The Plant Journal最新文献

{"title":"Natural variation in a FtMYB32-FtCES18 module drives Rhizoctonia solani resistance by reprogramming jasmonate and flavonoid metabolism in Tartary buckwheat","authors":"Yuanyuan Chen,&nbsp;Yang Liu,&nbsp;Xixu Peng,&nbsp;Haihua Wang,&nbsp;Zhengwu Fang,&nbsp;Jai Chand Rana,&nbsp;Nikhil Chrungoo,&nbsp;Maria D Logachev,&nbsp;Chaonan Guan,&nbsp;Meiliang Zhou","doi":"10.1111/tpj.71176","DOIUrl":"https://doi.org/10.1111/tpj.71176","url":null,"abstract":"<p>Tartary buckwheat <i>(Fagopyrum tataricum</i>) is renowned for its adaptability to complex growing conditions and stress tolerance. However, soil-borne necrotrophic pathogens such as <i>Rhizoctonia solani</i> frequently cause devastating diseases that severely compromise its yield and quality. In this study, through a genome-wide association study (GWAS), we identified a carboxylesterase gene, <i>FtCES18</i>, and demonstrated that it acts as a core positive regulator of disease resistance in Tartary buckwheat. Overexpression of <i>FtCES18</i> significantly enhanced plant resistance, whereas virus-induced gene silencing (VIGS) led to a highly susceptible phenotype. Further analyses revealed that FtCES18 efficiently catalyzes the hydrolysis of methyl jasmonate (MeJA) into free jasmonic acid (JA), which initiates downstream JA-Ile signaling and rapidly promotes endogenous jasmonate accumulation upon pathogen infection. This JA signaling cascade reprograms host flavonoid metabolism, promoting the substantial accumulation of downstream defensive flavonoids (such as rutin and quercetin). Furthermore, we found that the transcription factor FtMYB32 directly binds to the MBS cis-element in the <i>FtCES18</i> promoter to activate its expression. Notably, evolutionary analysis revealed a domestication-associated C-terminal truncation in the cultivated FtMYB32 that impairs its transactivation capacity, explaining the compromised basal resistance in cultivated accessions compared to their wild ancestors. Crucially, a natural single-nucleotide polymorphism (SNP) in the <i>FtMYB32</i> promoter defines a superior haplotype (hapC) conferring enhanced basal transcriptional activity. This natural variation in promoter activity controls the expression abundance of the <i>FtMYB32</i>-<i>FtCES18</i> module via a “dosage fine-tuning” effect, which is subsequently amplified by the downstream metabolic cascade, ultimately contributing to the natural variation in disease resistance among different Tartary buckwheat accessions. This study provides valuable genetic resources and a theoretical basis for breeding novel Tartary buckwheat varieties with high disease resistance.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71176","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149259352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstructing tissue culture to improve Agrobacterium-mediated transformation of maize","authors":"Seijiro Ono,&nbsp;Misato Ono,&nbsp;Reinhold Brettschneider,&nbsp;Dagmar Sauer,&nbsp;Katja Müller,&nbsp;Martina Balboni,&nbsp;Max van der Heide,&nbsp;Arp Schnittger","doi":"10.1111/tpj.71183","DOIUrl":"https://doi.org/10.1111/tpj.71183","url":null,"abstract":"<p>The ability to insert, delete, or modify genetic information is crucial for mechanistic studies and biotechnological applications. However, efficient genetic transformation remains a major bottleneck for research in maize and many other crops. Here, we report an optimized <i>Agrobacterium</i>-mediated transformation platform based on systematic reconstruction of tissue culture handling in the maize inbred line A188. Refinement of callus induction, selection, and regeneration substantially improved recovery of transgenic plantlets. To distinguish independent T-DNA insertion events, we developed TAFLP (T-DNA amplified fragment length polymorphism), a simple and inexpensive assay that amplifies T-DNA flanking sequences and can be performed using standard laboratory equipment. Our enhanced transformation pipeline was also applicable to the inbred line B104 as well as to hygromycin and G418 selection systems, demonstrating broad utility of our method. We validated the platform for CRISPR/Cas9 mutagenesis and reporter-line generation. Using this approach, we isolated new loss-of-function alleles of the maize-specific <i>MAC1</i> (<i>MULTIPE ARCHESPORIAL CELLS 1</i>) and F-box protein encoding <i>ACOZ1</i> (<i>ABNORMAL CHROMOSOME ORGANIZATION IN ZYGOTENE 1</i>), a homolog of the Arabidopsis <i>RMF1/2</i> (<i>REDUCED MALE FERTILITY 1/2</i>) and rice <i>ZYGO1</i> (<i>ZYGOTENE 1</i>). The concomitant generation of reporter lines for ACOZ1 and the nuclear lamin-like proteins NCH1 (NMCP/CROWN HOMOLOG1) and NCH2, as well as SUN1 (SUN DOMAIN PROTEIN 1) revealed that the function of this F-box protein class in releasing the somatic constraints of chromosome organization for meiotic recombination is highly conserved in flowering plants.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71183","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149258662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The MdVQ22-MdWRKY33d complex regulates MdPER55 and MdDREB1D expression to modulate apple salt tolerance by reactive oxygen species scavenging","authors":"Hongmin Hou,&nbsp;Shuxin Li,&nbsp;Qi Zhang,&nbsp;Guo Chen,&nbsp;Wengang Wu,&nbsp;Xueli Liu,&nbsp;Shenghui Jiang,&nbsp;Jihua Xu,&nbsp;Xiao Liang,&nbsp;Dingchang Meng,&nbsp;Abdulqahhor Toshpulatov Khusniddinugli,&nbsp;Farrukh Matkarimov Ilkhomovich,&nbsp;Yugang Zhang","doi":"10.1111/tpj.71191","DOIUrl":"https://doi.org/10.1111/tpj.71191","url":null,"abstract":"<p>Apple is a globally significant fruit tree with considerable economic value. However, it is severely affected by soil salinization, which leads to a reduction in both yield and quality. Since salt tolerance in grafted apple trees largely depends on the rootstock, this study compared transcriptomic responses between salt-tolerant (R5-5) and salt-sensitive (M9T337) rootstocks under salt stress. A key salt-responsive gene, <i>MdWRKY33d</i>, was identified. Overexpressing <i>MdWRKY33d</i> in apple improved salt tolerance, while silencing it had the opposite effect. Additionally, under salt stress, compared with the control, chlorophyll fluorescence values, superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) levels were elevated in <i>MdWRKY33d</i> transgenic apple and poplar materials. Functional analyses demonstrated that <i>MdWRKY33d</i> directly activates the expression of <i>Peroxidase55</i> (<i>MdPER55</i>) and <i>Dehydration-Responsive Element-Binding protein1D</i> (<i>MdDREB1D</i>), thereby enhancing reactive oxygen species (ROS) scavenging and salt tolerance in transgenic plants. Yeast two-hybrid screening identified MdVQ22 as an interacting partner of MdWRKY33d, which was confirmed by pull-down, bimolecular fluorescence complementation (BiFC), and luciferase complementation imaging (LCI) assays. <i>MdVQ22</i> negatively regulated apple salt tolerance by suppressing MdWRKY33d-mediated transcriptional activation of <i>MdPER55</i> and <i>MdDREB1D</i>. Collectively, this study explores a putative regulatory module MdVQ22-MdWRKY33d-<i>MdPER55</i>/<i>MdDREB1D</i> to coordinate the responses to apple salt stress and provides potential targets for engineering salt-tolerant varieties.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71191","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149258603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SDG26 integrates ABA-dependent and ABA-independent pathways to regulate cold stress responses in Arabidopsis via chromatin modification","authors":"Xue Zhang,&nbsp;Julie Lapierre,&nbsp;Julie Zumsteg,&nbsp;Mathieu Erhardt,&nbsp;Wen-Hui Shen,&nbsp;Alexandre Berr","doi":"10.1111/tpj.71180","DOIUrl":"https://doi.org/10.1111/tpj.71180","url":null,"abstract":"<p>Plants constantly face adverse environmental conditions, with temperature drops posing major threats to growth and productivity. To adapt, plants have evolved complex mechanisms of transcriptional reprogramming. While various cold-responsive pathways have been described, the contribution of chromatin-level regulation, particularly histone modifications, remains poorly understood. Here, we identify the histone methyltransferase SET DOMAIN GROUP 26 (SDG26) as a positive regulator of cold stress responses in <i>Arabidopsis thaliana</i>. We show that <i>SDG26</i> is transcriptionally induced and posttranscriptionally stabilized by cold, and that its loss of function compromises several abscisic acid (ABA)-related phenotypes. At the molecular level, SDG26 promotes the expression of cold-responsive genes, including members of the CBF-COR regulon, through direct chromatin binding and deposition of histone H3 lysine 36 trimethylation (H3K36me3). Additionally, SDG26 modulates ABA biosynthesis, catabolism, and transport, thereby promoting ABA accumulation, stomatal closure, and drought tolerance. Collectively, our results reveal that SDG26 integrates ABA-dependent and ABA-independent pathways to fine-tune Arabidopsis responses to abiotic stresses. We further establish SDG26 as a chromatin modifier contributing to stress-responsive H3K36me3 enrichment at specific loci. Together, our findings position SDG26 as a chromatin-based hub that coordinates cold acclimation and water conservation to enhance plant resilience.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71180","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149258605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MdMPK6a/b-mediated phosphorylation of MdANN2 restricts cytosolic Ca2+ influx and attenuates cold tolerance in apple","authors":"Jinzhu Wang,&nbsp;Mengyao Yang,&nbsp;Yehua Li,&nbsp;Lepu Jiang,&nbsp;Yanghao Long,&nbsp;Zhijun Zhang,&nbsp;Lina Qiu,&nbsp;Jie Yang,&nbsp;Fengwang Ma,&nbsp;Ke Mao","doi":"10.1111/tpj.71182","DOIUrl":"https://doi.org/10.1111/tpj.71182","url":null,"abstract":"<p>Annexins (ANNs) are Ca²⁺-dependent phospholipid-binding proteins that play important roles in plant responses to environmental stress. However, the apple <i>ANN</i> gene family and the regulatory mechanisms by which ANNs participate in cold-stress responses remain poorly understood. In this study, 15 MdANN family members were identified in the apple genome and divided into three subfamilies. Among them, <i>MdANN2</i> expression was strongly induced by low temperature. Functional analyses showed that <i>MdANN2</i> overexpression markedly enhanced cold tolerance in apple, whereas virus-induced gene silencing (VIGS) of <i>MdANN2</i> compromised cold tolerance. Subcellular localization assays revealed that MdANN2 localized to the plasma membrane, cytoplasm, and nucleus. Non-invasive micro-test technology (NMT) further showed that MdANN2 is associated with Ca²⁺-permeable channel activity: cold stimulation significantly enhanced cytosolic Ca²⁺ influx in <i>MdANN2</i>-overexpressing plants, whereas exogenous application of the Ca²⁺ channel blocker LaCl₃ or the Ca²⁺ chelator EGTA substantially inhibited this influx. The kinases MdMPK6a and MdMPK6b physically interacted with and phosphorylated MdANN2 both <i>in vitro</i> and <i>in vivo</i>. Silencing <i>MdMPK6a/b</i> significantly increased apple cold tolerance, whereas overexpression of <i>MdMPK6a/b</i> reduced apple cold tolerance. Moreover, transient overexpression of <i>MdMPK6a/b</i> in the <i>MdANN2</i>-overexpression background attenuated MdANN2-mediated cold tolerance and Ca²⁺ influx. In addition, co-localization assays showed that MdMPK6a/b decreased the accumulation of MdANN2 at the plasma membrane. Together, these findings demonstrate that MdANN2 positively regulates apple cold tolerance by promoting cold-induced Ca²⁺ influx, a process inhibited by MdMPK6a/b-mediated phosphorylation. This study identifies a novel MdMPK6a/b-MdANN2 module that governs Ca²⁺ signaling in apple under cold stress, thereby providing promising molecular targets for improving cold tolerance in apple and other crop species.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71182","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149258606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-peroxisomal allantoin biosynthesis reveals unexpected flexibility in plant purine catabolism","authors":"Yuta Takeuchi,&nbsp;Tamio Sumida,&nbsp;Hiroshi Shimada,&nbsp;Atsushi Sakamoto","doi":"10.1111/tpj.71178","DOIUrl":"https://doi.org/10.1111/tpj.71178","url":null,"abstract":"<p>Allantoin, a central intermediate of purine catabolism, plays key roles in nitrogen remobilization and is also implicated in stress protection in plants. As in other eukaryotes, allantoin biosynthesis in land plants has long been considered restricted to peroxisomes, where this process is catalyzed by ALLANTOIN SYNTHASE (ALNS). However, angiosperms produce not only the canonical peroxisomal isoform but also a shorter splice variant lacking a type 2 peroxisomal targeting signal (PTS2), raising the question of whether allantoin biosynthesis can occur outside peroxisomes. Through comparative sequence analyses across Archaeplastida, we show that PTS2-lacking ALNS exhibits a patchy distribution within Viridiplantae, including species without identifiable PTS2-containing ALNS homologs, suggesting the evolutionary significance of non-peroxisomal allantoin biosynthesis. Fluorescent protein fusion analysis showed that PTS2-lacking ALNS proteins from the angiosperm <i>Arabidopsis thaliana</i>, the monilophyte <i>Dryopteris erythrosora</i>, and the bryophyte <i>Marchantia polymorpha</i> localize outside peroxisomes, consistent with cytosolic localization. Furthermore, recombinant proteins from all three species catalyzed stereospecific (<i>S</i>)-allantoin formation. <i>Arabidopsis alns</i> knockout mutants accumulated racemic allantoin, indicating that ALNS ensures the stereospecific formation of (<i>S</i>)-allantoin while preventing the generation of poorly metabolizable (<i>R</i>)-allantoin, which likely arises through spontaneous decomposition of the unstable ALNS substrate 5-hydroxyisourate. Importantly, expression of either ALNS isoform restored normal allantoin metabolism and largely rescued the growth and physiological defects of the <i>alns</i> mutants. These findings demonstrate the functional equivalence of cytosolic and peroxisomal ALNS in <i>Arabidopsis</i> and reveal previously unrecognized flexibility in the subcellular organization of purine catabolism in plants.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71178","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149258604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome architecture modulates 35S and 5S rDNA homogenization in Asteraceae","authors":"Daniel Vitales,&nbsp;Joan Pere Pascual-Díaz,&nbsp;Veronika Zoulová,&nbsp;Ales Kovarik,&nbsp;Sònia Garcia","doi":"10.1111/tpj.71174","DOIUrl":"https://doi.org/10.1111/tpj.71174","url":null,"abstract":"<p>Concerted evolution is the model by which multicopy gene families are homogenized across genomes, with ribosomal DNA (rDNA) as its textbook example. However, the extent and efficiency of this process may vary depending on genomic factors. The plant family Asteraceae provides a natural comparative system to address the evolutionary dynamics of rDNA, as it is uniquely characterized by the coexistence of two contrasting genomic arrangements: a separate (S-type) and a linked (L-type) organization of 5S and 35S rRNA genes. Here we analyzed rDNA arrangements in 71 representative Asteraceae species (50 S-type and 21 L-type) and, using WGS data and repeatome analyses, we have reconstructed full rDNA units and quantified the intragenomic variability across coding (genic) and non-coding (spacer) regions. No intermediate (coexisting L-type+S-type) genotypes were found. Our results reveal contrasting patterns of 5S rDNA variation depending on its genomic context. S-type species exhibit high levels of 5S polymorphism in both genic and spacer regions, while L-type species show near-complete sequence homogeneity, consistent with variation in homogenization efficiency and selective constraints related to copy number and chromosomal position of 5S rRNA genes. In contrast, 35S rDNA shows a low polymorphism level overall. The findings support a context-dependent view of concerted evolution across rDNA and highlight the influence of genome architecture on rDNA evolution. In particular, the contrasting behavior of 5S (highly conserved when linked but highly variable when separate) emerges as a key example of how structural genomic context shapes the evolution of even the most conserved housekeeping genes.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71174","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149235349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens","authors":"Nancy Choudhary,&nbsp;Shakunthala Natarajan,&nbsp;Clara Morweiser,&nbsp;Nele Grünig,&nbsp;Marie Hagedorn,&nbsp;Jakob Franke,&nbsp;Boas Pucker","doi":"10.1111/tpj.71173","DOIUrl":"https://doi.org/10.1111/tpj.71173","url":null,"abstract":"<p>Specialised metabolism is an important factor in how plants cope with biotic and, to a lesser extent, abiotic stress. Current approaches to identify and study the genes involved in such metabolic pathways mainly leverage genomic and transcriptomic datasets of plants, in order to improve our understanding of plant resilience. Even though modern sequencing techniques have provided access to high-quality reference genome or transcriptome datasets, sequencing costs have for a long time forced a restriction to a selected reference accession. However, individual plants within a population often exhibit substantial differences in metabolic profiles, sometimes even leading to completely different chemotypes. This generated an urgent need to transition from single-reference accessions to the wider diversity of plant populations or even beyond the species level. Thanks to decreasing costs and improved reliability of sequencing techniques, this is now possible through pangenomic or pantranscriptomic approaches. In this review, we provide an introduction into the current state of the fields of pangenomics and pantranscriptomics and highlight recent examples on how these approaches have been used to elucidate and investigate specialised metabolic pathways in plants. We also provide an overview of database resources that might be useful for researchers in the field. Lastly, we present a critical summary and discussion of limitations and trends that are important for future innovations. With these developments in mind, we anticipate that pangenomics and pantranscriptomics will play a crucial role in exploring and harnessing the diversity of plant specialised metabolism beyond single individuals.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71173","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149235413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Red to green: catching gene silencing as it takes hold","authors":"Charlay Wood","doi":"10.1111/tpj.71188","DOIUrl":"10.1111/tpj.71188","url":null,"abstract":"&lt;p&gt;A green &lt;i&gt;Arabidopsis&lt;/i&gt; seedling that ought to be magenta looks like a failed transformation. Xin Wei, Yanming Hou, Yuyang Si and colleagues have turned it into a screen. They gave the plant's silencing machinery a pigment gene to switch off and then looked for mutants that switched it back on. The screen recovered more than twice as many post-transcriptional gene silencing (PTGS) alleles as any earlier reporter system has produced. Because the pigment can be scored on a living plant, from cotyledon to flower, it also shows when silencing takes hold, not just whether it does.&lt;/p&gt;&lt;p&gt;PTGS underpins antiviral immunity and endogenous gene regulation in plants (Hamilton &amp; Baulcombe, &lt;span&gt;1999&lt;/span&gt;), and its core components came out of forward genetic screens using GFP, GUS or luciferase reporters (Dalmay et al., &lt;span&gt;2000&lt;/span&gt;; Mourrain et al., &lt;span&gt;2000&lt;/span&gt;). However, GFP requires excitation and imaging equipment; GUS assays require a substrate and destructive sampling; luciferase needs a substrate and a sensitive detector; and none are easy to analyse across thousands of seedlings. Earlier screens also produced more limited allelic series and made weak, developmentally changing phenotypes harder to resolve.&lt;/p&gt;&lt;p&gt;&lt;i&gt;RUBY&lt;/i&gt; solves that a change in PTGS becomes a change in colour (He et al., &lt;span&gt;2020&lt;/span&gt;). However, a &lt;i&gt;35S::RUBY&lt;/i&gt; plant is already red, and picking a slightly redder seedling out of thousands is no easy feat. Wei and colleagues therefore crossed a stable &lt;i&gt;35S::RUBY&lt;/i&gt; line into &lt;i&gt;ein5-1&lt;/i&gt;, a mutant lacking the 5′→3′ exoribonuclease EIN5 (Olmedo et al., &lt;span&gt;2006&lt;/span&gt;), whose loss raises small RNA levels and strengthens silencing of coding genes (Wu et al., &lt;span&gt;2020&lt;/span&gt;; Zhang et al., &lt;span&gt;2015&lt;/span&gt;). In this background, the reporter's own aberrant transcripts trigger silencing of &lt;i&gt;RUBY&lt;/i&gt; itself. Plants accumulate &lt;i&gt;RUBY&lt;/i&gt;-derived 21- and 22-nt siRNAs and are fully green as early as 4–5 days after germination, early enough to screen seedlings by eye. Green is now the starting point, and a known &lt;i&gt;rdr6-11&lt;/i&gt; mutation turns the pigment back on (Figure 1a). Losing colour means silencing is working; regaining it means silencing has failed.&lt;/p&gt;&lt;p&gt;EMS mutagenesis and bulked segregant resequencing identified 162 non-redundant alleles. Most lie in the four core PTGS components: 68 in &lt;i&gt;RDR6&lt;/i&gt;, 22 in &lt;i&gt;SGS3&lt;/i&gt;, 11 in &lt;i&gt;AGO1&lt;/i&gt; and 12 in &lt;i&gt;SDE5&lt;/i&gt;, with 49 more spread across other loci. The latter represent candidate regulators distributed across 26 genes and remain to be functionally validated. The classic &lt;i&gt;35S::GUS&lt;/i&gt; system has produced 61 alleles across several studies on the same count, including a single &lt;i&gt;sde5&lt;/i&gt; allele against 12 identified by Wei et al. (Figure 1b). Every allele here was recovered because silencing was weakened, delayed or lost. The same logic sets this &lt;i&gt;RUBY&lt;/i&gt;-based screen's limitation: with no pigment left to lose in the green parental line, it ca","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13686652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149230876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Out of the shadows: Phosphatase PP2A promotes shade avoidance by dephosphorylating phytochrome-interacting factor 7","authors":"Brian C. Mooney","doi":"10.1111/tpj.71158","DOIUrl":"10.1111/tpj.71158","url":null,"abstract":"&lt;p&gt;In dense vegetation, plants fiercely compete with their neighbours for sunlight. Shade-avoiding species like &lt;i&gt;Arabidopsis thaliana&lt;/i&gt; respond to vegetative shade with a series of adaptations collectively known as shade-avoidance syndrome (SAS). SAS includes the elongation of hypocotyls and stems alongside upward leaf movement and a decrease in leaf blade area. These responses enable plants to grow beyond their neighbour's shadow and regain access to light (Casal, &lt;span&gt;2013&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;Leaves primarily absorb red (R) light while reflecting far-red (FR) wavelengths. Plants detect vegetative shade by monitoring the ratio of R:FR light using the photoreceptor phytochrome B (phyB) (Reed et al., &lt;span&gt;1993&lt;/span&gt;). When red light is abundant, the active ‘Pfr’ conformation of phyB translocates to the nucleus where it promotes the phosphorylation and subsequent degradation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factors. In shade (when R:FR &lt; 1), phyB is maintained in the cytosol in an inactive ‘Pr’ state, allowing PIFs to accumulate and drive the expression of genes that promote SAS.&lt;/p&gt;&lt;p&gt;PIF7 has emerged as the central regulator of the shade avoidance response (Li et al., &lt;span&gt;2012&lt;/span&gt;). Its regulatory activity is partly controlled by reversible phosphorylation. Under white light, both phosphorylated and unphosphorylated forms co-exist. Phosphorylated PIF7 is restricted to the cytoplasm, while the unphosphorylated form accumulates in the nucleus. However, nuclear phyB sequesters PIF7 in condensates leading to the suppression of its DNA-binding activity. In shade, PIF7 is largely dephosphorylated. Coupled with the exclusion of inactive phyB from the nucleus, this enables PIF7 to activate the transcription of auxin biosynthesis and signalling genes, thereby promoting SAS-related elongation. Despite the importance of this PIF7 phosphorylation switch, the enzymes responsible for its regulation have remained unknown.&lt;/p&gt;&lt;p&gt;Professor Enamul Huq at The University of Texas at Austin investigates how plants perceive and respond to light. Considering his group's long-standing interest in phytochromes and PIFs, elucidating the regulation of PIF7 was a natural progression. In their new study, Huq's group revealed that phosphatase PP2A dephosphorylates PIF7 to promote shade avoidance (Cai et al., &lt;span&gt;2026&lt;/span&gt;). This work also included a collaboration with researchers specialising in phosphatase biology at Hebei Normal University, the previous home of first author Xingbo Cai.&lt;/p&gt;&lt;p&gt;PP2A is a heterotrimeric phosphatase comprising scaffold (A), regulatory (B) and catalytic (C) subunits. The Arabidopsis genome encodes 17 B subunit isoforms which are responsible for substrate specificity and subcellular localisation. Huq's group recently identified four PP2A B subunits that dephosphorylate another PIF family member, PIF3 (Cai et al., &lt;span&gt;2024&lt;/span&gt;). To determine whether these subunits also regulate PIF7 during shade avoidance, Ca","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"127 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71158","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149190323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}