Plant Molecular Biology最新文献

{"title":"A novel QTL qRYM-7H for barley yellow mosaic resistance identified by GWAS and linkage analysis.","authors":"Juan Zhu, Hui Zhou, Mengna Zhang, Yi Hong, Yuhang Zhang, Chao Lv, Baojian Guo, Feifei Wang, Rugen Xu","doi":"10.1007/s11103-024-01529-7","DOIUrl":"https://doi.org/10.1007/s11103-024-01529-7","url":null,"abstract":"<p><p>Barley (Hordeum vulgare L.) is the fourth largest cereal crop in the world after rice, wheat and maize. Barley yellow mosaic disease (BYMD) is a serious threat to winter barley production. The evolution and mutation of virus strains lead to the breakdown of the resistance of the originally resistant varieties. It is therefore vital to explore new BYMD resistance genes. In this study, a natural population (334 barley varieties or lines) and a double haploid population derived from the cross between Tam407227 and Franklin were used to search for new quantitative trait loci (QTL) for BYMD resistance. Two major QTL on chromosomes 3H and 7H, respectively, were detected from the genome wide association study and validated in the DH population. Among them, The QTL on 3H (qRYM-3H/qTFRYM-3H) was confirmed to be the reported BYMD resistance gene eIF4E by haplotype analysis. And the QTL on 7H (qRYM-7H/qTFRYM-7H) is a novel QTL that has not been reported before. Another QTL on 2H was identified from the DH population. This QTL is more likely the Rmy16^Hb reported previously. These three QTL showed an additive effect on improving BYMD resistance with the average disease scores from 2.45 (all sensitive alleles for these three QTL) to 0.62 (all tolerant alleles for these three QTL). The candidate genes for the novel QTL qRYM-7H/qTFRYM-7H were predicted based on transcriptome sequencing and qPCR analysis.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"127"},"PeriodicalIF":3.9,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142688489","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":"Proteomic and metabolomic insights into the mechanisms of calcium-mediated salt stress tolerance in hemp.","authors":"Yang Yang, Zhenhua Lu, Hailong Ye, Jiafeng Li, Yan Zhou, Ling Zhang, Gang Deng, Zheng Li","doi":"10.1007/s11103-024-01525-x","DOIUrl":"10.1007/s11103-024-01525-x","url":null,"abstract":"<p><p>Industrial hemp (Cannabis sativa L.) is a multifaced crop that has the potential to be exploited for many industrial applications, and making use of salt lands is considered to be a sustainable development strategy for the hemp industry. However, no elite salt-tolerant hemp varieties have been developed, and therefore supplementing appropriate exogenous substances to saline soil is one possible solution. Calcium-containing compounds are well-known for their salt tolerance enhancing effects, but the underlying molecular mechanisms remain largely unclear. Here, we first assessed the ameliorative effects of calcium amendments on salt-stressed hemp plants and then investigated these mechanisms on hemp using integrative analysis of proteomics and metabolomics. The stress phenotypes could be lessened by Ca²⁺ treatment. Certain concentrations of Ca²⁺ maintained relative electrical conductivity and the contents of malondialdehyde and chlorophyll. Ca²⁺ treatment also generally led to greater accumulations of soluble proteins, soluble carbohydrates and proline, and enhanced the activities of superoxide dismutase and peroxidase. Through functional classification, pathway enrichment, and network analysis, our data reveal that accumulation of dipeptides is a prominent metabolic signature upon exogenous Ca²⁺ treatment, and that changes in mitochondrial properties may play an important role in enhancing the salt tolerance. Our results outline the complex metabolic alternations involved in calcium-mediated salt stress resistance, and these data and analyses would be useful for future functional studies.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"126"},"PeriodicalIF":3.9,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668670","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":"Publisher Correction: Alternative splicing and deletion in S-RNase confer stylar-part self-compatibility in the apple cultivar 'Vered'.","authors":"Kazuma Okada, Taku Shimizu, Shigeki Moriya, Masato Wada, Kazuyuki Abe, Yutaka Sawamura","doi":"10.1007/s11103-024-01526-w","DOIUrl":"https://doi.org/10.1007/s11103-024-01526-w","url":null,"abstract":"","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"125"},"PeriodicalIF":3.9,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625759","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":"Multi-omics analysis reveals the positive impact of differential chloroplast activity during in vitro regeneration of barley.","authors":"Parul Sirohi, Chanderkant Chaudhary, Mayank Sharma, Ravi Bodampalli Anjanappa, Suchi Baliyan, Ritika Vishnoi, Sumit Kumar Mishra, Reeku Chaudhary, Bhairavnath Waghmode, Anuj Kumar Poonia, Hugo Germain, Debabrata Sircar, Harsh Chauhan","doi":"10.1007/s11103-024-01517-x","DOIUrl":"https://doi.org/10.1007/s11103-024-01517-x","url":null,"abstract":"<p><p>Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. In this study, two contrasting cultivars differencing in their in vitro regeneration efficiency were identified. Tissue culture friendly cultivar Golden Promise (GP) and tissue culture resistant DWRB91(D91) were selected as contrasting cultivars to investigate the molecular basis of regeneration efficiency through multiomics analysis. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS/MS revealed 3062 protein groups and 16,989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. TEM analysis also revealed differential plastid development. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91. A comprehensive examination of gene expression, protein profiling and metabolite patterns unveiled a significant increase in the genes encompassing various functions, such as ion homeostasis, chlorophyll metabolic process, ROS regulation, and the secondary metabolic pathway.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"124"},"PeriodicalIF":3.9,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625756","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":"Transcriptomic responses of Solanum tuberosum cv. Pirol to arbuscular mycorrhiza and potato virus Y (PVY) infection.","authors":"Edyta Deja-Sikora, Marcin Gołębiewski, Katarzyna Hrynkiewicz","doi":"10.1007/s11103-024-01519-9","DOIUrl":"10.1007/s11103-024-01519-9","url":null,"abstract":"<p><p>Arbuscular mycorrhizal fungi (AMF) serve as both plant symbionts and allies in resisting pathogens and environmental stresses. Mycorrhizal colonization of plant roots can influence the outcomes of plant-pathogen interactions by enhancing specific host defense mechanisms. The transcriptional responses induced by AMF in virus-infected plants remain largely unexplored. In the presented study, we employed a comprehensive transcriptomic approach and qPCR to investigate the molecular determinants underlying the interaction between AMF and potato virus Y (PVY) in Solanum tuberosum L. Our primary goal was to identify the symbiosis- and defense-related determinants activated in mycorrhizal potatoes facing PVY. Through a comparative analysis of mRNA transcriptomes in experimental treatments comprising healthy and PVY-infected potatoes colonized by two AMF species, Rhizophagus regularis or Funneliformis mosseae, we unveiled the overexpression of genes associated with mycorrhiza, including nutrient exchange, lipid transfer, and cell wall remodeling. Furthermore, we identified several differentially expressed genes upregulated in all mycorrhizal treatments that encoded pathogenesis-related proteins involved in plant immune responses, thus verifying the bioprotective role of AMF. We investigated the relationship between mycorrhiza levels and PVY levels in potato leaves and roots. We found accumulation of the virus in the leaves of mycorrhizal plants, but our studies additionally showed a reduced PVY content in potato roots colonized by AMF, which has not been previously demonstrated. Furthermore, we observed that a virus-dependent reduction in nutrient exchange could occur in mycorrhizal roots in the presence of PVY. These findings provide an insights into the interplay between virus and AMF.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"123"},"PeriodicalIF":3.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625760","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}

{"title":"DArTseq genotyping facilitates identification of Aegilops biuncialis chromatin introgressed into bread wheat Mv9kr1.","authors":"Eszter Gaál, András Farkas, Edina Türkösi, Klaudia Kruppa, Éva Szakács, Kitti Szőke-Pázsi, Péter Kovács, Balázs Kalapos, Éva Darkó, Mahmoud Said, Adam Lampar, László Ivanizs, Miroslav Valárik, Jaroslav Doležel, István Molnár","doi":"10.1007/s11103-024-01520-2","DOIUrl":"10.1007/s11103-024-01520-2","url":null,"abstract":"<p><p>Wild wheat relative Aegilops biuncialis offers valuable traits for crop improvement through interspecific hybridization. However, gene transfer from Aegilops has been hampered by difficulties in detecting introgressed U^b- and M^b-genome chromatin in the wheat background at high resolution. The present study applied DArTseq technology to genotype two backcrossed populations (BC382, BC642) derived from crosses of wheat line Mv9kr1 with Ae. biuncialis accession, MvGB382 (early flowering and drought-tolerant) and MvGB642 (leaf rust-resistant). A total of 11,952 Aegilops-specific Silico-DArT markers and 8,998 wheat-specific markers were identified. Of these, 7,686 markers were assigned to U^b-genome chromosomes and 4,266 to M^b-genome chromosomes and were ordered using chromosome scale reference assemblies of hexaploid wheat and Ae. umbellulata. U^b-genome chromatin was detected in 5.7% of BC382 and 22.7% of BC642 lines, while 88.5% of BC382 and 84% of BC642 lines contained M^b-genome chromatin, predominantly the chromosomes 4M^b and 5M^b. The presence of alien chromatin was confirmed by microscopic analysis of mitotic metaphase cells using GISH and FISH, which allowed precise determination of the size and position of the introgression events. New Mv9kr1-Ae. biuncialis MvGB382 4M^b and 5M^b disomic addition lines together with a 5DS.5DL-5M^bL recombination were identified. A possible effect of the 5M^bL distal region on seed length has also been observed. Moreover, previously developed Mv9kr1-MvGB642 introgression lines were more precisely characterized. The newly developed cytogenetic stocks represent valuable genetic resources for wheat improvement, highlighting the importance of utilizing diverse genetic materials to enhance wheat breeding strategies.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"122"},"PeriodicalIF":3.9,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11543725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605881","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}

{"title":"Exploring the complexity of genome size reduction in angiosperms.","authors":"Akihiro Ezoe, Motoaki Seki","doi":"10.1007/s11103-024-01518-w","DOIUrl":"10.1007/s11103-024-01518-w","url":null,"abstract":"<p><p>The genome sizes of angiosperms decreased significantly more than the genome sizes of their ancestors (pteridophytes and gymnosperms). Decreases in genome size involve a highly complex process, with remnants of the genome size reduction scattered across the genome and not directly linked to specific genomic structures. This is because the associated mechanisms operate on a much smaller scale than the mechanisms mediating increases in genome size. This review thoroughly summarizes the available literature regarding the molecular mechanisms underlying genome size reductions and introduces Utricularia gibba and Arabidopsis thaliana as model species for the examination of the effects of these molecular mechanisms. Additionally, we propose that phosphorus deficiency and drought stress are the major external factors contributing to decreases in genome size. Considering these factors affect almost all land plants, angiosperms likely gained the mechanisms for genome size reductions. These environmental factors may affect the retention rates of deletions, while also influencing the mutation rates of deletions via the functional diversification of the proteins facilitating double-strand break repair. The biased retention and mutation rates of deletions may have synergistic effects that enhance deletions in intergenic regions, introns, transposable elements, duplicates, and repeats, leading to a rapid decrease in genome size. We suggest that these selection pressures and associated molecular mechanisms may drive key changes in angiosperms during recurrent cycles of genome size decreases and increases.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"121"},"PeriodicalIF":3.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11530473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562432","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}

{"title":"Multiple NADPH-cytochrome P450 reductases from Lycoris radiata involved in Amaryllidaceae alkaloids biosynthesis.","authors":"Yuqing Wu, Yifeng Zhang, Haitong Fan, Jie Gao, Siyu Shen, Jifan Jia, Rong Liu, Ping Su, Yating Hu, Wei Gao, Dan Li","doi":"10.1007/s11103-024-01516-y","DOIUrl":"https://doi.org/10.1007/s11103-024-01516-y","url":null,"abstract":"<p><p>Amaryllidaceae alkaloids (AAs), such as galanthamine and lycorine, are natural products of Lycoris radiata possessing various pharmacological activities including anti-acetylcholinesterase, anti-inflammatory, and antitumour activities. Elucidating the biosynthesis of these special AAs is crucial for understanding their production and potential modification for improved clinical application, of which cytochrome P450 enzymes catalyse the formation of key alkaloid skeletons and subsequent modification processes, with the NAPDH cytochrome P450 reductases (CPRs) serving as essential redox partners. This study identified three CPRs, LrCPR1, LrCPR2, and LrCPR3, encoding 700, 697 and 695 amino acids, respectively, which belong to Class II CPRs. The LrCPRs reduced cytochrome c and ferricyanide in an NADPH-dependent manner, and their activities all followed the typical Michaelis-Menten curve. In yeast, the co-expression of LrCPRs and CYP96T6 produced the galantamine-like alkaloid namely N-demethylnarwedine, suggesting that they support the catalytic activity of CYP96T6. Quantitative analysis of the transcriptional expression profiles showed that LrCPRs were expressed in all the examined tissues of L. radiata, and their gene expression patterns are consistent with other genes that may be involved in the biosynthetic pathway of AAs, including cinnamate 4-hydroxylase and phenylalanine ammonia-lyase. Our study firstly provides the functional characterization of LrCPRs in L. radiata, which will contribute to the discovery of biosynthetic pathways and heterologous production of AAs.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"120"},"PeriodicalIF":3.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562502","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":"Expression interplay of genes coding for calcium-binding proteins and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat.","authors":"Diana Duarte-Delgado, Inci Vogt, Said Dadshani, Jens Léon, Agim Ballvora","doi":"10.1007/s11103-024-01523-z","DOIUrl":"10.1007/s11103-024-01523-z","url":null,"abstract":"<p><p>Bread wheat is an important crop for the human diet, but the increasing soil salinization is reducing the yield. The Ca²⁺ signaling events at the early stages of the osmotic phase of salt stress are crucial for the acclimation response of the plants through the performance of calcium-sensing proteins, which activate or repress transcription factors (TFs) that affect the expression of downstream genes. Physiological, genetic mapping, and transcriptomics studies performed with the contrasting genotypes Syn86 (synthetic, salt-susceptible) and Zentos (elite cultivar, salt-tolerant) were integrated to gain a comprehensive understanding of the salt stress response. The MACE (Massive Analysis of cDNA 3'-Ends) based transcriptome analysis until 4 h after stress exposure revealed among the salt-responsive genes, the over-representation of genes coding for calcium-binding proteins. The functional and structural diversity within this category was studied and linked with the expression levels during the osmotic phase in the contrasting genotypes. The non-EF-hand category from calcium-binding proteins was found to be enriched for the susceptibility response. On the other side, the tolerant genotype was characterized by a faster and higher up-regulation of genes coding for proteins with EF-hand domain, such as RBOHD orthologs, and TF members. This study suggests that the interplay of calcium-binding proteins, WRKY, and AP2/ERF TF families in signaling pathways at the start of the osmotic phase can affect the expression of downstream genes. The identification of SNPs in promoter sequences and 3' -UTR regions provides insights into the molecular mechanisms controlling the differential expression of these genes through differential transcription factor binding affinity or altered mRNA stability.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"119"},"PeriodicalIF":3.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11530504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562435","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}

{"title":"Deep learning modeling of RNA ac4C deposition reveals the importance of plant alternative splicing.","authors":"Bintao Guo, Xinlin Wei, Shuangcheng Liu, Wenchao Cui, Chao Zhou","doi":"10.1007/s11103-024-01512-2","DOIUrl":"10.1007/s11103-024-01512-2","url":null,"abstract":"<p><p>The N4-acetylcytidine (ac4C) modification has recently been characterized as a noncanonical RNA marker in plants. While the precise installation of ac4C sites in individual plant transcripts continues to present challenges, the biological roles of ac4C in specific plant species are gradually being deciphered. Herein, we utilized a deep learning technique called iac4C (intelligent ac4C) to predict ac4C sites in mRNA. ac4C deposition was effectively forecasted by the iac4C model (AUROC = 0.948), revealing a reliable distribution pattern primarily situated in the transcribing area as opposed to regions that are not translated. The iac4C deep learning approach using a combination of BiGRU and self-attention mechanisms both validates previous studies showing a positive correlation between ac4C and RNA splicing in plant species and reveals new examples of other splicing events associated with ac4C. Our advanced deep learning algorithm for analyzing ac4C enables swift identification of important biological phenomena that would otherwise be challenging to uncover through traditional experimental approaches. These findings provide insight into the essential regulatory function of site-specific ac4C deposition in alternative splicing processes. The source code and datasets for iac4C are available at https://github.com/xlwei507/iac4C .</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 6","pages":"118"},"PeriodicalIF":3.9,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522596","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}