japonica</i> during domestication. This study not only provides a novel favourable gene for molecular breeding of CTF but also highlights the potential of <i>CTF1</i> in advancing rice breeding.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"45 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056341","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}
Jarst van Belle, Jan G. Schaart, Annemarie C. Dechesne, Danli Fei, Abraham Ontiveros Cisneros, Michele Serafini, Richard G.F. Visser, Eibertus N. van Loo
Mutants with simultaneous germline mutations were obtained in all three F5H genes and all three FAD2 genes (one to eleven mutated alleles) in order to improve the feed value of the seed meal and the fatty acid composition of the seed oil. In mutants with multiple mutated F5H alleles, sinapine in seed meal was reduced by up to 100%, accompanied by a sharp reduction in the S-monolignol content of lignin without causing lodging or stem break. A lower S-lignin monomer content in stems can contribute to improved stem degradability allowing new uses of stems. Mutants in all six FAD2 alleles showed an expected increase in MUFA from 8.7% to 74% and a reduction in PUFA from 53% to 13% in the fatty acids in seed oil. Remarkably, some full FAD2 mutants showed normal growth and seed production and not the dwarfing phenotype reported in previous studies. The relation between germline mutation allele dosage and phenotype was influenced by the still ongoing activity of the CRISPR/Cas9 system, leading to new somatic mutations in the leaves of flowering plants. The correlations between the total mutation frequency (germline plus new somatic mutations) for F5H with sinapine content, and FAD2 with fatty acid composition were higher than the correlations between germline mutation count and phenotypes. This shows the importance of quantifying both the germline mutations and somatic mutations when studying CRISPR/Cas9 effects in situations where the CRISPR/Cas9 system is not yet segregated out.
{"title":"Direct and indirect effects of multiplex genome editing of F5H and FAD2 in oil crop camelina","authors":"Jarst van Belle, Jan G. Schaart, Annemarie C. Dechesne, Danli Fei, Abraham Ontiveros Cisneros, Michele Serafini, Richard G.F. Visser, Eibertus N. van Loo","doi":"10.1111/pbi.14593","DOIUrl":"https://doi.org/10.1111/pbi.14593","url":null,"abstract":"Mutants with simultaneous germline mutations were obtained in all three <i>F5H</i> genes and all three <i>FAD2</i> genes (one to eleven mutated alleles) in order to improve the feed value of the seed meal and the fatty acid composition of the seed oil. In mutants with multiple mutated <i>F5H</i> alleles, sinapine in seed meal was reduced by up to 100%, accompanied by a sharp reduction in the S-monolignol content of lignin without causing lodging or stem break. A lower S-lignin monomer content in stems can contribute to improved stem degradability allowing new uses of stems. Mutants in all six <i>FAD2</i> alleles showed an expected increase in MUFA from 8.7% to 74% and a reduction in PUFA from 53% to 13% in the fatty acids in seed oil. Remarkably, some full <i>FAD2</i> mutants showed normal growth and seed production and not the dwarfing phenotype reported in previous studies. The relation between germline mutation allele dosage and phenotype was influenced by the still ongoing activity of the CRISPR/Cas9 system, leading to new somatic mutations in the leaves of flowering plants. The correlations between the total mutation frequency (germline plus new somatic mutations) for <i>F5H</i> with sinapine content, and <i>FAD2</i> with fatty acid composition were higher than the correlations between germline mutation count and phenotypes. This shows the importance of quantifying both the germline mutations and somatic mutations when studying CRISPR/Cas9 effects in situations where the CRISPR/Cas9 system is not yet segregated out.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"38 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>Wood, one of the most abundant renewable natural resources globally, plays a crucial role in the timber, papermaking and bioenergy industries (Chutturi <i>et al</i>., <span>2023</span>). Wood (i.e. secondary xylem) is derived from vascular cambium, which is pivotal in determining the wood biomass in woody plants (Tang <i>et al</i>., <span>2022</span>). Reactive oxygen species (ROS) act as signalling molecules that regulate plant development, growth and responses to abiotic and biotic stresses (Wang <i>et al</i>., <span>2024</span>). Numerous studies underscore the significance of ROS in maintaining the root and shoot stem cell niches (Wang <i>et al</i>., <span>2024</span>). A recent study has indicated that LATERAL ORGAN BOUNDARIES DOMAIN 11 (LBD11) governs several ROS metabolic genes to manage the specific distribution of ROS within the cambium, thus affecting cambial cell proliferation in <i>Arabidopsis</i> root and shoot (Dang <i>et al</i>., <span>2023</span>). However, there remains a lack of clarity on the biological functions of ROS accumulation in tree vascular cambium activity. Additionally, the localized accumulation of ROS is required for lignin biosynthesis (Wang <i>et al</i>., <span>2024</span>). Therefore, ROS homeostasis enables woody plants to fine-tune the activity of cambium, increase wood yield and improve their quality.</p> <p>In plants, various forms of ROS exist, including singlet oxygen (<sup>1</sup>O<sub>2</sub>), superoxide anion (O<sub>2</sub><sup>·−</sup>), hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), hydroxyl radical (HO<sup>·</sup>) and others. Among them, O<sub>2</sub><sup>·−</sup> and H<sub>2</sub>O<sub>2</sub> play a crucial role in regulating stem cell fate in shoot apical meristem (SAM) and root apical meristem (RAM) (Wang <i>et al</i>., <span>2024</span>). Superoxide dismutases (SODs) are a group of metalloenzymes that scavenge ROS by converting O<sub>2</sub><sup>·−</sup> radicals into H<sub>2</sub>O<sub>2</sub>. In SAM and RAM, the balance between O<sub>2</sub><sup>·−</sup> and H<sub>2</sub>O<sub>2</sub> plays a critical role in the maintenance and differentiation of stem cells (Zeng <i>et al</i>., <span>2017</span>). Since the development of vascular cambium originates from the peripheral region of SAM, the balance between O<sub>2</sub><sup>·−</sup> and H<sub>2</sub>O<sub>2</sub> may also contribute significantly to vascular cambium activity. In this study, 11 <i>SOD</i> genes were identified in <i>Populus</i> genome (Figure S1). As revealed by the cell-type transcriptome analysis of the poplar stem (Dai <i>et al</i>., <span>2023</span>), among the 11 <i>SOD</i> genes, <i>CSD2</i> has a higher specific expression level in the cambium other than in the xylem or phloem, indicating a potential role of <i>CSD2</i> in vascular cambium development (Figure 1a).</p> <figure><picture> <source media="(min-width: 1650px)" srcset="/cms/asset/780ef7f0-e5c7-4432-ab01-3e7f86656935/pbi14590-fig-0001-m.jpg"/><img alt="Det
{"title":"Engineering transgenic Populus with enhanced biomass, wood quality and pest resistance through dual gene expression","authors":"Dian Wang, Fumei Liu, Mengyan Zhao, Xihao Yu, Jiping Feng, Wei Wang, Mengzhu Lu, Wei Li, Xianfeng Tang, Congpeng Wang, Gongke Zhou","doi":"10.1111/pbi.14590","DOIUrl":"https://doi.org/10.1111/pbi.14590","url":null,"abstract":"<p>Wood, one of the most abundant renewable natural resources globally, plays a crucial role in the timber, papermaking and bioenergy industries (Chutturi <i>et al</i>., <span>2023</span>). Wood (i.e. secondary xylem) is derived from vascular cambium, which is pivotal in determining the wood biomass in woody plants (Tang <i>et al</i>., <span>2022</span>). Reactive oxygen species (ROS) act as signalling molecules that regulate plant development, growth and responses to abiotic and biotic stresses (Wang <i>et al</i>., <span>2024</span>). Numerous studies underscore the significance of ROS in maintaining the root and shoot stem cell niches (Wang <i>et al</i>., <span>2024</span>). A recent study has indicated that LATERAL ORGAN BOUNDARIES DOMAIN 11 (LBD11) governs several ROS metabolic genes to manage the specific distribution of ROS within the cambium, thus affecting cambial cell proliferation in <i>Arabidopsis</i> root and shoot (Dang <i>et al</i>., <span>2023</span>). However, there remains a lack of clarity on the biological functions of ROS accumulation in tree vascular cambium activity. Additionally, the localized accumulation of ROS is required for lignin biosynthesis (Wang <i>et al</i>., <span>2024</span>). Therefore, ROS homeostasis enables woody plants to fine-tune the activity of cambium, increase wood yield and improve their quality.</p>\u0000<p>In plants, various forms of ROS exist, including singlet oxygen (<sup>1</sup>O<sub>2</sub>), superoxide anion (O<sub>2</sub><sup>·−</sup>), hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), hydroxyl radical (HO<sup>·</sup>) and others. Among them, O<sub>2</sub><sup>·−</sup> and H<sub>2</sub>O<sub>2</sub> play a crucial role in regulating stem cell fate in shoot apical meristem (SAM) and root apical meristem (RAM) (Wang <i>et al</i>., <span>2024</span>). Superoxide dismutases (SODs) are a group of metalloenzymes that scavenge ROS by converting O<sub>2</sub><sup>·−</sup> radicals into H<sub>2</sub>O<sub>2</sub>. In SAM and RAM, the balance between O<sub>2</sub><sup>·−</sup> and H<sub>2</sub>O<sub>2</sub> plays a critical role in the maintenance and differentiation of stem cells (Zeng <i>et al</i>., <span>2017</span>). Since the development of vascular cambium originates from the peripheral region of SAM, the balance between O<sub>2</sub><sup>·−</sup> and H<sub>2</sub>O<sub>2</sub> may also contribute significantly to vascular cambium activity. In this study, 11 <i>SOD</i> genes were identified in <i>Populus</i> genome (Figure S1). As revealed by the cell-type transcriptome analysis of the poplar stem (Dai <i>et al</i>., <span>2023</span>), among the 11 <i>SOD</i> genes, <i>CSD2</i> has a higher specific expression level in the cambium other than in the xylem or phloem, indicating a potential role of <i>CSD2</i> in vascular cambium development (Figure 1a).</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/780ef7f0-e5c7-4432-ab01-3e7f86656935/pbi14590-fig-0001-m.jpg\"/><img alt=\"Det","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"1 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>Cotton serves as not only a crucial natural textile crop, with cotton fibre accounting for approximately 95% of fibre usage in the textile industry but also a valuable model for the investigation of plant cell elongation (Cao <i>et al</i>., <span>2020</span>; Wang <i>et al</i>., <span>2019</span>). The plant hormones brassinosteroid (BR) and gibberellic acid (GA) promote fibre cell development (He <i>et al</i>., <span>2024</span>; Huang <i>et al</i>., <span>2021</span>; Shan <i>et al</i>., <span>2014</span>; Zhu <i>et al</i>., <span>2023</span>). Despite the positive role of BR and GA in fibre cell development that has been reported, the cross-talk between BR and GA biosynthesis pathway and signalling pathway in fibre growth remains largely unknown. In this study, our results reveal that BR stimulates GA biosynthesis during fibre elongation in cotton.</p> <p>BR and GA considerably promote cotton fibre development, whereas their respective inhibitors, brassinazole (BRZ, a BR biosynthesis inhibitor) and paclobutrazol (PAC, a GA biosynthesis inhibitor), impede fibre growth (Yang <i>et al</i>., <span>2023</span>; Zhu <i>et al</i>., <span>2022</span>). To explore the potential regulatory mechanisms between BR and GA, we treated wild-type (WT) ovules to with BR, BRZ, GA<sub>3</sub>, and PAC using an <i>in vitro</i> ovule culture system. Our observations reveal that BR and GA improved fibre development, and BRZ and PAC impeded it. In addition, GA<sub>3</sub> mitigated the inhibitory effects of BRZ on fibre development, whereas PAC treatment considerably inhibited the fibre-promoting effect of BR Figure 1a,b. Moreover, the GA levels were increased after the BR treatment and decreased after the BRZ treatment (ovule with fibres; Figure 1c). <i>BES1</i> (Gh_D02G0939) is the critical regulator in BR signalling (Zhu <i>et al</i>., <span>2023</span>). Overexpression of <i>BES1</i> notably stimulated the GA content in fibres (Figure 1d), accompanied with the considerably increased fibre length (Figure 1e,f and S1a,b). PAC significantly inhibited the promotion of fibre length after <i>BES1</i> overexpression (Figure S2a,b). These results suggest that BR acts upstream of GA in the context of fibre development.</p> <figure><picture> <source media="(min-width: 1650px)" srcset="/cms/asset/39103016-aadc-4499-87bf-3d0aa70332d7/pbi14579-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/39103016-aadc-4499-87bf-3d0aa70332d7/pbi14579-fig-0001-m.jpg" loading="lazy" src="/cms/asset/2969d54d-45ef-4a46-95b5-fcdb7ca1f7f4/pbi14579-fig-0001-m.png" title="Details are in the caption following the image"/></picture><figcaption> <div><strong>Figure 1<span style="font-weight:normal"></span></strong><div>Open in figure viewer<i aria-hidden="true"></i><span>PowerPoint</span></div> </div> <div>BR enhances GA biosynthesis to promote fibre cell growth in cotton. (a) Phenotypes of fibres derived from ovules cultured with 0.5 μM GA<sub>3</
棉花不仅是一种重要的天然纺织作物，棉纤维约占纺织工业纤维使用量的95%，而且是研究植物细胞伸长的有价值的模型(Cao等人，2020；Wang等人，2019)。植物激素油菜素类固醇（BR）和赤霉素酸（GA）促进纤维细胞发育(He et al., 2024；Huang et al., 2021；Shan et al., 2014；朱等人，2023)。尽管已经报道了BR和GA在纤维细胞发育中的积极作用，但BR和GA生物合成途径和信号通路在纤维生长中的相互作用仍是未知的。在本研究中，我们的研究结果表明，在棉花纤维伸长过程中，BR刺激了GA的生物合成。BR和GA显著促进棉纤维发育，而它们各自的抑制剂，油菜素唑（BRZ， BR生物合成抑制剂）和多效唑（PAC， GA生物合成抑制剂）阻碍纤维生长(Yang等，2023；朱等人，2022)。为了探索BR和GA之间的潜在调控机制，我们在离体胚珠培养系统中使用BR、BRZ、GA3和PAC处理野生型（WT）胚珠。我们的观察结果表明，BR和GA促进了纤维的发育，而BRZ和PAC则阻碍了纤维的发育。此外，GA3减轻了BRZ对纤维发育的抑制作用，而PAC处理显著抑制了BR的促纤维作用（图1a，b）。BR处理后GA水平升高，BRZ处理后GA水平降低(胚珠有纤维；图1 c)。BES1 （Gh_D02G0939）是BR信号传导的关键调节因子（Zhu et al., 2023）。过表达BES1显著刺激了纤维中的GA含量（图1d），同时纤维长度显著增加（图1e、f和S1a、b）。PAC显著抑制BES1过表达后纤维长度的增加（图S2a，b）。这些结果表明，在纤维发育的背景下，BR作用于GA的上游。br增强GA生物合成，促进棉花纤维细胞生长。(a) 0.5 μM GA3、1 μM PAC、5 μM BR、15 μM BRZ、0.5 μM GA3 + 15 μM BRZ和5 μM BR + 1 μM PAC培养10天胚珠纤维的表型。Bar = 5mm。(b) (a)中纤维长度统计。(c)经BR或BRZ处理的胚珠所得纤维的GA1和GA4含量。(d)野生型和过表达BES1棉纤维中GA1和GA4的含量。(e) BES1过表达棉花的成熟纤维表型。Bar = 10mm。(f) (e) (g) BES1与15个GA生物合成基因启动子间的Y1H测定。(h)和(i)烟草瞬时表达实验显示，在GA20OX1D和GA3OX1D启动子控制下，通过共表达BES1， LUC报告基因转录激活。(j)和(k)电泳迁移率转移试验（EMSA）显示BES1直接结合GA20OX1D启动子L1片段(j)和GA3OX1D启动子L2片段(k)。(l)和(m)竞争性EMSA试验使用生物素标记的GA20OX1D启动子L1片段(l)和生物素标记的GA3OX1D启动子L2片段(m)与BES1孵卵。与含有完整或突变结合位点(L1m （l)或L2m (m)）的不同浓度的冷探针（没有生物素标记）竞争。(n) - (q) WT、GA20OX1D (n)和(p)以及GA3OX1D (o)和(q)过表达和敲除系的纤维表型(n)和(o)以及长度测量(p)和(q)。Bar = 10mm。(r)和(t)用荧光白(r)或S4B (t)染色的WT、GA3OX1D过表达系和敲除系石蜡包埋成熟纤维的横截面。(s)和(u) WT、GA3OX1D过表达系和敲除系纤维的细胞壁厚度测量。(v)示意图模型。CK、控制。野生型。OE,超表达。KO,淘汰赛。DPA，花后日。给出的值为mean±SD， n = 10 (b), n = 20 (f), n = 3 (c)和(d)。各比较具有统计学意义（t检验）(*P≤0.05；** p≤0.01；*** p≤0.001)。在陆地棉花中鉴定出26个GA合成基因，其中15个基因的启动子中含有BES1结合位点（E-box顺式元件）。利用酵母单杂交法研究了BES1与15个候选基因启动子的相互作用。因此，BES1能够与两个基因启动子（pGA20OX1D和pGA3OX1D）相互作用（图1g）。烟草双荧光素酶实验表明，BES1激活了GA20OX1D和GA3OX1D的启动子，导致LUC基因的表达增强（图1h、i和S3a、b）。根据E-box顺式元件的分布将GA20OX1D和GA3OX1D的启动子分为三个片段。发现BES1分别特异性结合GA20OX1D和GA3OX1D启动子的P2和F3片段（图S4和S5a-d）。 值得注意的是，这种结合相互作用在P2或F3片段的第一个E-box突变时被取消（图S4和S5e-h）。此外，电泳迁移率转移实验揭示了BES1与pGA20OX1D-L1和pGA3OX1D-L2片段与E-box的特异性结合亲和力（图1j，k）。此外，不含生物素的竞争性结合探针分别显著降低了BES1蛋白与pGA20OX1D-L1和pGA3OX1D-L2的结合（图11，m）。此外，染色质免疫沉淀（ChIP）、测序和ChIP-定量PCR （qPCR）分析表明，BES1被选择性地招募到含有E-box的启动子片段上（图S6a-d）。BR处理或过表达BES1后，纤维中GA20OX1D和GA3OX1D的表达水平显著升高，BRZ处理或敲除BES1后，GA20OX1D和GA3OX1D的表达水平下降（图S7a-d）。此外，在棉纤维发育过程中，GA20OX1D和GA3OX1D的表达水平升高，表明这些基因在纤维细胞发育过程中发挥了功能作用（图S7e，f）。为了进一步研究GA20OX1D和GA3OX1D在棉纤维发育中的作用，我们制备了GA20OX1D和GA3OX1D转基因棉花植株（图S8a-f）。此外，我们检测了GA20OX1D和GA3OX1D转基因棉纤维中的GA含量，发现过表达GA20OX1D或GA3OX1D增加了GA的积累（图S9a，b）。在GA20OX1D或GA3OX1D过表达植株中，纤维长度显著增加，而在敲除系中，纤维长度显著减少（图1n-q）。此外，在GA3OX1D过表达系中，纤维的细胞壁厚度大大增加，而在GA3OX1D敲除系中，纤维的壁厚度减少（图1r-u和S10a，b）。然而，GA20OX1D转基因系的纤维细胞壁厚度与WT植株相当（图S10c-h）。更重要的是，外源应用GA3成功地挽救了GA20OX1D或GA3OX1D突变导致的短纤维表型。相反，PAC抑制了GA20OX1D或GA3OX1D过表达导致的纤维伸长促进（图S11a-d）。先前的研究表明，GA通过促进甚长链脂肪酸（VLCFAs）的生物合成来促进棉纤维的伸长(He et al., 2024；田等，2022；Xiao et al., 2016)。我们推测GA20OX1D和GA3OX1D可能通过调节VLCFAs的生物合成来提高纤维的伸长。总的来说，我们的研究结果表明，BR通过BES1调节GA20OX1D和GA3OX1D的转录，而BES1反过来调节GA的生物合成以促进纤维的发育（图1v）。
{"title":"Brassinosteroids enhance gibberellic acid biosynthesis to promote cotton fibre cell elongation","authors":"Liyong Hou, Liping Zhu, Miaomiao Hao, Yufei Liang, Guanghui Xiao","doi":"10.1111/pbi.14579","DOIUrl":"https://doi.org/10.1111/pbi.14579","url":null,"abstract":"<p>Cotton serves as not only a crucial natural textile crop, with cotton fibre accounting for approximately 95% of fibre usage in the textile industry but also a valuable model for the investigation of plant cell elongation (Cao <i>et al</i>., <span>2020</span>; Wang <i>et al</i>., <span>2019</span>). The plant hormones brassinosteroid (BR) and gibberellic acid (GA) promote fibre cell development (He <i>et al</i>., <span>2024</span>; Huang <i>et al</i>., <span>2021</span>; Shan <i>et al</i>., <span>2014</span>; Zhu <i>et al</i>., <span>2023</span>). Despite the positive role of BR and GA in fibre cell development that has been reported, the cross-talk between BR and GA biosynthesis pathway and signalling pathway in fibre growth remains largely unknown. In this study, our results reveal that BR stimulates GA biosynthesis during fibre elongation in cotton.</p>\u0000<p>BR and GA considerably promote cotton fibre development, whereas their respective inhibitors, brassinazole (BRZ, a BR biosynthesis inhibitor) and paclobutrazol (PAC, a GA biosynthesis inhibitor), impede fibre growth (Yang <i>et al</i>., <span>2023</span>; Zhu <i>et al</i>., <span>2022</span>). To explore the potential regulatory mechanisms between BR and GA, we treated wild-type (WT) ovules to with BR, BRZ, GA<sub>3</sub>, and PAC using an <i>in vitro</i> ovule culture system. Our observations reveal that BR and GA improved fibre development, and BRZ and PAC impeded it. In addition, GA<sub>3</sub> mitigated the inhibitory effects of BRZ on fibre development, whereas PAC treatment considerably inhibited the fibre-promoting effect of BR Figure 1a,b. Moreover, the GA levels were increased after the BR treatment and decreased after the BRZ treatment (ovule with fibres; Figure 1c). <i>BES1</i> (Gh_D02G0939) is the critical regulator in BR signalling (Zhu <i>et al</i>., <span>2023</span>). Overexpression of <i>BES1</i> notably stimulated the GA content in fibres (Figure 1d), accompanied with the considerably increased fibre length (Figure 1e,f and S1a,b). PAC significantly inhibited the promotion of fibre length after <i>BES1</i> overexpression (Figure S2a,b). These results suggest that BR acts upstream of GA in the context of fibre development.</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/39103016-aadc-4499-87bf-3d0aa70332d7/pbi14579-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/39103016-aadc-4499-87bf-3d0aa70332d7/pbi14579-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/2969d54d-45ef-4a46-95b5-fcdb7ca1f7f4/pbi14579-fig-0001-m.png\" title=\"Details are in the caption following the image\"/></picture><figcaption>\u0000<div><strong>Figure 1<span style=\"font-weight:normal\"></span></strong><div>Open in figure viewer<i aria-hidden=\"true\"></i><span>PowerPoint</span></div>\u0000</div>\u0000<div>BR enhances GA biosynthesis to promote fibre cell growth in cotton. (a) Phenotypes of fibres derived from ovules cultured with 0.5 μM GA<sub>3</","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"41 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020988","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}
Haoyang Xin, Luke W. Strickland, John P. Hamilton, Jacob K. Trusky, Chao Fang, Nathaniel M. Butler, David S. Douches, C. Robin Buell, Jiming Jiang
Potato (Solanum tuberosum) is the third-most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags behind that of other major food crops, largely due to the lack of a model experimental potato line. Here, we present a diploid potato line, ‘Jan,’ which possesses all essential characteristics for facile functional genomics studies. Jan exhibits a high level of homozygosity after seven generations of self-pollination. Jan is vigorous, highly fertile and produces tubers with outstanding traits. Additionally, it demonstrates high regeneration rates and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated its genes and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two ‘mini-Jan’ lines with compact and dwarf plant stature through CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes involved in growth. One mini-Jan mutant, mini-JanE, is fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan offer a robust model system that can be leveraged for gene editing and functional genomics research in potato.
马铃薯（Solanum tuberosum）是世界上第三重要的粮食作物。虽然马铃薯基因组已经完全测序，但马铃薯的功能基因组学研究滞后于其他主要粮食作物，主要原因是缺乏马铃薯模型实验品系。在这里，我们提出了一个二倍体马铃薯系，‘ Jan ’，它具有所有必要的特征，便于功能基因组学研究。自花授粉7代后，简表现出高水平的纯合子。Jan生机勃勃，肥力强，块茎产量高，性状突出。此外，它还具有较高的再生速率和优异的转化效率。我们为Jan建立了染色体尺度的基因组组装，对其基因进行了注释，并鉴定了与马铃薯参考基因组组装DMv6.1相关的同源物，以促进功能基因组学。为了使植物结构小型化，我们通过CRISPR/ cas9介导的靶向矮秆和直立基因的诱变，开发了两个紧凑和矮秆的“mini-Jan”品系。一个迷你简突变体，迷你简，是完全肥沃的，将允许在有限的生长室和温室空间进行更高通量的研究。因此，Jan和mini-Jan提供了一个强大的模型系统，可以用于马铃薯的基因编辑和功能基因组学研究。
{"title":"Jan and mini-Jan, a model system for potato functional genomics","authors":"Haoyang Xin, Luke W. Strickland, John P. Hamilton, Jacob K. Trusky, Chao Fang, Nathaniel M. Butler, David S. Douches, C. Robin Buell, Jiming Jiang","doi":"10.1111/pbi.14582","DOIUrl":"https://doi.org/10.1111/pbi.14582","url":null,"abstract":"Potato (<i>Solanum tuberosum</i>) is the third-most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags behind that of other major food crops, largely due to the lack of a model experimental potato line. Here, we present a diploid potato line, ‘Jan,’ which possesses all essential characteristics for facile functional genomics studies. Jan exhibits a high level of homozygosity after seven generations of self-pollination. Jan is vigorous, highly fertile and produces tubers with outstanding traits. Additionally, it demonstrates high regeneration rates and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated its genes and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two ‘mini-Jan’ lines with compact and dwarf plant stature through CRISPR/Cas9-mediated mutagenesis targeting the <i>Dwarf</i> and <i>Erecta</i> genes involved in growth. One mini-Jan mutant, mini-Jan<sup>E</sup>, is fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan offer a robust model system that can be leveraged for gene editing and functional genomics research in potato.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"136 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020989","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}
Jianping Liu, Xin Li, Ke Wang, Tao Wang, Yang Meng, Zhi Peng, Jinli Huang, Jiaohan Huo, Xiaoqi Zhu, Jinyong Yang, Yongxi Fan, Feiyun Xu, Qian Zhang, Zhengrui Wang, Ya Wang, Hao Chen, Weifeng Xu
Heat stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of heat resistance in rice. U2AF (U2 snRNP auxiliary factor) is an essential splicing complex with critical roles in recognizing the 3′-splice site of precursor messenger RNAs (pre-mRNAs). The U2AF small subunit (U2AF35) can bind to the 3′-AG intron border and promote U2 snRNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit (U2AF65). However, the functions of U2AF35 in plants are poorly understood. In this study, we discovered that the OsU2AF35a gene was vigorously induced by heat stress and could positively regulate rice thermotolerance during both the seedling and reproductive growth stages. OsU2AF35a interacts with OsU2AF65a within the nucleus, and both of them can form condensates through liquid–liquid phase separation (LLPS) following heat stress. The intrinsically disordered regions (IDR) are accountable for their LLPS. OsU2AF35a condensation is indispensable for thermotolerance. RNA-seq analysis disclosed that, subsequent to heat treatment, the expression levels of several genes associated with water deficiency and oxidative stress in osu2af35a-1 were markedly lower than those in ZH11. In accordance with this, OsU2AF35a is capable of positively regulating the oxidative stress resistance of rice. The pre-mRNAs of a considerable number of genes in the osu2af35a-1 mutant exhibited defective splicing, among which was the OsHSA32 gene. Knocking out OsHSA32 significantly reduced the thermotolerance of rice, while overexpressing OsHSA32 could partially rescue the heat sensitivity of osu2af35a-1. Together, our findings uncovered the essential role of OsU2AF35a in rice heat stress response through protein separation and regulating alternative pre-mRNA splicing.
{"title":"The splicing auxiliary factor OsU2AF35a enhances thermotolerance via protein separation and promoting proper splicing of OsHSA32 pre-mRNA in rice","authors":"Jianping Liu, Xin Li, Ke Wang, Tao Wang, Yang Meng, Zhi Peng, Jinli Huang, Jiaohan Huo, Xiaoqi Zhu, Jinyong Yang, Yongxi Fan, Feiyun Xu, Qian Zhang, Zhengrui Wang, Ya Wang, Hao Chen, Weifeng Xu","doi":"10.1111/pbi.14587","DOIUrl":"https://doi.org/10.1111/pbi.14587","url":null,"abstract":"Heat stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of heat resistance in rice. U2AF (<span style=\"text-decoration:underline\">U2</span> snRNP <span style=\"text-decoration:underline\">a</span>uxiliary <span style=\"text-decoration:underline\">f</span>actor) is an essential splicing complex with critical roles in recognizing the 3′-splice site of precursor messenger RNAs (pre-mRNAs). The U2AF small subunit (U2AF35) can bind to the 3′-AG intron border and promote U2 snRNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit (U2AF65). However, the functions of U2AF35 in plants are poorly understood. In this study, we discovered that the <i>OsU2AF35a</i> gene was vigorously induced by heat stress and could positively regulate rice thermotolerance during both the seedling and reproductive growth stages. OsU2AF35a interacts with OsU2AF65a within the nucleus, and both of them can form condensates through liquid–liquid phase separation (LLPS) following heat stress. The intrinsically disordered regions (IDR) are accountable for their LLPS. OsU2AF35a condensation is indispensable for thermotolerance. RNA-seq analysis disclosed that, subsequent to heat treatment, the expression levels of several genes associated with water deficiency and oxidative stress in <i>osu2af35a-1</i> were markedly lower than those in ZH11. In accordance with this, OsU2AF35a is capable of positively regulating the oxidative stress resistance of rice. The pre-mRNAs of a considerable number of genes in the <i>osu2af35a-1</i> mutant exhibited defective splicing, among which was the <i>OsHSA32</i> gene. Knocking out <i>OsHSA32</i> significantly reduced the thermotolerance of rice, while overexpressing <i>OsHSA32</i> could partially rescue the heat sensitivity of <i>osu2af35a-1</i>. Together, our findings uncovered the essential role of OsU2AF35a in rice heat stress response through protein separation and regulating alternative pre-mRNA splicing.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"12 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020865","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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