{"title":"Exploring the drought-responsive miRNAs and their corresponding target genes in chickpea root tissue.","authors":"Lalbahadur Singh, Deshika Kohli, Yashwant K Yadava, Sheel Yadav, Kishor Gaikwad, Chellapilla Bharadwaj, Pradeep Kumar Jain","doi":"10.1007/s11103-025-01572-y","DOIUrl":"10.1007/s11103-025-01572-y","url":null,"abstract":"<p><p>Chickpea is an important pulse crop globally, with major production in Southeast Asia. However, the production of chickpea is hampered due to various biotic and abiotic stressors. In response to such stressors, microRNAs which are small non-coding regulatory RNA molecules have been observed as key players. The present study evaluates the role of drought-responsive microRNAs in the root tissues of chickpea genotypes contrasting for drought tolerance. This study led to the generation of 146.7 million short-read sequences from small RNA libraries constructed from the root tissues of the two genotypes. Upon analysis, 224 conserved and 155 novel miRNA sequences were identified. The miR156 family was found to be the most abundant among the 51 families identified for the conserved miRNAs. Quantitative real-time PCR (qRT-PCR) was used to validate eleven conserved and six novel miRNAs. The identification of drought-induced expression of specific miRNAs and their related target genes suggests miRNA-mediated response mechanisms in chickpea. Furthermore, this research investigated the role of drought-responsive miRNAs, specifically miR171 and miR166 and their target genes, SCL27 (scarecrow-like protein 27) and ATHB15 (Homeobox-leucine zipper family protein), respectively. The study validated the miR171 and miR166 directed cleavage of SCL27 and ATHB15, respectively, in drought-stressed root tissues using 5´RLM-RACE (5' RNA Ligase-Mediated Rapid Amplification of cDNA Ends) analysis. The study highlights the role of diverse miRNAs in chickpea for mitigating drought.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"43"},"PeriodicalIF":3.9,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143616780","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}
Amr Elkelish, Ahmad M Alqudah, Abdulrahman M Alhudhaibi, Hussain Alqahtani, Andreas Börner, Samar G Thabet
{"title":"Inherited endurance: deciphering genetic associations of transgenerational and intergenerational heat stress memory in barley.","authors":"Amr Elkelish, Ahmad M Alqudah, Abdulrahman M Alhudhaibi, Hussain Alqahtani, Andreas Börner, Samar G Thabet","doi":"10.1007/s11103-025-01571-z","DOIUrl":"10.1007/s11103-025-01571-z","url":null,"abstract":"<p><p>Barley (Hordeum vulgare L.), a cornerstone of global cereal crops, is increasingly vulnerable to concurrent heat stress, a critical abiotic factor that is intensified by climate change. This study employed genome-wide association studies (GWAS) to investigate \"stress memory,\" a phenomenon where prior stress exposure enhances a plant's response to subsequent stress events. In this study, we analyzed essential agronomic traits, including plant height, spike length, grain number, and thousand-kernel weight, in conjunction with biochemical markers such as chlorophyll content, proline, and soluble proteins. These assessments spanned three successive generations under heat stress, capturing transgenerational and intergenerational effects and uncovering the cumulative impacts of prolonged stress in the third generation. Markedly, our findings highlight the critical influence of heat stress on plant physiology across generational scales, showcasing significant reductions in chlorophyll content, which reflect stress-induced limitations on photosynthetic capacity. In contrast, the observed consistent and substantial increases in proline and soluble protein content across transgenerational, intergenerational, and third-generation stress memory stages underscore their vital roles in stress mitigation and cellular homeostasis. These results provide compelling evidence of generational stress memory, suggesting potential adaptive strategies that plants employ to cope with harsh environmental conditions. Interestingly, identifying significant SNP markers within key genomic regions using GWAS analysis further highlights the potential for harnessing these loci in breeding programs. These results shed light on the intricate mechanisms of barley's stress tolerance and underscore the potential of integrating genomic, epigenomic, and advanced phenotyping tools into breeding programs to develop heat-resilient cultivars.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"42"},"PeriodicalIF":3.9,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597560","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}
Muhammad Arif, Muhammad Haroon, Ayesha Fazal Nawaz, Hina Abbas, Ruhong Xu, Luhua Li
{"title":"Enhancing wheat resilience: biotechnological advances in combating heat stress and environmental challenges.","authors":"Muhammad Arif, Muhammad Haroon, Ayesha Fazal Nawaz, Hina Abbas, Ruhong Xu, Luhua Li","doi":"10.1007/s11103-025-01569-7","DOIUrl":"10.1007/s11103-025-01569-7","url":null,"abstract":"<p><p>Climate change, with its increasing temperatures, is significantly disrupting global agricultural systems, and wheat, a key cereal crop faces severe challenges. Heat stress has emerged as a critical threat, accelerating wheat growth, leading to premature maturation, reduced grain filling, and ultimately lower yields. The situation is exacerbated by more frequent and intense heat waves, particularly in regions already struggling with water scarcity. Maintaining the delicate balance of temperature and water necessary for optimal wheat production is becoming challenging, posing a serious risk to global food security. Therefore, there is an urgent need to develop adaptive strategies with innovations in breeding and transgenic technologies crucial to improving wheat resilience to environmental stresses, especially to combat the growing impacts of heat stress. Modern tools like CRISPR/Cas9, Transcription Activator-Like Effector Nucleases, and Zinc Finger Nucleases have been instrumental in developing wheat varieties with improved traits. However, the future of wheat cultivation requires more than just resistance to a single stressor. As climate change intensifies, there is an urgent need for wheat varieties that can withstand multiple stresses, including heat, drought, and pests. Developing these multi-stress-tolerant cultivars is crucial for ensuring food security in a rapidly changing climate.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"41"},"PeriodicalIF":3.9,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586684","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}
{"title":"Disruption of the endoplasmic reticulum-localized fatty acyl-ACP thioesterase IPF1 caused partial male sterility in rice.","authors":"Wenye Tan, Jingfei Tian, Wenfeng Zhao, Jianxin Wei, Yibo Xu, Shixu Zhou, Zihan Wei, Zejun Shen, Minghang Wu, Lianguang Shang, Rongbai Li, Yongfei Wang, Baoxiang Qin","doi":"10.1007/s11103-025-01574-w","DOIUrl":"10.1007/s11103-025-01574-w","url":null,"abstract":"<p><p>The fatty acyl ACP thioesterases, catalyzing the final step of fatty acid synthesis in the plastid, regulate various critical processes in plants, including seed oil accumulation, seed development, plant growth, and drought tolerance. However, their roles in male fertility have seldom been demonstrated. In this study, the function of a newly FAT, Impaired Pollen Fertility 1 (IPF1) in male fertility was investigated. IPF1 expressed prominently in microspores and tapetum. IPF1 specifically located in the endoplasmic reticulum. IPF1 knock-out mutants produced by the CRISPR/Cas9 system displayed significant reduction in seed-setting rate compared to WT. The decreased seed-setting rate in the ipf1 mutants was found to be attributed to the defects of pollen viability, not the female gamete fertility. The aborted pollen in the ipf1 mutants showed impaired pollen wall formation and diminished lipid deposition. Consistently, the expression levels of six genes critical to pollen wall formation and lipid metabolism (GPAT3, OsC6, DPW2, OsPKS1, OsPKS2, and OsSTRL2) were significantly decreased in the ipf1 mutant. Taken together, these results demonstrate that IPF1 regulates rice pollen fertility through the modulation of lipid synthesis.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"40"},"PeriodicalIF":3.9,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582348","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}
{"title":"Phenylpropanoids for the control of fungal diseases of postharvest fruit.","authors":"Yijie Sun, Xiaohan Wang, Zhengyu Huang, Xiaoyang Zhao, Linxiang Qiao, Caie Wu, Zhaohui Xue, Xiaohong Kou","doi":"10.1007/s11103-025-01568-8","DOIUrl":"10.1007/s11103-025-01568-8","url":null,"abstract":"<p><p>In recent years, there has been a growing interest in developing greener and safer substances for the control of postharvest fungal diseases of fruit. Secondary metabolic pathways play an important role in plant defense responses, and the phenylpropanoid metabolic pathway is one of the most important secondary metabolic pathways in plant defense. More and more studies have shown that exogenous phenylpropanoids treatments can inhibit postharvest fungal diseases. On the one hand, these biologically active phenylpropanoids are fungistatic and can act directly on the fungal cells infesting the postharvest fruit to inhibit spore germination and mycelial growth. On the other hand, phenylpropanoids treatment can improve plant resistance. In this review, we summarize recent achievements in the mechanisms and applications of phenylpropanoids, including cinnamic acid, p-coumaric acid and esters, caffeic acid, ferulic acid, and chlorogenic acid, in the inhibition of fungal pathogens and the reduction of postharvest losses. In addition, we propose further research hotspots and development directions based on combining nanomaterials and biotechnology.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"39"},"PeriodicalIF":3.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531116","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}
{"title":"Barley young leaf chlorina, a putative pentatricopeptide repeat gene, is essential for chloroplast development in young leaves.","authors":"Biguang Huang, Daiqing Huang, Jianchun Zhang, Jiwei Xiong, Shiyu Wu, Xinrong Zheng, Likun Huang, Jinbin Lin, Yu Li, Zonglie Hong, J Allan Feurtado, Weiren Wu","doi":"10.1007/s11103-025-01561-1","DOIUrl":"10.1007/s11103-025-01561-1","url":null,"abstract":"<p><p>A spontaneous barley mutant, young leaf chlorina (ylc), was identified in this study. Young leaves of ylc exhibited a yellow base and green tip, with reduced chlorophyll content, and altered chlorophyll fluorescence pattern, and underdeveloped grana in chloroplasts. The color of mutant leaves gradually transitioned to pale green and then became green in mature leaves. The ylc phenotype was found to be controlled by a recessive locus mapped to a 2.4 Mb interval on chromosome 7HS using bulked-segregant analysis with deep sequencing and further fine mapped to a 410 kb interval using polymorphic markers. The YLC locus co-segregated with a molecular marker that led to identification of HORVU7Hr1G011570 as the most likely candidate gene. As compared to the barley reference genome, the candidate ylc allele contained nucleotide changes that would lead to functional alterations of its protein product. The candidate YLC gene encodes a DYW-type pentatricopeptide repeat (PPR) protein, implicated in RNA cleavage and RNA editing in chloroplasts. Chlorophyll fluorescence analysis suggests that the PPR protein may regulate chloroplast development through the function of NAD(P)H dehydrogenase (NDH) complex and plays a pivotal role in mediating electron flow in thylakoid membranes during leaf growth in barley.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"36"},"PeriodicalIF":3.9,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143503379","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}
{"title":"Tomato miR398 knockout disrupts ROS dynamics during stress conferring heat tolerance but hypersusceptibility to necrotroph infection.","authors":"Shreya Chowdhury, Ananya Mukherjee, Raghuvir Singh, Sushmita Talukdar, Shrabani Basak, Rohit Das, Sayan Mal, Pallob Kundu","doi":"10.1007/s11103-025-01563-z","DOIUrl":"10.1007/s11103-025-01563-z","url":null,"abstract":"<p><p>An imbalance between ROS production and scavenging during stress results in oxidative bursts, which causes cellular damage. miR398 is a regulator of ROS scavenging since it targets crucial Cu/Zn superoxide dismutases (CSDs). Established functional studies aligned miR398 with plants' heat and heavy metal stress fitness. However, a knowledge gap in the dynamics of miR398-CSD interaction for redox regulation during pathogenic development impeded their use in crop improvement programmes. We use tomato, Solanum lycopersicum, plants, and necrotrophic and biotrophic pathogens to show that a complex transcriptional and post-transcriptional regulatory circuit maintains SlmiR398 and its target SlCSD genes' level. The interaction is indispensable for ROS regulation in either the pathogenic outcome, thermal stress, or a combination of both stresses, as observed in the cultivation field. The SlmiR398 knockout plants display feeble O2<sup>∙-</sup> accumulation but enhanced levels of H<sub>2</sub>O<sub>2</sub>, several defense-related genes, metabolites, and vital HSFs and HSPs, which were heightened upon stress. Depletion of SlmiR398, although it renders thermotolerance and resilience to biotrophic pathogens likely due to the augmented hypersensitive response, facilitates necrotrophy. Thus, SlmiR398-mediated ROS regulation seemingly works at the interface of abiotic and biotic stress response for a sustainable reaction of tomato plants.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"35"},"PeriodicalIF":3.9,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483907","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}
Shankar K Bhujbal, Archana N Rai, Archana Joshi-Saha
{"title":"Dwarfs standing tall: breeding towards the 'Yellow revolution' through insights into plant height regulation.","authors":"Shankar K Bhujbal, Archana N Rai, Archana Joshi-Saha","doi":"10.1007/s11103-025-01565-x","DOIUrl":"10.1007/s11103-025-01565-x","url":null,"abstract":"<p><p>High oilseed production is an exigency due to the increasing edible oil consumption of the growing population. Rapeseed and mustard are cultivated worldwide and contribute significantly to the world's total oilseed production. Already a plateau is reached in terms of area and yield in most of the existing cultivars. Most of the commercially cultivated high yielding rapeseed and mustard varieties are tall, mainly due to a wider use of heterosis. However, they are susceptible to lodging and consequent yield losses. Plant yield is strongly dependent upon its architecture; therefore, 'ideotype breeding' is the key approach adopted to develop new varieties with enhanced yield potential, which is less explored in these crops. Dwarf/ semi dwarf plant type varieties has shown its improved yield potential over tall plant type in cereals which further leads to 'Green revolution' in Asian countries. Although, many induced dwarf mutants in rapeseed and mustard were isolated, unlike dwarf green-revolution varieties of cereals, most of them had undesirable plant types with defects including extreme dwarfism and sterility, leading to poor yield potential. Understanding the genetic and molecular mechanisms governing plant height and its correlation with yield and yield contributing characters is crucial. In this review, recent insights into genetic, molecular, and anatomical regulation of plant height have been discussed. The role of hormones, their crosstalk, and hormonal control for cell division and expansion have been delineated with respect to plant architecture. Many dwarfing genes are identified as being part of various phytohormone pathways. Parallelly, molecular links between plant height and flowering time have been explored. The overall synthesis of the review points out some key target pathways and genes that will be useful for plant breeders as well as biotechnologists for targeted genome editing for improving plant architecture without a yield penalty.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"34"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mengyu Su, Yi Yang, Caicai Lin, Wenjun Liu, Xuesen Chen
{"title":"WRKY transcription factor MdWRKY71 regulates flowering time in apple.","authors":"Mengyu Su, Yi Yang, Caicai Lin, Wenjun Liu, Xuesen Chen","doi":"10.1007/s11103-024-01544-8","DOIUrl":"10.1007/s11103-024-01544-8","url":null,"abstract":"<p><p>In plants, flowering is crucial to reproductive success. Receiving limited attention in apple research is the function of WRKY transcription factors in regulating flowering time. We characterized a WRKY transcription factor, MdWRKY71, from red-fleshed apple in this study, and ectopically expressed it in Arabidopsis thaliana, which revealed its role in flowering. The sequence of MdWRKY71 exhibited similarity to that of AtWRKY71, and its protein comprised a WRKY domain and a C<sub>2</sub>H<sub>2</sub> zinc finger-like motif, placing it within subgroup IIc of the WRKY family. The similar changing trends demonstrated a significant positive correlation between the expression level of MdWRKY71 and the key flower transition genes in apical buds of apple in flower transition stage. Overexpression of MdWRKY71 promoted the upregulation of certain flower transition genes in apple calli. The ectopic expression of MdWRKY71 in A. thaliana was observed to induce early flowering. Additionally, MdWRKY71 could bind to the promoters of several floral pathway integrators directly and interact with them to enhance their expression levels. These results contribute to our understanding of the molecular mechanism through which MdWRKY71 regulates the flowering process in fruit trees, such as red-fleshed apple.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"32"},"PeriodicalIF":3.9,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409853","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}
{"title":"Identification and expression pattern analysis of BpGRAS gene family in Bergenia purpurascens and functional characterization of BpGRAS9 in salt tolerance.","authors":"Xin Lyu, Nuomei Xu, Jie Chen, Wenqing Wang, Feiyang Yan, Zongxiang Jiang, Qiankun Zhu","doi":"10.1007/s11103-025-01562-0","DOIUrl":"10.1007/s11103-025-01562-0","url":null,"abstract":"<p><p>Bergenia purpurascens is an important medicinal, edible, and ornamental plant. It generally grows in extreme environments with complex stresses. The GRAS transcription factors play a crucial role in regulating plant stress tolerance and growth-development. There is no research on GRAS transcription factors in B. purpurascens. In this study, 29 B. purpurascens GRAS (BpGRAS) genes were identified based on B. purpurascens transcriptome data. These BpGRAS genes were classified into seven subfamilies according to phylogenetic analysis, while BpGRAS1 was not classified into any other subfamilies. The motif analysis showed that the protein motifs in the same subfamily were relatively conserved. The expression pattern analysis of BpGRAS genes in different tissues and under salt stress showed that eight BpGRAS genes were differentially expressed under salt stress. The expression profiles showed that BpGRAS9 might play an important role in salt response and the transgenic Arabidopsis thaliana lines with overexpressed BpGRAS9 showed the enhanced salt tolerance. Root length and fresh weight were significantly increased in transgenic lines under salt conditions. The studies enhanced our comprehension of the function of BpGRAS and established a more foundation for exploring the molecular mechanisms underlying plant salt tolerance.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"33"},"PeriodicalIF":3.9,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409677","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}