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Epigenetic regulation of ISPL10 enhances regional adaptability of rice varieties
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-25 DOI: 10.1111/tpj.70109
Zhiwen Yu, Xiaoche Wang, Yongzheng Wang, Jiahao Lu, Hao Chen, Xiang Li, Hai Xu, Fengcheng Li, Wenfu Chen, Quan Xu

Suppressing the heading date of rice under short-day (SD) conditions while promoting it under long-day (LD) conditions can significantly enhance the regional adaptability of rice varieties. However, rice germplasm resources with these traits are scarce. In this study, we report the Jumonji C (jmjC) protein-encoding gene ISPL10. The ispl10 mutant exhibited heading 7 days later under SD and 14 days earlier under LD compared with the wild type (WT). ISPL10 decreased H3 lysine 9 dimethylation (H3K9me2) levels at the OsMADS51 locus and activated the expression of OsMADS51, which then enhanced the expression of Ehd1 and up-regulated Hd3a under SD conditions. By contrast, ISPL10 is directly bound to the promoter of OsVIL2 to suppress its expression, thereby inhibiting Ehd1 expression and reducing RFT1 expression under LD conditions. Additionally, ISPL10 interacted with Se14, another jmjC protein that controlled H3K4me3 states in the RFT1 chromatin. The field tests showed that the ispl10 mutant not only extended the growth period in low-latitude regions but also shortened the maturity duration in high-latitude regions, and thus significantly increased grain yield in both low- and high-latitude regions compared with WT. Therefore, the ISPL10 locus could be a crucial factor in improving the regional adaptability of rice varieties.

{"title":"Epigenetic regulation of ISPL10 enhances regional adaptability of rice varieties","authors":"Zhiwen Yu,&nbsp;Xiaoche Wang,&nbsp;Yongzheng Wang,&nbsp;Jiahao Lu,&nbsp;Hao Chen,&nbsp;Xiang Li,&nbsp;Hai Xu,&nbsp;Fengcheng Li,&nbsp;Wenfu Chen,&nbsp;Quan Xu","doi":"10.1111/tpj.70109","DOIUrl":"https://doi.org/10.1111/tpj.70109","url":null,"abstract":"<div>\u0000 \u0000 <p>Suppressing the heading date of rice under short-day (SD) conditions while promoting it under long-day (LD) conditions can significantly enhance the regional adaptability of rice varieties. However, rice germplasm resources with these traits are scarce. In this study, we report the Jumonji C (jmjC) protein-encoding gene <i>ISPL10</i>. The <i>ispl10</i> mutant exhibited heading 7 days later under SD and 14 days earlier under LD compared with the wild type (WT). ISPL10 decreased H3 lysine 9 dimethylation (H3K9me2) levels at the <i>OsMADS51</i> locus and activated the expression of <i>OsMADS51</i>, which then enhanced the expression of <i>Ehd1</i> and up-regulated <i>Hd3a</i> under SD conditions. By contrast, ISPL10 is directly bound to the promoter of <i>OsVIL2</i> to suppress its expression, thereby inhibiting <i>Ehd1</i> expression and reducing <i>RFT1</i> expression under LD conditions. Additionally, ISPL10 interacted with Se14, another jmjC protein that controlled H3K4me3 states in the <i>RFT1</i> chromatin. The field tests showed that the <i>ispl10</i> mutant not only extended the growth period in low-latitude regions but also shortened the maturity duration in high-latitude regions, and thus significantly increased grain yield in both low- and high-latitude regions compared with WT. Therefore, the <i>ISPL10</i> locus could be a crucial factor in improving the regional adaptability of rice varieties.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690134","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}
引用次数: 0
The chromatin accessibility landscape during early maize seed development
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-24 DOI: 10.1111/tpj.70073
Guang Ming Zheng, Jia Wen Wu, Jun Li, Ya Jie Zhao, Chao Zhou, Ru Chang Ren, Yi Ming Wei, Xian Sheng Zhang, Xiang Yu Zhao

Cis-regulatory elements (CREs) are enriched in accessible chromatin regions (ACRs) of eukaryotes. Despite extensive research on genome-wide ACRs in various plant tissues, the global impact of these changes on developmental processes in maize seeds remains poorly understood. In this study, we employed the assay for transposase-accessible chromatin sequencing (ATAC-seq) to reveal the chromatin accessibility profile throughout the genome during the early stages of maize seed development. We identified a total of 37 952 to 59 887 high-quality ACRs in maize seeds at 0 to 8 days after pollination (DAP). Furthermore, we examined the correlation between the identified ACRs and gene expression. We observed a positive correlation between the open degree of promoter-ACRs and the expression of most genes. Moreover, we identified binding footprints of numerous transcription factors (TFs) within chromatin accessibility regions and revealed key TF families involved in different stages. Through the footprints of accessible chromatin regions, we predicted transcription factor regulatory networks during early maize embryo development. Additionally, we discovered that DNA sequence diversity was notably reduced at ACRs, yet trait-associated SNPs were more likely to be located within ACRs. We edited the ACR containing the trait-associated SNP of NKD1. Both NKD1pro-1 and NKD1pro-2 showed phenotypes corresponding to the trait-associated SNP. Our results suggest that alterations in chromatin accessibility play a crucial role in maize seed development and highlight the potential contribution of open chromatin regions to advancements in maize breeding.

{"title":"The chromatin accessibility landscape during early maize seed development","authors":"Guang Ming Zheng,&nbsp;Jia Wen Wu,&nbsp;Jun Li,&nbsp;Ya Jie Zhao,&nbsp;Chao Zhou,&nbsp;Ru Chang Ren,&nbsp;Yi Ming Wei,&nbsp;Xian Sheng Zhang,&nbsp;Xiang Yu Zhao","doi":"10.1111/tpj.70073","DOIUrl":"https://doi.org/10.1111/tpj.70073","url":null,"abstract":"<p><i>Cis</i>-regulatory elements (CREs) are enriched in <i>accessible chromatin regions</i> (ACRs) of eukaryotes. Despite extensive research on genome-wide ACRs in various plant tissues, the global impact of these changes on developmental processes in maize seeds remains poorly understood. In this study, we employed the assay for transposase-accessible chromatin sequencing (ATAC-seq) to reveal the chromatin accessibility profile throughout the genome during the early stages of maize seed development. We identified a total of 37 952 to 59 887 high-quality ACRs in maize seeds at 0 to 8 days after pollination (DAP). Furthermore, we examined the correlation between the identified ACRs and gene expression. We observed a positive correlation between the open degree of promoter-ACRs and the expression of most genes. Moreover, we identified binding footprints of numerous transcription factors (TFs) within chromatin accessibility regions and revealed key TF families involved in different stages. Through the footprints of accessible chromatin regions, we predicted transcription factor regulatory networks during early maize embryo development. Additionally, we discovered that DNA sequence diversity was notably reduced at ACRs, yet trait-associated SNPs were more likely to be located within ACRs. We edited the ACR containing the trait-associated SNP of <i>NKD1</i>. Both <i>NKD1</i><sup><i>pro</i></sup><i>-1</i> and <i>NKD1</i><sup><i>pro</i></sup><i>-2</i> showed phenotypes corresponding to the trait-associated SNP. Our results suggest that alterations in chromatin accessibility play a crucial role in maize seed development and highlight the potential contribution of open chromatin regions to advancements in maize breeding.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70073","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689728","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}
引用次数: 0
The role of DNA content in shaping chromatin architecture and gene expression
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-24 DOI: 10.1111/tpj.70116
Alfonso Carlos Barragán-Rosillo, Ricardo A. Chávez Montes, Luis Herrera-Estrella

Whole-genome duplication is an evolutionary force that drives speciation in all living kingdoms and is notably prevalent in plants. The evolutionary history of plants involved at least two genomic duplications that significantly expanded the plant morphology and physiology spectrum. Many important crops are polyploids, showing valuable features relative to morphological and stress response traits. After genome duplication, diploidization processes facilitate genomic adjustments to restore disomic inheritance. However, little is known about the chromatin changes triggered by nuclear DNA content alterations. Here, we report that synthetically induced genome duplication leads to chromatinization and significant changes in gene expression, resulting in a transcriptional landscape resembling a natural tetraploid. Interestingly, synthetic diploidization elicits only minor alterations in transcriptional activity and chromatin accessibility compared to the more pronounced effects of tetraploidization. We identified epigenetic factors, including specific histone variants, that showed increased expression following genome duplication and decreased expression after genome reduction. These changes may play a key role in the epigenetic mechanisms underlying the phenotypic complexity after tetraploidization in plants. Our findings shed light on the mechanisms that modulate chromatin accessibility remodeling and gene transcription regulation underlying plant genome adaptation in response to changes in genome size.

{"title":"The role of DNA content in shaping chromatin architecture and gene expression","authors":"Alfonso Carlos Barragán-Rosillo,&nbsp;Ricardo A. Chávez Montes,&nbsp;Luis Herrera-Estrella","doi":"10.1111/tpj.70116","DOIUrl":"https://doi.org/10.1111/tpj.70116","url":null,"abstract":"<p>Whole-genome duplication is an evolutionary force that drives speciation in all living kingdoms and is notably prevalent in plants. The evolutionary history of plants involved at least two genomic duplications that significantly expanded the plant morphology and physiology spectrum. Many important crops are polyploids, showing valuable features relative to morphological and stress response traits. After genome duplication, diploidization processes facilitate genomic adjustments to restore disomic inheritance. However, little is known about the chromatin changes triggered by nuclear DNA content alterations. Here, we report that synthetically induced genome duplication leads to chromatinization and significant changes in gene expression, resulting in a transcriptional landscape resembling a natural tetraploid. Interestingly, synthetic diploidization elicits only minor alterations in transcriptional activity and chromatin accessibility compared to the more pronounced effects of tetraploidization. We identified epigenetic factors, including specific histone variants, that showed increased expression following genome duplication and decreased expression after genome reduction. These changes may play a key role in the epigenetic mechanisms underlying the phenotypic complexity after tetraploidization in plants. Our findings shed light on the mechanisms that modulate chromatin accessibility remodeling and gene transcription regulation underlying plant genome adaptation in response to changes in genome size.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689727","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}
引用次数: 0
Deletion of GhSCY2D Causes Impaired Chloroplast Development and Temperature-Dependent Leaf Yellowing in Cotton (Gossypium hirsutum L.).
IF 6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-24 DOI: 10.1111/pce.15476
Xiaokang Feng, Yanmei Ma, Qian Liang, Yanlong Jin, Xuefeng Wang, Jianhang Wang, Feng Liu, Xinyu Zhang, Dongnan Shao, Jie Sun, Qian-Hao Zhu, Fei Xue

Leaf colour mutants play an important role in understanding chlorophyll metabolism and photosynthesis. In this study, we characterised a temperature-sensitive yellow leaf cotton mutant. Genome re-sequencing and comparison identified a 10.327 Kb deletion on the D12 chromosome (D12:670726-681053) in the mutant. The deletion region contains two annotated genes, GH_D12G0047 and GH_D12G0048. Investigations integrating gene mapping, comparative transcriptome analysis, gene annotation, virus-induced gene silencing and gene complementation, found deletion of GH_D12G0047 or GhSCY2D, a crucial constituent of the Sec2 complex essential for the function of chloroplasts, being responsible for the yellow leaf phenotype. The yellow leaf mutant had disrupted chloroplast structure and hindered chlorophyll synthesis when temperature was below 28°C but regained normal green leaf colour at 32°C. By analysing the transcriptome data and hormonal level changes of the mutant under conditions of 25°C and 32°C, it was found that the jasmonic acid signalling pathway and GhSCY2 work in concert to maintain the structural integrity of chloroplasts. The outcomes of the study reveal the indispensable role of GhSCY2 and jasmonic acid in sustaining chloroplast homoeostasis, providing new insights into the regulation of cotton leaf colour and paving the way for advancement in high photosynthetic efficiency breeding strategies.

{"title":"Deletion of GhSCY2D Causes Impaired Chloroplast Development and Temperature-Dependent Leaf Yellowing in Cotton (Gossypium hirsutum L.).","authors":"Xiaokang Feng, Yanmei Ma, Qian Liang, Yanlong Jin, Xuefeng Wang, Jianhang Wang, Feng Liu, Xinyu Zhang, Dongnan Shao, Jie Sun, Qian-Hao Zhu, Fei Xue","doi":"10.1111/pce.15476","DOIUrl":"https://doi.org/10.1111/pce.15476","url":null,"abstract":"<p><p>Leaf colour mutants play an important role in understanding chlorophyll metabolism and photosynthesis. In this study, we characterised a temperature-sensitive yellow leaf cotton mutant. Genome re-sequencing and comparison identified a 10.327 Kb deletion on the D12 chromosome (D12:670726-681053) in the mutant. The deletion region contains two annotated genes, GH_D12G0047 and GH_D12G0048. Investigations integrating gene mapping, comparative transcriptome analysis, gene annotation, virus-induced gene silencing and gene complementation, found deletion of GH_D12G0047 or GhSCY2D, a crucial constituent of the Sec2 complex essential for the function of chloroplasts, being responsible for the yellow leaf phenotype. The yellow leaf mutant had disrupted chloroplast structure and hindered chlorophyll synthesis when temperature was below 28°C but regained normal green leaf colour at 32°C. By analysing the transcriptome data and hormonal level changes of the mutant under conditions of 25°C and 32°C, it was found that the jasmonic acid signalling pathway and GhSCY2 work in concert to maintain the structural integrity of chloroplasts. The outcomes of the study reveal the indispensable role of GhSCY2 and jasmonic acid in sustaining chloroplast homoeostasis, providing new insights into the regulation of cotton leaf colour and paving the way for advancement in high photosynthetic efficiency breeding strategies.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690433","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}
引用次数: 0
OsPHP1 as a Negative Regulator of Cytokinin Signaling in Rice Stress Responses.
IF 6 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-24 DOI: 10.1111/pce.15498
Hongfei Li, Yanjie Xie
{"title":"OsPHP1 as a Negative Regulator of Cytokinin Signaling in Rice Stress Responses.","authors":"Hongfei Li, Yanjie Xie","doi":"10.1111/pce.15498","DOIUrl":"https://doi.org/10.1111/pce.15498","url":null,"abstract":"","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690364","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}
引用次数: 0
The F box protein INHIBITOR FOR BROWN FURROWS 1 (IBF1) regulates flavonoid accumulation in rice hull by promoting degradation of chalcone synthase 1
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-23 DOI: 10.1111/tpj.70105
Weiyan Li, Jingjing Zhang, Wan Zhang, Qiuxin Zhang, Haoyuan Wang, Tingting Xu, Zhongxian Chen, Zemin Zhang

Flavonoids are secondary metabolites of plants that play various roles in plants. The transcriptional level regulation of flavonoid synthesis in plants has been extensively studied, but research on the protein level of flavonoid synthesis in plants is still limited. In the present study, a brown hull mutant, bh2, was screened from an ethane methyl sulfonate (EMS)-induced bank from the seeds of the indica cultivar RH2B. The bh2 mutant exhibited a brown hull phenotype and higher levels of total flavonoids and anthocyanins compared with wild-type plants. We identified the gene INHIBITOR FOR BROWN FURROWS 1 (IBF1) in the bh2 mutant through MutMap analysis and subsequently cloned it. IBF1 encodes an F-box protein and is involved in the formation of an SCF (S-phase kinase-associated protein 1 [SKP1], Cullin, and F-box) complex with the Oryza sativa SKP1-like proteins OSK1/OSK20. Through yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays, the interaction of IBF1 with chalcone synthase 1 (CHS1) was confirmed. This interaction facilitated the degradation of CHS1 through the ubiquitin-26S proteasome system. The ibf1 chs1 double mutants exhibited normal hull color, restoring the phenotype of ibf1. Genetic analysis suggested that IBF1 regulates hull color in a CHS1-dependent manner. Collectively, our study suggests that IBF1 serves as a crucial negative regulator that controls flavonoid biosynthesis by mediating CHS1 degradation, thereby regulating hull color.

{"title":"The F box protein INHIBITOR FOR BROWN FURROWS 1 (IBF1) regulates flavonoid accumulation in rice hull by promoting degradation of chalcone synthase 1","authors":"Weiyan Li,&nbsp;Jingjing Zhang,&nbsp;Wan Zhang,&nbsp;Qiuxin Zhang,&nbsp;Haoyuan Wang,&nbsp;Tingting Xu,&nbsp;Zhongxian Chen,&nbsp;Zemin Zhang","doi":"10.1111/tpj.70105","DOIUrl":"https://doi.org/10.1111/tpj.70105","url":null,"abstract":"<div>\u0000 \u0000 <p>Flavonoids are secondary metabolites of plants that play various roles in plants. The transcriptional level regulation of flavonoid synthesis in plants has been extensively studied, but research on the protein level of flavonoid synthesis in plants is still limited. In the present study, a brown hull mutant, <i>bh2</i>, was screened from an ethane methyl sulfonate (EMS)-induced bank from the seeds of the indica cultivar RH2B. The <i>bh2</i> mutant exhibited a brown hull phenotype and higher levels of total flavonoids and anthocyanins compared with wild-type plants. We identified the gene <i>INHIBITOR FOR BROWN FURROWS 1</i> (<i>IBF1</i>) in the <i>bh2</i> mutant through MutMap analysis and subsequently cloned it. <i>IBF1</i> encodes an F-box protein and is involved in the formation of an SCF (S-phase kinase-associated protein 1 [SKP1], Cullin, and F-box) complex with the <i>Oryza sativa</i> SKP1-like proteins OSK1/OSK20. Through yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays, the interaction of IBF1 with chalcone synthase 1 (CHS1) was confirmed. This interaction facilitated the degradation of CHS1 through the ubiquitin-26S proteasome system. The <i>ibf1 chs1</i> double mutants exhibited normal hull color, restoring the phenotype of <i>ibf1</i>. Genetic analysis suggested that IBF1 regulates hull color in a CHS1-dependent manner. Collectively, our study suggests that IBF1 serves as a crucial negative regulator that controls flavonoid biosynthesis by mediating CHS1 degradation, thereby regulating hull color.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689250","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}
引用次数: 0
Comparative tissue-specific transcriptomics reveals the regulatory control of convergent seed shattering in independently evolved weedy rice lineages
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-23 DOI: 10.1111/tpj.70083
Xiang Li, Ana L. Caicedo

The repeated evolution of high seed shattering during multiple independent de-domestications of cultivated Asian rice (Oryza sativa) into weedy rice (Oryza spp.) is a prime example of convergent evolution. Weedy rice populations converge in histological features of the abscission zone (AZ), a crucial structure for seed abscission, while ancestral cultivated rice populations exhibit varied AZ morphology and levels of shattering. However, the genetic bases of these phenotypic patterns remain unclear. We examined the expression profiles of the AZ region and its surrounding tissues at three developmental stages in two low-shattering cultivars of aus and temperate japonica domesticated groups and in two genotypes of their derived high-shattering weed groups, Blackhull Awned (BHA) and Spanish Weedy Rice (SWR), respectively. Consistent with the greater alteration of AZ morphology during the de-domestication of SWR than BHA, fewer genes exhibited a comparable AZ-region exclusive expression pattern between weed and crop in the temperate japonica lineage than in the aus lineage. Transcription factors related to the repression of lignin and secondary cell wall deposition, such as, OsWRKY102 and OsXND-1-like, along with certain known shattering genes involved in AZ formation, likely played a role in maintaining AZ region identity in both lineages. Meanwhile, most genes exhibiting AZ-region exclusive expression patterns do not overlap between the two lineages and the genes exhibiting differential expression in the AZ region between weed and crop across the two lineages are enriched for different gene ontology terms. Our findings suggest genetic flexibility in shaping AZ morphology, while genetic constraints on AZ identity determination in these two lineages.

{"title":"Comparative tissue-specific transcriptomics reveals the regulatory control of convergent seed shattering in independently evolved weedy rice lineages","authors":"Xiang Li,&nbsp;Ana L. Caicedo","doi":"10.1111/tpj.70083","DOIUrl":"https://doi.org/10.1111/tpj.70083","url":null,"abstract":"<div>\u0000 \u0000 <p>The repeated evolution of high seed shattering during multiple independent de-domestications of cultivated Asian rice (<i>Oryza sativa</i>) into weedy rice (<i>Oryza</i> spp.) is a prime example of convergent evolution. Weedy rice populations converge in histological features of the abscission zone (AZ), a crucial structure for seed abscission, while ancestral cultivated rice populations exhibit varied AZ morphology and levels of shattering. However, the genetic bases of these phenotypic patterns remain unclear. We examined the expression profiles of the AZ region and its surrounding tissues at three developmental stages in two low-shattering cultivars of <i>aus</i> and <i>temperate japonica</i> domesticated groups and in two genotypes of their derived high-shattering weed groups, Blackhull Awned (BHA) and Spanish Weedy Rice (SWR), respectively. Consistent with the greater alteration of AZ morphology during the de-domestication of SWR than BHA, fewer genes exhibited a comparable AZ-region exclusive expression pattern between weed and crop in the <i>temperate japonica</i> lineage than in the <i>aus</i> lineage. Transcription factors related to the repression of lignin and secondary cell wall deposition, such as, <i>OsWRKY102</i> and <i>OsXND-1-like</i>, along with certain known shattering genes involved in AZ formation, likely played a role in maintaining AZ region identity in both lineages. Meanwhile, most genes exhibiting AZ-region exclusive expression patterns do not overlap between the two lineages and the genes exhibiting differential expression in the AZ region between weed and crop across the two lineages are enriched for different gene ontology terms. Our findings suggest genetic flexibility in shaping AZ morphology, while genetic constraints on AZ identity determination in these two lineages.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689700","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}
引用次数: 0
OsGSK1 interacts with OsbZIP72 to regulate salt response in rice
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-23 DOI: 10.1111/tpj.70112
Xi Liu, Xin Guo, Tingjing Li, Xue Wang, Yulu Guan, Di Wang, Yinjie Wang, Xiaonan Ji, Qingsong Gao, Jianhui Ji

Soil salinity remains a continuing threat to agriculture worldwide, greatly affecting seedling development and reducing crop yield. Thus, the cultivation of salt-resistant crops on salinized land is an excellent strategy to ensure food security. The rice GSK3-like protein kinase, OsGSK1, is known to play a role in the response to various abiotic stressors; however, the underlying molecular mechanism of this response remains unclear. Here, we aimed to elucidate the mechanism by which OsGSK1 regulates the salt stress response. We found that OsGSK1 interacts with OsbZIP72 to negatively regulate salt stress tolerance in rice plants. OsGSK1 is specifically induced by cold, salt stress, and abscisic acid (ABA) treatment. OsGSK1 was found to be localized in the nucleus and cytoplasm, where it physically interacts with OsbZIP72 – a positive regulator of the rice salt stress response. OsbZIP72 directly binds to the ABA response element in the OsNHX1 promoter to regulate its expression under salt stress, whereas OsGSK1 interacts with OsbZIP72 to repress OsNHX1 expression. The knockout of OsGSK1 increased salt tolerance without affecting the main agronomic traits of the mutant plants. Therefore, OsGSK1 could be used to maintain rice yield in salinized soil.

{"title":"OsGSK1 interacts with OsbZIP72 to regulate salt response in rice","authors":"Xi Liu,&nbsp;Xin Guo,&nbsp;Tingjing Li,&nbsp;Xue Wang,&nbsp;Yulu Guan,&nbsp;Di Wang,&nbsp;Yinjie Wang,&nbsp;Xiaonan Ji,&nbsp;Qingsong Gao,&nbsp;Jianhui Ji","doi":"10.1111/tpj.70112","DOIUrl":"https://doi.org/10.1111/tpj.70112","url":null,"abstract":"<div>\u0000 \u0000 <p>Soil salinity remains a continuing threat to agriculture worldwide, greatly affecting seedling development and reducing crop yield. Thus, the cultivation of salt-resistant crops on salinized land is an excellent strategy to ensure food security. The rice GSK3-like protein kinase, OsGSK1, is known to play a role in the response to various abiotic stressors; however, the underlying molecular mechanism of this response remains unclear. Here, we aimed to elucidate the mechanism by which OsGSK1 regulates the salt stress response. We found that OsGSK1 interacts with OsbZIP72 to negatively regulate salt stress tolerance in rice plants. <i>OsGSK1</i> is specifically induced by cold, salt stress, and abscisic acid (ABA) treatment. OsGSK1 was found to be localized in the nucleus and cytoplasm, where it physically interacts with OsbZIP72 – a positive regulator of the rice salt stress response. OsbZIP72 directly binds to the ABA response element in the <i>OsNHX1</i> promoter to regulate its expression under salt stress, whereas OsGSK1 interacts with OsbZIP72 to repress <i>OsNHX1</i> expression. The knockout of <i>OsGSK1</i> increased salt tolerance without affecting the main agronomic traits of the mutant plants. Therefore, OsGSK1 could be used to maintain rice yield in salinized soil.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689440","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}
引用次数: 0
Efficient targeted T-DNA integration for gene activation and male germline-specific gene tagging in Arabidopsis
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-23 DOI: 10.1111/tpj.70104
Peng Xu, Jilei Huang, Xiaojing Chen, Qi Wang, Bo Yin, Qing Xian, Chuxiong Zhuang, Yufei Hu

Site-specific DNA integration is an important tool in plant genetic engineering. Traditionally, this process relies on homologous recombination (HR), which is known for its low efficiency in plant cells. In contrast, Agrobacterium-mediated T-DNA integration is highly efficient for plant transformation. However, T-DNA is typically inserted randomly into double-strand breaks within the plant genome via the non-homologous end-joining (NHEJ) DNA repair pathway. In this study, we developed an approach of CRISPR/Cas9-mediated targeted T-DNA integration in Arabidopsis, which was more rapid and efficient than the HR-mediated method. This targeted T-DNA integration aided in gene activation and male germline-specific gene tagging. Gene activation was accomplished by positioning the CaMV35S promoter at the left border of T-DNA, thereby activating specific downstream genes. The activation of FT and MYB26 significantly increased their transcriptional expression, which resulted in early flowering and an altered pattern of cell wall thickening in the anther endothelium, respectively. Male germline-specific gene tagging incorporates two reporters, namely, NeoR and MGH3::mCherry, within the T-DNA. This design facilitates the creation of insertional mutants, simplifies the genetic analysis of mutated alleles, and allows for cellular tracking of male germline cells during fertilization. We successfully applied this system to target the male germline-specific gene GEX2. In conclusion, our results demonstrated that site-specific integration of DNA fragments in the plant genome can be rapidly and efficiently achieved through the NHEJ pathway, making this approach broadly applicable in various contexts.

位点特异性 DNA 整合是植物基因工程的重要工具。传统上,这一过程依赖于同源重组(HR),众所周知,HR 在植物细胞中的效率较低。相比之下,农杆菌介导的 T-DNA 整合在植物转化中效率很高。然而,T-DNA 通常是通过非同源末端连接(NHEJ)DNA 修复途径随机插入植物基因组内的双链断裂处。在这项研究中,我们在拟南芥中开发了一种 CRISPR/Cas9 介导的靶向 T-DNA 整合方法,这种方法比 HR 介导的方法更快速、更高效。这种靶向 T-DNA 整合有助于基因激活和雄性生殖系特异性基因标记。基因激活是通过将 CaMV35S 启动子定位在 T-DNA 的左边界来实现的,从而激活了特定的下游基因。FT 和 MYB26 的激活显著增加了它们的转录表达,分别导致了花药内皮细胞的早花和细胞壁增厚模式的改变。雄性生殖系特异性基因标记在 T-DNA 中加入了两个报告基因,即 NeoR 和 MGH3::mCherry。这种设计有利于产生插入突变体,简化了突变等位基因的遗传分析,并能在受精过程中对雄性生殖细胞进行细胞追踪。我们成功地将这一系统用于靶向雄性生殖细胞特异基因 GEX2。总之,我们的研究结果表明,DNA片段在植物基因组中的位点特异性整合可以通过NHEJ途径快速高效地实现,因此这种方法可广泛应用于各种情况。
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引用次数: 0
StNF-YA8-YB20-YC5 module regulates potato tuber dormancy by modulating gibberellin and abscisic acid pathways
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-03-23 DOI: 10.1111/tpj.70106
Xiao Wang, Han Wei, Ning Zhang, Shigui Li, Huaijun Si

The molecular mechanisms involved in the regulation of potato tuber dormancy are complex, involving a variety of related genes and enzymes, which modulate multiple signaling pathways. Nuclear factor-Y (NF-Y) transcription factors (TFs) are widely found in eukaryotes and are involved in the regulation of plant embryonic development, seed germination, fruit ripening, and in response to biotic and abiotic stress. Previously, we found that StNF-YA8 gene expression was increasing with the release of potato tuber dormancy. In this study, it was found that StNF-YA8 overexpressed tubers broke dormancy earlier than non-transgenic (NT) and StNF-YA8 downregulated tubers. Changes in abscisic acid (ABA) and gibberellin (GA) content of different types of tubers at different dormancy periods confirmed that both GA and ABA hormones influenced the differences in dormancy time. This was confirmed by the expression of GA pathway genes StGA3ox1 and StGA20ox1 genes and ABA pathway genes StCYP707A2 and StPP2CA1 genes in different tubers. The four genes described above were further shown to be target genes of the StNF-YA8 TF, which transcriptionally activates the expression of these genes. In addition, we verified the involvement of StNF-YA8 in the tuber dormancy release process by the interacting proteins StNF-YB20 and StNF-YC5, which are able to bind to the StNF-YA8-B20-C5 module to activate the transcription of GA and ABA pathway genes. Our study reveals the StNF-YA8-C5 module activates the transcription of the StCYP707A2, StPP2CA1, StGA3ox1, and StGA20ox1 genes and alters GA and ABA content, accelerating the release of dormancy in potato tubers.

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引用次数: 0
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