Plant Methods最新文献

{"title":"Enhanced Bayesian model for multienvironmental selection of winter hybrids maize: assessing grain yield using 'ProbBreed'.","authors":"Bikas Basnet, Chitra Bahadur Kunwar, Umisha Upreti","doi":"10.1186/s13007-025-01327-2","DOIUrl":"10.1186/s13007-025-01327-2","url":null,"abstract":"<p><strong>Background: </strong>Crossover interactions stemming from phenotypic plasticity complicate selection decisions when evaluating hybrid maize with superior grain yield and consistent performance. Consequently, a two-year, region-wide investigation of 45 hybrids maize across Nepal was performed with the aim of disclosing both site and wide adapted hybrids. Utilizing an innovative \"ProbBreed\" package, based on Bayesian probability analysis of randomized complete block designs with three replicated trials at each station, this study substantively streamlines hybrids maize selection.</p><p><strong>Results: </strong>This finding revealed substantial genetic, environmental, and interactive influences on grain yield (p < 0.05). Among the hybrids, DKC9149 (8.8 tons/ha) emerged as the elite with probability coefficient of (0.39), followed by NK6607(0.35 & 8.6 tons/ha). Joint probability analysis identified RMH1899 super (0.23 & 8.3 tons/ha), followed by RMH 666 (0.15 & 8.4 tons/ha) and Uttam 121 (0.11 & 8.6 tons/ha), all of which accounted for overall environmental conditions. Additionally, over the years, DKC 9149, NK 6607(0.18 & 8.6 tons/ha), GK 3254(0.18 & 8.5 tons/ha), Shann 111(0.12 & 8.4 tons/ha), Sweety 1(0.13 & 8.4 tons/ha), and ADV 756(0.10 & 8.2 tons/ha) consistently demonstrated superior performance and stability. Delving with site specific recommendations include Nepalgunj: RMH 9999(8.5 tons/ha), NK 6607(8.6 tons/ha); Parwanipur: DKC 9149, MM 2033(8.5 tons/ha); Rampur: ADV 756, DKC 9149, MM 2929(8.6 tons/ha); and Tarahara: GK 3254(8.5 tons/ha), NK 6607(8.6 tons/ha), Uttam 121.</p><p><strong>Conclusion: </strong>Thus, Selected hybrids are predicted to outperform within the recommended domain. Over and above, integrating genomic information into Bayesian models expected to enhance prediction accuracy and expedite breeding progress.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"8"},"PeriodicalIF":4.7,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067307","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":"Correction: Minirhizotron measurements can supplement deep soil coring to evaluate root growth of winter wheat when certain pitfalls are avoided.","authors":"Jessica Arnhold, Facundo R Ispizua Yamati, Henning Kage, Anne-Katrin Mahlein, Heinz-Josef Koch, Dennis Grunwald","doi":"10.1186/s13007-025-01328-1","DOIUrl":"10.1186/s13007-025-01328-1","url":null,"abstract":"","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"7"},"PeriodicalIF":4.7,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11771108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047556","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":"A simple new method to determine leaf specific heat capacity.","authors":"Jiayu Zhang, Elias Kaiser, Hanyi Zhang, Leo F M Marcelis, Silvere Vialet-Chabrand","doi":"10.1186/s13007-025-01326-3","DOIUrl":"10.1186/s13007-025-01326-3","url":null,"abstract":"<p><strong>Background: </strong>Quantifying plant transpiration via thermal imaging is desirable for applications in agriculture, plant breeding, and plant science. However, thermal imaging under natural non-steady state conditions is currently limited by the difficulty of quantifying thermal properties of leaves, especially specific heat capacity (C_p). Existing literature offers only rough estimates of C_p and lacks simple and accurate methods to determine it.</p><p><strong>Results: </strong>We developed a non-invasive method to quantify k (the product of leaf thickness (lt), leaf density(ρ), and C_p), by fitting a leaf energy balance model to a leaf temperature (T_leaf) transient during and after a ~ 10 s light pulse. C_p was then estimated by dividing k by lt*ρ. Using this method, we quantified C_p for 13 horticultural and tropical plant species, and explored the relationship between C_p and leaf water content, specific leaf area and T_leaf response rate during the light pulse. Values of C_p ranged between 3200-4000 J kg^-1 K^-1, and were positively correlated with leaf water content. In species with very thick leaves, such as Phalaenopsis amabilis, we found leaf thickness to be a major factor in the temperature response to a short light pulse.</p><p><strong>Conclusions: </strong>Our method allows for easy determination of leaf C_p of different species, and may help pave the way to apply more accurate thermal imaging under natural non-steady state conditions.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"6"},"PeriodicalIF":4.7,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040964","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":"A simple and highly efficient protocol for ¹³C-labeling of plant cell wall for structural and quantitative analyses via solid-state nuclear magnetic resonance.","authors":"Tasleem Javaid, Akshayaa Venkataraghavan, Matrika Bhattarai, Debkumar Debnath, Wancheng Zhao, Tuo Wang, Ahmed Faik","doi":"10.1186/s13007-024-01310-3","DOIUrl":"10.1186/s13007-024-01310-3","url":null,"abstract":"<p><strong>Background: </strong>Plant cell walls are made of a complex network of interacting polymers that play a critical role in plant development and responses to environmental changes. Thus, improving plant biomass and fitness requires the elucidation of the structural organization of plant cell walls in their native environment. The ¹³C-based multi-dimensional solid-state nuclear magnetic resonance (ssNMR) has been instrumental in revealing the structural information of plant cell walls through 2D and 3D correlation spectral analyses. However, the requirement of enriching plants with ¹³C limits the applicability of this method. To our knowledge, there is only a very limited set of methods currently available that achieve high levels of ¹³C-labeling of plant materials using ¹³CO_2, and most of them require large amounts of ¹³CO₂ in larger growth chambers.</p><p><strong>Results: </strong>In this study, a simplified protocol for ¹³C-labeling of plant materials is introduced that allows ca 60% labeling of the cell walls, as quantified by comparison with commercially labeled samples. This level of ¹³C-enrichment is sufficient for all conventional 2D and 3D correlation ssNMR experiments for detailed analysis of plant cell wall structure. The protocol is based on a convenient and easy setup to supply both ¹³C-labeled glucose and ¹³CO₂ using a vacuum-desiccator. The protocol does not require large amounts of ¹³CO₂.</p><p><strong>Conclusion: </strong>This study shows that our ¹³C-labeling of plant materials can make the accessibility to ssNMR technique easy and affordable. The derived high-resolution 2D and 3D correlation spectra are used to extract structural information of plant cell walls. This helps to better understand the influence of polysaccharide-polysaccharide interaction on plant performance and allows for a more precise parametrization of plant cell wall models.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"5"},"PeriodicalIF":4.7,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143009865","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":"Apnet: Lightweight network for apricot tree disease and pest detection in real-world complex backgrounds.","authors":"Minglang Li, Zhiyong Tao, Wentao Yan, Sen Lin, Kaihao Feng, Zeyi Zhang, Yurong Jing","doi":"10.1186/s13007-025-01324-5","DOIUrl":"10.1186/s13007-025-01324-5","url":null,"abstract":"<p><p>Apricot trees, serving as critical agricultural resources, hold a significant role within the agricultural domain. Conventional methods for detecting pests and diseases in these trees are notably labor-intensive. Many conditions affecting apricot trees manifest distinct visual symptoms that are ideally suited for precise identification and classification via deep learning techniques. Despite this, the academic realm currently lacks extensive, realistic datasets and deep learning strategies specifically crafted for apricot trees. This study introduces ATZD01, a publicly accessible dataset encompassing 11 categories of apricot tree pests and diseases, meticulously compiled under genuine field conditions. Furthermore, we introduce an innovative detection algorithm founded on convolutional neural networks, specifically devised for the management of apricot tree pests and diseases. To enhance the accuracy of detection, we have developed a novel object detection framework, APNet, alongside a dedicated module, the Adaptive Thresholding Algorithm (ATA), tailored for the detection of apricot tree afflictions. Experimental evaluations reveal that our proposed algorithm attains an accuracy rate of 87.1% on ATZD01, surpassing the performance of all other leading algorithms tested, thereby affirming the effectiveness of our dataset and model. The code and dataset will be made available at https://github.com/meanlang/ATZD01 .</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"4"},"PeriodicalIF":4.7,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11721285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142953006","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":"Correction: BerryPortraits: phenotyping of ripening traits in cranberry (Vaccinium macrocarpon Ait.) With YOLOv8.","authors":"Jenyne Loarca, Tyr Wiesner-Hanks, Hector Lopez-Moreno, Andrew F Maule, Michael Liou, Maria Alejandra Torres-Meraz, Luis Diaz-Garcia, Jennifer Johnson-Cicalese, Jeffrey Neyhart, James Polashock, Gina M Sideli, Christopher F Strock, Craig T Beil, Moira J Sheehan, Massimo Iorizzo, Amaya Atucha, Juan Zalapa","doi":"10.1186/s13007-025-01323-6","DOIUrl":"https://doi.org/10.1186/s13007-025-01323-6","url":null,"abstract":"","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"3"},"PeriodicalIF":4.7,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142953009","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":"Effects of hormone concentrations on anther cultures and the acquisition of regenerated plants of five awnless triticale genotypes.","authors":"Jun Ma, Fangyuan Zhao, Yinxia Zhang, Xinhui Tian, Wenhua Du","doi":"10.1186/s13007-024-01322-z","DOIUrl":"https://doi.org/10.1186/s13007-024-01322-z","url":null,"abstract":"<p><strong>Background: </strong>The rapid production of doubled haploids by anther culture technology is an important breeding method for awnless triticale. The aim of this study was to explore the effects of triticale genotype and the types and ratios of exogenous hormones in the medium on the efficiency of triticale anther culture.</p><p><strong>Results: </strong>Anthers of five triticale genotypes were cultured on four different callus induction media and the calli were induced to differentiate into green plants by culture on three different differentiation media. The triticale genotype T8004 showed the best performance in anther culture, with a callus induction rate of 28.64%, a green plantlet differentiation frequency of 33.33%, and a green plantlet production rate of 2.78%. The highest callus induction rates were obtained by culturing anthers on C3 medium (the main components were potassium nitrate, glutamine, inositol, etc.), and the highest green plantlet differentiation frequency was obtained by culturing calli on D2 differentiation medium (the main components were potassium nitrate, ammonium nitrate, calcium chloride dihydrate, etc.). Flow cytometry analyses showed that 15 of the 20 DH0 generation plants that grew normally in the field were doubled haploids. The average chromosome doubling success rate was 55.6%. Analyses of agronomic traits showed that the 11 DH1 doubled haploid plants reached the standard for awnless triticale, so they are candidate materials for breeding new awnless triticale varieties.</p><p><strong>Conclusion: </strong>The anther culture technology of triticale was optimized in this paper, which made it possible to rapidly breed homozygous varieties of awnless triticale.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"2"},"PeriodicalIF":4.7,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142953014","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":"Development of a robust and efficient virus-induced gene silencing system for reverse genetics in recalcitrant Camellia drupifera capsules.","authors":"Hongjian Shen, Huajie Chen, Weimeng Li, Shan He, Boyong Liao, Wanyu Xiong, Yang Shen, Yongjuan Li, Yanru Gao, Yong Quan Li, Bipei Zhang","doi":"10.1186/s13007-024-01320-1","DOIUrl":"10.1186/s13007-024-01320-1","url":null,"abstract":"<p><strong>Background: </strong>Virus-induced gene silencing (VIGS) is a rapid and powerful method for gene functional analysis in plants that pose challenges in stable transformation. Numerous VIGS systems based on Agrobacterium infiltration has been widely developed for tender tissues of various plant species, yet none is available for recalcitrant perennial woody plants with firmly lignified capsules, such as tea oil camellia. Therefore, there is an urgent need for an efficient, robust, and cost-effective VIGS system for recalcitrant tissues.</p><p><strong>Results: </strong>Herein, we initiated the Tobacco rattle virus (TRV)-elicited VIGS in Camellia drupifera capsules with an orthogonal analysis including three factors: silencing target, virus inoculation approach, and capsule developmental stage. To facilitate observation and statistical analysis, two genes predominantly involved in pericarp pigmentation were selected for silencing efficiency: CdCRY1 (coding for a key photoreceptor affecting light-responsive perceivable anthocyanin accumulation in exocarps) and CdLAC15 (coding for an oxidase catalyzing the oxidative polymerization of proanthocyanidins in mesocarps, resulting in unperceivable red-hued mesocarps). The infiltration efficiency achieved for each gene was ~ 93.94% by pericarp cutting immersion. The optimal VIGS effect for each gene was observed at early (~ 69.80% for CdCRY1) and mid stages (~ 90.91% for CdLAC15) of capsule development.</p><p><strong>Conclusions: </strong>Using our optimized VIGS system, CdCRY1 and CdLAC15 expression was successfully knocked down in Camellia drupifera pericarps, leading to fading phenotypes in exocarps and mesocarps, respectively. The established VIGS system may facilitate functional genomic studies in tea oil camellia and other recalcitrant fruits of woody plants.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"1"},"PeriodicalIF":4.7,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927755","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":"Agrobacterium-mediated transient transformation of Flaveria bidentis leaves: a novel method to examine the evolution of C₄ photosynthesis.","authors":"Christopher J Baros, Jeremy Beerkens, Martha Ludwig","doi":"10.1186/s13007-024-01306-z","DOIUrl":"10.1186/s13007-024-01306-z","url":null,"abstract":"<p><p>The genus Flaveria has been studied extensively as a model for the evolution of C₄ photosynthesis. Thus far, molecular analyses in this genus have been limited due to a dearth of genomic information and the lack of a rapid and efficient transformation protocol. Since their development, Agrobacterium-mediated transient transformation protocols have been instrumental in understanding many biological processes in a range of plant species. However, this technique has not been applied to the genus Flaveria. Here, an efficient protocol for the Agrobacterium-mediated transient transformation of the leaves of the C₄ species Flaveria bidentis is presented. This technique has the distinct advantages of rapid turnaround, the ability to co-transform with multiple constructs, and the capacity to assay coding and non-coding regions of Flaveria genomes in a homologous context. To illustrate the utility of this protocol, the quantitative transcriptional regulation of phosphoenolpyruvate carboxylase, the primary carboxylase of C₄ plants, was investigated. A 24 bp region in the ppcA1 proximal promoter was found to elicit high levels of reporter gene expression. The Agrobacterium-mediated transient transformation of F. bidentis leaves will accelerate the understanding of the biology and evolution of C₄ photosynthesis in the genus Flaveria as well as in other C₄ lineages.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"193"},"PeriodicalIF":4.7,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11674322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142896306","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":"Development of a web-based high-throughput marker design program: CAPS (cleaved amplified polymorphic sequence) Maker.","authors":"Joo-Seok Park, Yoram Choi, Jin-Hyun Kim, Chaeyoung Lee, Min-Gyun Jeong, Yeong-Il Jeong, Yang Jae Kang, Young-Soo Chung, Hong-Kyu Choi","doi":"10.1186/s13007-024-01319-8","DOIUrl":"10.1186/s13007-024-01319-8","url":null,"abstract":"<p><strong>Background: </strong>Genetic markers are crucial for breeding crops with desired agronomic traits, and their development can be expedited using next-generation sequencing (NGS) and bioinformatics tools. Numerous tools have been developed to design molecular markers, enhancing the convenience, accuracy, and efficiency of molecular breeding. However, these tools primarily focus on genetic variants within short user-input sequences, despite the availability of extensive omics data for genomic variants. To design molecular markers encompassing a vast number of genetic variants at the genome-wide scale in soybean, an automatic system capable of handling NGS-based big data is necessary.</p><p><strong>Results: </strong>In this study, we developed a robust digital platform, the CAPS Maker, for designing cleaved amplified polymorphic sequence (CAPS)/derived CAPS (dCAPS) markers in soybeans. This platform simplifies the systematic design of genomic markers with a user-friendly graphical interface, featuring a 'SNP Browser' and 'Primer Table', along with internal programs (e.g., the eHT-PCR module) to design unique primer pairs for highly duplicated genomes like soybean.</p><p><strong>Conclusions: </strong>The CAPS Maker's efficiency and reliability were experimentally verified by comparing its marker predictions with actual experimental results. Consequently, breeders can easily design CAPS/dCAPS markers using the CAPS Maker platform to develop new soybean cultivars with beneficial agronomic traits. This platform is freely accessible at https://tgil.donga.ac.kr/CAPSMaker .</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"192"},"PeriodicalIF":4.7,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886061","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}