Pub Date : 2026-05-01Epub Date: 2026-02-18DOI: 10.1016/j.plantsci.2026.113062
Xingliang Duan , Guanjie Wang , Qinglin Song , Jiale Liu , Huilin Ding , Jing Che , Wei Xuan
Flowering time is of great significance for crop yield, reproduction and regional adaptability, which is regulated by complex gene network and environmental signals, such as nitrogen (N) nutrition. Long hypocotyl 1 (HY1) encodes a heme oxygenase, which is necessary for the biosynthesis of phytochrome chromophore biosynthesis, and promotes photomorphogenesis in plants. It has been reported that HY1 regulates rice flowering time, though the molecular mechanism remains elusive. Meanwhile, whether HY1 involves in N-regulated flowering is also unclear. Here, we found that HY1 knock-out mutant showed early flowering and decreased grain yield. HY1 is highly expressed in young rice leaf tissues, and its expression is induced by both light and N supply. We also revealed that HY1 follows a circadian rhythm, and alters the expression of circadian-clock genes to regulate following time. In rice, high N supply delayed flowering time, while the flowering time of hy1 mutant is insensitive to N supply in comparison to WT. Furthermore, HY1 knock-out decreases N uptake and use efficiency at both low N and high N levels under long-day conditions. These results suggested a critical role of HY1 in N-dependent signaling to regulate the function of clock and thus flowering under long-day conditions.
{"title":"Long Hypocotyl 1 mediates nitrogen regulation of flowering time and nitrogen use efficiency","authors":"Xingliang Duan , Guanjie Wang , Qinglin Song , Jiale Liu , Huilin Ding , Jing Che , Wei Xuan","doi":"10.1016/j.plantsci.2026.113062","DOIUrl":"10.1016/j.plantsci.2026.113062","url":null,"abstract":"<div><div>Flowering time is of great significance for crop yield, reproduction and regional adaptability, which is regulated by complex gene network and environmental signals, such as nitrogen (N) nutrition. <em>Long hypocotyl 1 (HY1)</em> encodes a heme oxygenase, which is necessary for the biosynthesis of phytochrome chromophore biosynthesis, and promotes photomorphogenesis in plants. It has been reported that <em>HY1</em> regulates rice flowering time, though the molecular mechanism remains elusive. Meanwhile, whether <em>HY1</em> involves in N-regulated flowering is also unclear. Here, we found that <em>HY1</em> knock-out mutant showed early flowering and decreased grain yield. <em>HY1</em> is highly expressed in young rice leaf tissues, and its expression is induced by both light and N supply. We also revealed that <em>HY1</em> follows a circadian rhythm, and alters the expression of circadian-clock genes to regulate following time. In rice, high N supply delayed flowering time, while the flowering time of <em>hy1</em> mutant is insensitive to N supply in comparison to WT. Furthermore, <em>HY1</em> knock-out decreases N uptake and use efficiency at both low N and high N levels under long-day conditions. These results suggested a critical role of <em>HY1</em> in N-dependent signaling to regulate the function of clock and thus flowering under long-day conditions.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113062"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146228221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-19DOI: 10.1016/j.plantsci.2026.113068
Jingnan Luo , Jiangsong Jin , Yangyang Ma , Yanwen Jiang , Fengxue Zhu , Lanyan Zhang , Yingqiang Wen , Jiayue Feng
The magnesium chelatase subunit CHLI is well-characterized in chlorophyll biosynthesis, but its role in plant immunity remains unclear. In this study, we generated chimeric Fvchli mutant strawberries via CRISPR/Cas9 and obtained T1-T3 progeny with a wide range of editing efficiencies through self-pollination. Mutants with higher editing efficiency exhibited more leaf spots. Following inoculation with Xanthomonas fragariae, Fvchli mutants showed increased susceptibility, with both lesion area and disease incidence positively correlating with editing efficiency. We further demonstrated that stomata in Fvchli mutants closed significantly more slowly in response to ABA compared to the WT. After 1.5 h of ABA treatment, the stomatal aperture (width-to-length ratio) of the wild type (WT) decreased from 32 % to 2.3 %, whereas in the mutant line with 70 % editing efficiency, it only reduced from 32 % to 16 %. In the edited plants, the expression levels of genes related to ABA biosynthesis and signal transduction were significantly lower than those in the wild type. After pathogen infection, ABA levels increased in both WT and mutant plants, but remained significantly lower in Fvchli mutant. Scanning electron microscopy revealed that Fvchli mutants had wider stomatal apertures at 5 and 12 hpi, facilitating extensive bacterial colonization, whereas WT plants effectively restricted invasion through stomatal closure. Our results reveal a previously unrecognized role for Fvchli in stomatal immunity, where its deficiency impairs ABA accumulation and responsiveness, compromising stomatal defense and promoting bacterial infection.
{"title":"Fvchli deficiency impairs ABA-mediated stomatal closure and enhances susceptibility to Xanthomonas fragariae in strawberry","authors":"Jingnan Luo , Jiangsong Jin , Yangyang Ma , Yanwen Jiang , Fengxue Zhu , Lanyan Zhang , Yingqiang Wen , Jiayue Feng","doi":"10.1016/j.plantsci.2026.113068","DOIUrl":"10.1016/j.plantsci.2026.113068","url":null,"abstract":"<div><div>The magnesium chelatase subunit CHLI is well-characterized in chlorophyll biosynthesis, but its role in plant immunity remains unclear. In this study, we generated chimeric <em>Fvchli</em> mutant strawberries via CRISPR/Cas9 and obtained T1-T3 progeny with a wide range of editing efficiencies through self-pollination. Mutants with higher editing efficiency exhibited more leaf spots. Following inoculation with <em>Xanthomonas fragariae</em>, <em>Fvchli</em> mutants showed increased susceptibility, with both lesion area and disease incidence positively correlating with editing efficiency. We further demonstrated that stomata in <em>Fvchli</em> mutants closed significantly more slowly in response to ABA compared to the WT. After 1.5 h of ABA treatment, the stomatal aperture (width-to-length ratio) of the wild type (WT) decreased from 32 % to 2.3 %, whereas in the mutant line with 70 % editing efficiency, it only reduced from 32 % to 16 %. In the edited plants, the expression levels of genes related to ABA biosynthesis and signal transduction were significantly lower than those in the wild type. After pathogen infection, ABA levels increased in both WT and mutant plants, but remained significantly lower in <em>Fvchli</em> mutant. Scanning electron microscopy revealed that <em>Fvchli</em> mutants had wider stomatal apertures at 5 and 12 hpi, facilitating extensive bacterial colonization, whereas WT plants effectively restricted invasion through stomatal closure. Our results reveal a previously unrecognized role for <em>Fvchli</em> in stomatal immunity, where its deficiency impairs ABA accumulation and responsiveness, compromising stomatal defense and promoting bacterial infection.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113068"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146776485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-23DOI: 10.1016/j.plantsci.2026.113071
Suchong Deng, Qiang Ding, Xilin Hou
Watercress (Nasturtium officinale R.Br.) is a kind of aquatic or semi-aquatic vegetable, which is rich in a variety of metabolites beneficial to human body. The R2R3-MYB gene family plays a key role in the biosynthesis of metabolites such as anthocyanins, but has not been characterized in watercress. Here, we identified 118 R2R3-NoMYB genes in the watercress genome and classified them into 35 subgroups. High-light treatment simultaneously enhanced anthocyanin accumulation in both lateral stems and upper main stems and strongly up-regulated the expression of subgroup S6 member NoMYB90 as well as the anthocyanin biosynthetic structural genes. Subcellular localization showed that NoMYB90 was located in the nucleus and cell membrane. Transient overexpression of NoMYB90 in tobacco leaves promoted anthocyanin accumulation, confirming its role as a positive regulator of anthocyanin biosynthesis. Dual-luciferase assay showed that NoMYB90 transactivates the anthocyanin biosynthetic genes NoCHS, NoF3H, NoDFR, and NoUF3GT. This study presented the first genome-wide analysis of the R2R3-MYB family in watercress and identified NoMYB90 as a positive regulator of anthocyanin biosynthesis. The findings provided a reference for further investigations of R2R3-NoMYB genes and established a foundation for the study of anthocyanin biosynthesis in watercress.
{"title":"Genome-wide study of the R2R3-MYB gene family and analysis of NoMYB90 promoting anthocyanin biosynthesis in watercress (Nasturtium officinale R.Br.)","authors":"Suchong Deng, Qiang Ding, Xilin Hou","doi":"10.1016/j.plantsci.2026.113071","DOIUrl":"10.1016/j.plantsci.2026.113071","url":null,"abstract":"<div><div>Watercress (<em>Nasturtium officinale</em> R.Br.) is a kind of aquatic or semi-aquatic vegetable, which is rich in a variety of metabolites beneficial to human body. The R2R3-MYB gene family plays a key role in the biosynthesis of metabolites such as anthocyanins, but has not been characterized in watercress. Here, we identified 118 R2R3-NoMYB genes in the watercress genome and classified them into 35 subgroups. High-light treatment simultaneously enhanced anthocyanin accumulation in both lateral stems and upper main stems and strongly up-regulated the expression of subgroup S6 member <em>NoMYB90</em> as well as the anthocyanin biosynthetic structural genes. Subcellular localization showed that NoMYB90 was located in the nucleus and cell membrane. Transient overexpression of <em>NoMYB90</em> in tobacco leaves promoted anthocyanin accumulation, confirming its role as a positive regulator of anthocyanin biosynthesis. Dual-luciferase assay showed that NoMYB90 transactivates the anthocyanin biosynthetic genes <em>NoCHS</em>, <em>NoF3H</em>, <em>NoDFR</em>, and <em>NoUF3GT</em>. This study presented the first genome-wide analysis of the R2R3-MYB family in watercress and identified <em>NoMYB90</em> as a positive regulator of anthocyanin biosynthesis. The findings provided a reference for further investigations of R2R3-NoMYB genes and established a foundation for the study of anthocyanin biosynthesis in watercress.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113071"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147309397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-19DOI: 10.1016/j.plantsci.2026.113066
Qian Li , Bo Chen , Ziyu Yang , ChenJing Li , Qing Jing , Qinghong Lu , Rui Ni , Pengzhi Mao , Li Zhang , Xinyong Guo
Soybean (Glycine max (Linn.) Merr), an important economic crop, is significantly impacted by alkaline stress, but the regulatory networks involved under such stress remain largely unclear. This study aimed to elucidate the regulatory mechanisms of alkaline stress using alkaline-tolerant (Heihe 35) and alkaline-sensitive (Zhonghuang 911) soybean varieties, employing phenotypic, physiological, and multi-omics approaches. The results indicated that the Heihe 35 soybean variety exhibited superior growth compared to the Zhonghuang 911 variety, with increased 41.86 %-46.71 % biomass, 51.04 %-92.68 % antioxidant enzyme activity and 15.74 %-20.49 % osmotic regulators. Compared to Heihe 35, Zhonghuang 911 showed a 36.81 % higher relative conductivity, a 19.13–23.93 % increase in reactive oxygen species levels, and a 26.39 % higher malondialdehyde content. Metabolomic and transcriptomic analyses revealed that flavonoids were the most abundant metabolites in soybeans under alkaline stress, with key regulatory pathways in flavonoid, linoleic acid, and amino acid metabolism identified as crucial for the soybean response to alkaline stress. Notably, several key differential genes and metabolites showed significantly upregulated expression under alkaline stress compared to the control group, including formononetin (C00858), 9(s)-hotre (C16326), and adenine (C00147), which were upregulated by 1.65–10.56 times, as well as LOC100808944 (K01904), SDP1–4 (K14674), and LOC100819617 (K01679), which were upregulated by 1.61–8.75 times. The findings of this study enhance our understanding of the physiological and molecular mechanisms underlying soybean responses to alkaline stress, highlighting the significant roles of key metabolic pathways. These insights provide a theoretical foundation for improving alkaline tolerance in soybeans and lay the groundwork for breeding alkaline-resistant varieties.
{"title":"Integrative analysis of physiology, transcriptomics, and metabolomics unveils mechanisms in soybean (Glycine max (Linn.) Merr) response to alkaline stress","authors":"Qian Li , Bo Chen , Ziyu Yang , ChenJing Li , Qing Jing , Qinghong Lu , Rui Ni , Pengzhi Mao , Li Zhang , Xinyong Guo","doi":"10.1016/j.plantsci.2026.113066","DOIUrl":"10.1016/j.plantsci.2026.113066","url":null,"abstract":"<div><div>Soybean (<em>Glycine max</em> (Linn.) Merr), an important economic crop, is significantly impacted by alkaline stress, but the regulatory networks involved under such stress remain largely unclear. This study aimed to elucidate the regulatory mechanisms of alkaline stress using alkaline-tolerant (Heihe 35) and alkaline-sensitive (Zhonghuang 911) soybean varieties, employing phenotypic, physiological, and multi-omics approaches. The results indicated that the Heihe 35 soybean variety exhibited superior growth compared to the Zhonghuang 911 variety, with increased 41.86 %-46.71 % biomass, 51.04 %-92.68 % antioxidant enzyme activity and 15.74 %-20.49 % osmotic regulators. Compared to Heihe 35, Zhonghuang 911 showed a 36.81 % higher relative conductivity, a 19.13–23.93 % increase in reactive oxygen species levels, and a 26.39 % higher malondialdehyde content. Metabolomic and transcriptomic analyses revealed that flavonoids were the most abundant metabolites in soybeans under alkaline stress, with key regulatory pathways in flavonoid, linoleic acid, and amino acid metabolism identified as crucial for the soybean response to alkaline stress. Notably, several key differential genes and metabolites showed significantly upregulated expression under alkaline stress compared to the control group, including formononetin (C00858), 9(s)-hotre (C16326), and adenine (C00147), which were upregulated by 1.65–10.56 times, as well as <em>LOC100808944</em> (K01904), <em>SDP1–4</em> (K14674), and <em>LOC100819617</em> (K01679), which were upregulated by 1.61–8.75 times. The findings of this study enhance our understanding of the physiological and molecular mechanisms underlying soybean responses to alkaline stress, highlighting the significant roles of key metabolic pathways. These insights provide a theoretical foundation for improving alkaline tolerance in soybeans and lay the groundwork for breeding alkaline-resistant varieties.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113066"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146776523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-24DOI: 10.1016/j.plantsci.2026.113064
Qiugui You , Wanqin Chen , Jinjing Pan , Diqiu Yu
Seed dormancy is a key adaptive trait that prevents germination under unfavorable conditions. In Arabidopsis, DELAY OF GERMINATION 1 (DOG1) serves as a master regulator of dormancy, primarily controlled through post-translational modifications. However, whether it interacts with other crucial transcriptional regulators remains to be investigated. Here, we identify WRKY25 as an interaction partner of DOG1. WRKY25 is mainly expressed in mature seeds during seed development, and wrky25 mutant display reduced primary dormancy, while overexpression enhances dormancy. Genetic analyses reveal that WRKY25 promotes primary seed dormancy through DOG1. Furthermore, WRKY25 modulates abscisic acid (ABA) responsiveness, as wrky25 mutants exhibit hyposensitivity to ABA during germination and early seedling growth. Mechanistically, WRKY25 physically interacts with the core ABA signaling component ABSCISIC ACID-INSENSITIVE5 (ABI5), and genetic assays confirm ABI5's necessity for WRKY25-mediated ABA hypersensitivity. Molecular characterization establishes WRKY25 as a transcriptional activator of both DOG1 and ABI5, binding to their promoters via conserved W-box elements. Additionally, WRKY25's regulatory functions require functional DOG1 and ABI5, positioning it as a pivotal integrator of dormancy and ABA signaling pathways. Overall, our study identified WRKY25 as a regulator of seed dormancy and germination that plays a crucial role in governing these processes through the DOG1 and ABA pathways.
{"title":"The transcription factor WRKY25 promotes seed dormancy and mediates abscisic acid signaling in Arabidopsis","authors":"Qiugui You , Wanqin Chen , Jinjing Pan , Diqiu Yu","doi":"10.1016/j.plantsci.2026.113064","DOIUrl":"10.1016/j.plantsci.2026.113064","url":null,"abstract":"<div><div>Seed dormancy is a key adaptive trait that prevents germination under unfavorable conditions. In Arabidopsis, DELAY OF GERMINATION 1 (DOG1) serves as a master regulator of dormancy, primarily controlled through post-translational modifications. However, whether it interacts with other crucial transcriptional regulators remains to be investigated. Here, we identify WRKY25 as an interaction partner of DOG1. <em>WRKY25</em> is mainly expressed in mature seeds during seed development, and <em>wrky25</em> mutant display reduced primary dormancy, while overexpression enhances dormancy. Genetic analyses reveal that WRKY25 promotes primary seed dormancy through DOG1. Furthermore, WRKY25 modulates abscisic acid (ABA) responsiveness, as <em>wrky25</em> mutants exhibit hyposensitivity to ABA during germination and early seedling growth. Mechanistically, WRKY25 physically interacts with the core ABA signaling component ABSCISIC ACID-INSENSITIVE5 (ABI5), and genetic assays confirm ABI5's necessity for WRKY25-mediated ABA hypersensitivity. Molecular characterization establishes WRKY25 as a transcriptional activator of both DOG1 and ABI5, binding to their promoters via conserved W-box elements. Additionally, WRKY25's regulatory functions require functional DOG1 and ABI5, positioning it as a pivotal integrator of dormancy and ABA signaling pathways. Overall, our study identified WRKY25 as a regulator of seed dormancy and germination that plays a crucial role in governing these processes through the DOG1 and ABA pathways.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113064"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147309411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-16DOI: 10.1016/j.plantsci.2026.113058
Gaoyang Qu , Ruibo Shen , Mingwan Sun , Di Zhao , Wei Wang , Shixiang Wei , Biao Wang , Hongbo Li
Salvia miltiorrhiza Bge. (S. miltiorrhiza) is a traditional Chinese herbal medicine, primarily used for treating cardiovascular diseases. Tanshinones as the main medicinal components of S. miltiorrhiza, their content is an important factor affecting the medicinal and economic value. Reasonable post-harvest techniques are the critical means to improve the effective components, and short-term low-temperature can induce the synthesis of plant secondary metabolites. However, the molecular mechanisms of low-temperature regulation of tanshinones remain unclear. This study found that post-harvest low-temperature can significantly accumulate the tanshinone components, simultaneously, it markedly enhances the expression of key enzyme genes involved in tanshinone biosynthesis. Analysis of the NAC gene family revealed that SmNAC68 is predominantly active in roots, with a marked decrease in expression under low-temperature. Genetic transformation experiments demonstrated that the accumulation of four tanshinones in SmNAC68 overexpression individual was significantly downregulated, with the key enzyme gene SmCPS1 showing the most significant downregulation. Protein interaction experiments revealed that SmNAC68 can interact with the promoter of SmCPS1 and inhibit its transcription. The results reveal the molecular mechanism of low-temperature regulation of tanshinone biosynthesis, which is of great significance for improving the post-harvest processing and quality enhancement of S. miltiorrhiza.
{"title":"SmNAC68 transcription factor negatively regulate tanshinone biosynthesis under low-temperature conditions in Salvia miltiorrhiza","authors":"Gaoyang Qu , Ruibo Shen , Mingwan Sun , Di Zhao , Wei Wang , Shixiang Wei , Biao Wang , Hongbo Li","doi":"10.1016/j.plantsci.2026.113058","DOIUrl":"10.1016/j.plantsci.2026.113058","url":null,"abstract":"<div><div><em>Salvia miltiorrhiza</em> Bge. (<em>S. miltiorrhiza</em>) is a traditional Chinese herbal medicine, primarily used for treating cardiovascular diseases. Tanshinones as the main medicinal components of <em>S. miltiorrhiza</em>, their content is an important factor affecting the medicinal and economic value. Reasonable post-harvest techniques are the critical means to improve the effective components, and short-term low-temperature can induce the synthesis of plant secondary metabolites. However, the molecular mechanisms of low-temperature regulation of tanshinones remain unclear. This study found that post-harvest low-temperature can significantly accumulate the tanshinone components, simultaneously, it markedly enhances the expression of key enzyme genes involved in tanshinone biosynthesis. Analysis of the NAC gene family revealed that <em>SmNAC68</em> is predominantly active in roots, with a marked decrease in expression under low-temperature. Genetic transformation experiments demonstrated that the accumulation of four tanshinones in <em>SmNAC68</em> overexpression individual was significantly downregulated, with the key enzyme gene <em>SmCPS1</em> showing the most significant downregulation. Protein interaction experiments revealed that <em>SmNAC68</em> can interact with the promoter of <em>SmCPS1</em> and inhibit its transcription. The results reveal the molecular mechanism of low-temperature regulation of tanshinone biosynthesis, which is of great significance for improving the post-harvest processing and quality enhancement of <em>S. miltiorrhiza</em>.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113058"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146220888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-27DOI: 10.1016/j.plantsci.2026.113070
Yanju Zhu , Qile Sun , Shanshan Wang , Fengxia Liu
Cold stress severely limits rice growth and yield, making it crucial to identify cold-tolerant QTLs and genes for effective molecular breeding. In this study, we detected four QTLs for seedling cold tolerance using the introgression lines derived from wild rice (Oryza nivara) and identified an introgression line Ra47 harboring the major QTL qSCT12, which exhibited a higher seedling survival rate under cold stress than its recipient parent 9311 (an elite indica cultivar). Using the F2:3 population developed by backcrossing Ra47 with 9311, we confirmed the major QTL qSCT12 for seedling cold tolerance, which explained up to 29.92% of the phenotypic variation in cold tolerance traits, and which allele from wild rice could enhance seedling cold tolerance. Using additional 2744 F2 individuals, we narrowed the QTL qSCT12 to a 21.8-kb region on chromosome 12 between markers CT321 and 3-F. This interval contains 2 candidate genes LOC_Os12g10700 and LOC_Os12g10710. Further RNA-seq analysis of Ra47 and 9311 before and after cold treatment revealed that DEGs were enriched in primary metabolic process, cellular metabolic process, hydrolase activity and pyrophosphatase activity. These findings will provide important insights into the genetic basis of cold tolerance in rice seedlings and offer new genetic resources for developing cold-tolerant rice varieties.
{"title":"Fine mapping of the qSCT12 locus conferring seedling cold tolerance in Oryza nivara","authors":"Yanju Zhu , Qile Sun , Shanshan Wang , Fengxia Liu","doi":"10.1016/j.plantsci.2026.113070","DOIUrl":"10.1016/j.plantsci.2026.113070","url":null,"abstract":"<div><div>Cold stress severely limits rice growth and yield, making it crucial to identify cold-tolerant QTLs and genes for effective molecular breeding. In this study, we detected four QTLs for seedling cold tolerance using the introgression lines derived from wild rice (<em>Oryza nivara</em>) and identified an introgression line Ra47 harboring the major QTL <em>qSCT12</em>, which exhibited a higher seedling survival rate under cold stress than its recipient parent 9311 (an elite <em>indica</em> cultivar). Using the F<sub>2:3</sub> population developed by backcrossing Ra47 with 9311, we confirmed the major QTL <em>qSCT12</em> for seedling cold tolerance, which explained up to 29.92% of the phenotypic variation in cold tolerance traits, and which allele from wild rice could enhance seedling cold tolerance. Using additional 2744 F<sub>2</sub> individuals, we narrowed the QTL <em>qSCT12</em> to a 21.8-kb region on chromosome 12 between markers CT321 and 3-F. This interval contains 2 candidate genes <em>LOC_Os12g10700</em> and <em>LOC_Os12g10710</em>. Further RNA-seq analysis of Ra47 and 9311 before and after cold treatment revealed that DEGs were enriched in primary metabolic process, cellular metabolic process, hydrolase activity and pyrophosphatase activity. These findings will provide important insights into the genetic basis of cold tolerance in rice seedlings and offer new genetic resources for developing cold-tolerant rice varieties.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113070"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-27DOI: 10.1016/j.plantsci.2026.113084
Mahta Mohamadiaza , Naser Farrokhi , Asadollah Ahmadikhah , Pär K. Ingvarsson , Mehdi Jahanfar
Rice stem performs assimilate transport and promises sturdiness due to cell wall structure and composition. However, less is known about the genetic basis of its structural characteristics. In this study, for the first time, the scanning electron microscope (SEM) imaging technique was developed to capture digital phenotypes to assess 18 straw traits collected from the cross-sections of 147 rice accessions. Genome-wide association studies (GWAS) identified 54 significant single-nucleotide polymorphisms (SNPs; integrated into 28 quantitative trait loci) residing in the genic sequences of rice (promoter and coding DNA sequence), and classified into three groups: 1) cell wall-defining genes, 2) cell size-defining genes, and 3) transcription factors. DUF246 and DUF1218, galactose oxidase, mitochondrial Rho GTPase, WUSCHEL-related homeobox 5 and scarecrow-like 9 are the novel genes identified among the 21 candidate genes. These genes may play roles in stem development traits, specifically the distance from the vascular bundle to the end of the parenchymal cells (DVBEPC) and the thickness of the straw cell wall in the protruding part (TSCWP). Post-GWAS analyses showed one significant haplotype on chromosome 4 and 25 significant epistatic interactions. Most notably, nine TF families were repeatedly detected among the significant QTL. Os07g0644300 (XPA-binding protein 2), located in the q7–1 genomic segment and associated with DVBEPC, was found to have a missense mutation. Phenotyping via SEM imaging provides precise genome-phenome association in understanding rice stem cell size and cell wall architecture, which ultimately can define biomass and lodging resistance.
水稻茎秆的细胞壁结构和组成决定了茎秆的同化物运输和茎秆的坚固性。然而，对其结构特征的遗传基础知之甚少。本研究首次利用扫描电镜（SEM）成像技术，对147份水稻材料的18个秸秆性状进行了数字表型分析。全基因组关联研究（GWAS）鉴定了水稻基因序列（启动子和编码DNA序列）中54个显著的单核苷酸多态性（snp；整合到28个数量性状位点），并将其分为三类：1)细胞壁定义基因，2)细胞大小定义基因和3)转录因子。DUF246和DUF1218、半乳糖氧化酶、线粒体Rho GTPase、wuschel相关同源盒5和稻草人样9是21个候选基因中鉴定出的新基因。这些基因可能在茎发育性状中发挥作用，特别是从维管束到实质细胞末端的距离（DVBEPC）和秸秆细胞壁突出部分的厚度（TSCWP）。gwas分析显示，4号染色体上有1个显著的单倍型，25个显著的上位性相互作用。最值得注意的是，在显著QTL中重复检测到9个TF家族。与DVBEPC相关的q7-1基因组片段Os07g0644300 （XPA-binding protein 2）存在错义突变。通过扫描电镜成像进行表型分析，为理解水稻干细胞的大小和细胞壁结构提供了精确的基因组-表型关联，最终可以确定生物量和抗倒伏性。
{"title":"Integrating SEM-based phenotyping with GWAS reveals the genetic architecture of rice straw secondary cell wall and internode cell features","authors":"Mahta Mohamadiaza , Naser Farrokhi , Asadollah Ahmadikhah , Pär K. Ingvarsson , Mehdi Jahanfar","doi":"10.1016/j.plantsci.2026.113084","DOIUrl":"10.1016/j.plantsci.2026.113084","url":null,"abstract":"<div><div>Rice stem performs assimilate transport and promises sturdiness due to cell wall structure and composition. However, less is known about the genetic basis of its structural characteristics. In this study, for the first time, the scanning electron microscope (SEM) imaging technique was developed to capture digital phenotypes to assess 18 straw traits collected from the cross-sections of 147 rice accessions. Genome-wide association studies (GWAS) identified 54 significant single-nucleotide polymorphisms (SNPs; integrated into 28 quantitative trait loci) residing in the genic sequences of rice (promoter and coding DNA sequence), and classified into three groups: 1) cell wall-defining genes, 2) cell size-defining genes, and 3) transcription factors. <em>DUF246</em> and <em>DUF1218</em>, <em>galactose oxidase</em>, <em>mitochondrial Rho GTPase</em>, <em>WUSCHEL-related homeobox 5</em> and <em>scarecrow-like 9</em> are the novel genes identified among the 21 candidate genes. These genes may play roles in stem development traits, specifically the distance from the vascular bundle to the end of the parenchymal cells (DVBEPC) and the thickness of the straw cell wall in the protruding part (TSCWP). Post-GWAS analyses showed one significant haplotype on chromosome 4 and 25 significant epistatic interactions. Most notably, nine TF families were repeatedly detected among the significant QTL. <em>Os07g0644300</em> (XPA-binding protein 2), located in <em>the q7–1</em> genomic segment and associated with DVBEPC, was found to have a missense mutation. Phenotyping via SEM imaging provides precise genome-phenome association in understanding rice stem cell size and cell wall architecture, which ultimately can define biomass and lodging resistance.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113084"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-18DOI: 10.1016/j.plantsci.2026.113063
Xinmeng Geng, Zesheng Liu, Caiting An, Min Cao, Qi Wang, Mengkun Liu, Qianbing Li, Chunlei Wang, Linli Hu
DNA methylation, as a central mechanism of epigenetic regulation, plays a key role in coordinating plant growth and stress responses. Simultaneously, the gaseous phytohormone ethylene is also a crucial regulator in these processes. Both form a metabolic competition through S-adenosyl-L-methionine (SAM) and mutually regulate each other at the level of gene expression. Studies demonstrate that DNA methylation functions to either enhance or block ethylene synthesis and ethylene signal transduction, thereby regulating a spectrum of developmental processes including seed development, root growth, flower opening and senescence, flower sex differentiation, and fruit maturation. Conversely, ethylene acts to reprogram DNA methylation patterns to accelerate seedling development, leaf senescence, fruit ripening, and abscission. Under abiotic stresses, alterations in DNA methylation affect the ethylene pathway, thereby enhancing plant tolerance to cold, heat, herbicides, sulfur dioxide, and salinity. During pathogen infection, DNA methylation enhances ethylene biosynthesis and signalling, thereby reinforcing disease defence mechanisms. Additionally, studies have shown that DNA methylation regulates the ethylene pathway in processes such as embryonic development, domestication, fruit softening, and the accumulation of aromatic compounds and pigments. Although there still exist unclear specific effects and causal mechanisms concerning DNA methylation and ethylene, the current knowledge we summarized may provide new insights into ethylene and epigenetic modification in plants.
{"title":"Relationship between DNA methylation and ethylene in plants: A review","authors":"Xinmeng Geng, Zesheng Liu, Caiting An, Min Cao, Qi Wang, Mengkun Liu, Qianbing Li, Chunlei Wang, Linli Hu","doi":"10.1016/j.plantsci.2026.113063","DOIUrl":"10.1016/j.plantsci.2026.113063","url":null,"abstract":"<div><div>DNA methylation, as a central mechanism of epigenetic regulation, plays a key role in coordinating plant growth and stress responses. Simultaneously, the gaseous phytohormone ethylene is also a crucial regulator in these processes. Both form a metabolic competition through <em>S</em>-adenosyl-<span>L</span>-methionine (SAM) and mutually regulate each other at the level of gene expression. Studies demonstrate that DNA methylation functions to either enhance or block ethylene synthesis and ethylene signal transduction, thereby regulating a spectrum of developmental processes including seed development, root growth, flower opening and senescence, flower sex differentiation, and fruit maturation. Conversely, ethylene acts to reprogram DNA methylation patterns to accelerate seedling development, leaf senescence, fruit ripening, and abscission. Under abiotic stresses, alterations in DNA methylation affect the ethylene pathway, thereby enhancing plant tolerance to cold, heat, herbicides, sulfur dioxide, and salinity. During pathogen infection, DNA methylation enhances ethylene biosynthesis and signalling, thereby reinforcing disease defence mechanisms. Additionally, studies have shown that DNA methylation regulates the ethylene pathway in processes such as embryonic development, domestication, fruit softening, and the accumulation of aromatic compounds and pigments. Although there still exist unclear specific effects and causal mechanisms concerning DNA methylation and ethylene, the current knowledge we summarized may provide new insights into ethylene and epigenetic modification in plants.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113063"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-01Epub Date: 2026-02-20DOI: 10.1016/j.plantsci.2026.113067
Beata Chmielewska, Marek Marzec, Iwona Szarejko, Agata Daszkowska-Golec
Root hairs, tubular extensions of the rhizodermal cells, facilitate nutrient uptake, yet their role in water acquisition remains debated and may be species- and soil-specific. To elucidate the genetic basis of root hair development and assess their physiological relevance in barley (Hordeum vulgare L.), particularly under water-limited conditions, we characterized a mutant with a changed root hairs phenotype. The HvRTH3 gene, a barley homolog of the maize COBRA gene roothairless3 (rth3) encoding a COBRA protein (Hochholdinger et al., 2008), was subjected to TILLING analysis. In the hvrth3.h mutant, the mutation was identified in 804 bp position (transition of G to A), which results in premature STOP codon, that caused a reduction of protein length by 405 aa. The sparsely located root hairs in a barley hvrth3.h mutant, otherwise than in maize, where short root hairs were observed, was a result of a smaller number of trichoblasts in comparison to WT. The newly identified hvrth3.h mutant was not allelic to any characterized barley mutant isolated in our lab. It showed diminished root traits and yield under greenhouse and field conditions but did not exhibit pronounced disadvantage under severe drought. The expression of HvRTH3 gene was observed in all analyzed tissues, with the highest expression level in root elongation zone. HvRTH3 is essential for root hair development, but apparently dispensable for water uptake under severe drought.
根毛是根皮细胞的管状延伸，促进营养吸收，但它们在水分获取中的作用仍存在争议，可能是物种和土壤特异性的。为了阐明大麦（Hordeum vulgare L.）根毛发育的遗传基础，并评估其生理相关性，特别是在水分限制条件下，我们鉴定了一个根毛表型改变的突变体。HvRTH3基因是玉米COBRA基因无根3 （rth3）的大麦同源物，编码COBRA蛋白（Hochholdinger et al., 2008），对其进行TILLING分析。在hvrth3.h突变体中，在804bp位置（G向A过渡）发现突变，导致STOP密码子过早产生，导致蛋白长度减少405 aa。在大麦hvrth3.h突变体中，根毛稀少，而在玉米中，根毛较短，这是由于与WT相比，毛原细胞数量较少。新发现的hvrth3.h突变体与我们实验室分离的任何特征大麦突变体都没有等位基因。在温室和田间条件下，其根系性状和产量均下降，但在严重干旱条件下，根系性状和产量下降不明显。HvRTH3基因在所有组织中均有表达，其中根伸长区表达量最高。HvRTH3对根毛发育至关重要，但对严重干旱条件下的水分吸收显然是必不可少的。
{"title":"Functional analysis of barley HvRTH3 reveals its role in root hair patterning with no detectable impact on drought response","authors":"Beata Chmielewska, Marek Marzec, Iwona Szarejko, Agata Daszkowska-Golec","doi":"10.1016/j.plantsci.2026.113067","DOIUrl":"10.1016/j.plantsci.2026.113067","url":null,"abstract":"<div><div>Root hairs, tubular extensions of the rhizodermal cells, facilitate nutrient uptake, yet their role in water acquisition remains debated and may be species- and soil-specific. To elucidate the genetic basis of root hair development and assess their physiological relevance in barley (<em>Hordeum vulgare</em> L.), particularly under water-limited conditions, we characterized a mutant with a changed root hairs phenotype. The <em>HvRTH3</em> gene, a barley homolog of the maize <em>COBRA</em> gene <em>roothairless3</em> (<em>rth3</em>) encoding a COBRA protein (Hochholdinger et al., 2008), was subjected to TILLING analysis. In the <em>hvrth3.h</em> mutant, the mutation was identified in 804 bp position (transition of G to A), which results in premature STOP codon, that caused a reduction of protein length by 405 aa. The sparsely located root hairs in a barley <em>hvrth3.h</em> mutant, otherwise than in maize, where short root hairs were observed, was a result of a smaller number of trichoblasts in comparison to WT. The newly identified <em>hvrth3.h</em> mutant was not allelic to any characterized barley mutant isolated in our lab. It showed diminished root traits and yield under greenhouse and field conditions but did not exhibit pronounced disadvantage under severe drought. The expression of <em>HvRTH3</em> gene was observed in all analyzed tissues, with the highest expression level in root elongation zone. <em>HvRTH3</em> is essential for root hair development, but apparently dispensable for water uptake under severe drought.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113067"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147271396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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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