Plant Methods最新文献

{"title":"A Bayesian framework to model variance of grain yield response to plant density.","authors":"Nicolas Giordano, Dustin Hayes, Trevor J Hefley, Josefina Lacasa, Brian L Beres, Lucas A Haag, Romulo P Lollato","doi":"10.1186/s13007-025-01355-y","DOIUrl":"10.1186/s13007-025-01355-y","url":null,"abstract":"<p><strong>Background: </strong>The expected grain yield response to plant density in winter wheat (Triticum aestivum L.) follows a diminishing returns function. To our knowledge, all previous studies dealing with plant density have assumed constant variance. The gap relies on quantifying the optimum plant density that optimizes grain yield at the lowest risk. Here, we propose a Bayesian hierarchical framework to model the variance of grain yield response to plant density. We demonstrate our framework by identifying the plant density in each seed size, seed treatment and environment combination that maximizes the expected yield and minimizes yield variance.</p><p><strong>Results: </strong>To fit the model, we used data from field experiments conducted in the Canadian Prairies to identify informative priors and Kansas experiments to demonstrate and validate our framework. Kansas experiments were conducted in 25 environments and consisted of a complete factorial combination of three seed cleaning methods leading to three different seed sizes (light, moderate, heavy), two or three seeding rates, and two seed chemical treatments (insecticide + fungicide vs. none). We described both expected yield and variance of yield in response to plant density. The proposed model allowed us to quantify the minimum risk plant density (minRPD), which represents the minimum plant density at which grain yield variance becomes constant. Plant density at the minRPD was always greater than the agronomic optimum plant density (AOPD, i.e.: the plant density that maximizes expected yield); thus, minRPD could be used to estimate the minimum plant density that maximizes expected yield and minimizes yield variance. When compared at the AOPD, four seed cleaning × chemical treatments combinations resulted in similar yield advantages over the control under high and low yielding environments. However, in low-yielding environments, only two cleaning × chemical treatments combinations resulted in smaller variance when compared at the minRPD against the control. All seed cleaning × chemical treatments combinations resulted in similar AOPD. However, two cleaning × chemical treatments combinations had greater minRPD in low-yield environments compared to the control.</p><p><strong>Conclusion: </strong>Modeling grain yield response to plant density with the proposed framework is suitable for heteroscedastic data scenarios. Future research may focus on exploring how genotypes, environments and their interaction modulate the difference between AOPD and minRPD and, extend the framework to a variety of processes involving crop management decisions.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"38"},"PeriodicalIF":4.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143649904","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 cotton organ segmentation method with phenotypic measurements from a point cloud using a transformer.","authors":"Fu-Yong Liu, Hui Geng, Lin-Yuan Shang, Chun-Jing Si, Shi-Quan Shen","doi":"10.1186/s13007-025-01357-w","DOIUrl":"10.1186/s13007-025-01357-w","url":null,"abstract":"<p><p>Cotton phenomics plays a crucial role in understanding and managing the growth and development of cotton plants. The segmentation of point clouds, a process that underpins the measurement of plant organ structures through 3D point clouds, is necessary for obtaining precise phenotypic parameters. This study proposes a cotton point cloud organ semantic segmentation method named TPointNetPlus, which combines PointNet++ and Transformer algorithms. Firstly, a dedicated point cloud dataset for cotton plants is constructed using multi-view images. Secondly, the attention module Transformer is introduced into the PointNet++ model to increase the accuracy of feature extraction. Finally, organ-level cotton plant point cloud segmentation is performed using the HDBSCAN algorithm, successfully segmenting cotton leaves, bolls, and branches from the entire plant, and obtaining their phenotypic feature parameters. The research results indicate that the TPointNetPlus model achieved a high accuracy of 98.39% in leaf semantic segmentation. The correlation coefficients between the measured values of four phenotypic parameters (plant height, leaf area, and boll volume) ranged from 0.95 to 0.97, demonstrating the accurate predictive capability of the model for these key traits. The proposed method, which enables automated data analysis from a plant's 3D point cloud to phenotypic parameters, provides a reliable reference for in-depth studies of plant phenotypes.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"37"},"PeriodicalIF":4.7,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143649906","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":"Tracing meristem cell lineages during plant development and regeneration by the all-in-one CRE/LOX system.","authors":"Shengnan Wang, Yu Li, Zijuan Li, Chao Li, Lin Xu, Ning Zhai","doi":"10.1186/s13007-025-01352-1","DOIUrl":"10.1186/s13007-025-01352-1","url":null,"abstract":"<p><p>The root apical meristem (RAM) and the shoot apical meristem (SAM), which contain stem cells and their lineages, are the centers for underground and aboveground organ formation in vascular plants. Accurately tracing stem cell lineage is important to understand how the RAM and SAM are formed and how they give rise to new organs. Here, we introduce the all-in-one CRE/LOX system, which is assembled in a single plasmid and can be used to efficiently trace cell lineage during de novo formation of meristems and cell differentiation within meristems in Arabidopsis thaliana. Using the CRE/LOX-GUS system driven by the WUSCHEL-RELATED HOMEOBOX5 (WOX5) promoter (i.e., WOX5_pro-CRE/LOX-GUS), we show that cell division of the quiescent center (QC) within the stem cell niche of the RAM might replenish initial/stem cells in plants grown on mannitol-containing medium or in soil. The results obtained using WOX5_pro-CRE/LOX-GUS also show that a group of shoot progenitor cells acts together to initiate the SAM during de novo shoot regeneration from callus in tissue culture. We also demonstrate the use of the CRE/LOX-RUBY system for real-time in vivo tracing of cell lineages in live organs. Overall, this paper not only introduces the all-in-one CRE/LOX tool, but also reveals the cell lineages during meristem development and regeneration.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"36"},"PeriodicalIF":4.7,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625633","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":"Genetic transformation of the oilseed crop camelina using immature zygotic embryos.","authors":"Barno Ruzimurodovna Rezaeva, Ingrid Otto, Götz Hensel, Pouneh Pouramini, Anton Peterson, Jochen Kumlehn","doi":"10.1186/s13007-025-01351-2","DOIUrl":"10.1186/s13007-025-01351-2","url":null,"abstract":"<p><strong>Background: </strong>Camelina is an oilseed crop with particularly useful fatty acid and amino acid profiles of its seeds, high resilience to abiotic and biotic stresses, and a short life cycle. Previous genetic engineering approaches in camelina have largely relied on the floral dip method which is, however, associated with genotype-dependent efficiency and incompatibility with methods of direct biomolecule delivery.</p><p><strong>Results: </strong>Here, we established a novel method of transgenesis for camelina, taking advantage of the high regenerative capacity of immature embryos. Various culture conditions and treatments were experimentally validated, which included the duration of explant pre-cultivation, wounding of explants and its time of application, Agrobacterium strain and density of inoculum, acetosyringone concentration, duration of explant-Agrobacterium co-cultivation, as well as application time and concentration of the selective agent hygromycin. We provide convergent evidence of stable transgenicity and transgene inheritance by (1) selection for resistance to hygromycin, (2) PCR, (3) detection of the transgene product GFP, and (4) DNA gel blot analysis involving primary transgenic plants and segregating progeny. Primary transgenics examined in detail featured one to three T-DNA integration loci, with one to seven T-DNA copies being integrated in total per plant. The established method proved efficient across all three tested accessions including two current cultivars, whereby transformation efficiencies, determined as PCR-positive primary transgenic plants related to agro-inoculated explants, of between 13 and 17% were obtained.</p><p><strong>Conclusion: </strong>With this method, we provide a viable platform for the functional validation of genes-of-interest and for biotechnological improvements of plant performance and quality features in camelina.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"35"},"PeriodicalIF":4.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143615443","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":"Spectral estimation of the aboveground biomass of cotton under water-nitrogen coupling conditions.","authors":"Shunyu Qiao, Jiaqiang Wang, Fuqing Li, Jing Shi, Chongfa Cai","doi":"10.1186/s13007-025-01358-9","DOIUrl":"10.1186/s13007-025-01358-9","url":null,"abstract":"<p><strong>Aims: </strong>Hyperspectral remote sensing technology can quickly obtain above-ground biomass (AGB) information of cotton, playing an important role in realizing accurate management for cotton cultivation.</p><p><strong>Methods: </strong>Using Tahe-2 as the research object, nitrogen application rates and irrigation amounts were set to 0 (N₀), 100 (N₁), 150 (N₂), 200 (N₃), 250 (N₄) kg ha^- 1 and 4500 (W₁), 6000 (W₂), 7500 (W₃) m³ ha^- 1 under the coupled conditions of water and nitrogen. Through correlation analysis between cotton AGB and canopy spectral reflectance, the intersection of feature wavelengths screened by the successive projection algorithm (SPA) and highly significant wavelengths was used as the input vector for modeling. Support vector machine (SVM), regression tree (RT), and convolutional neural network (CNN) were employed to verify the accuracy.</p><p><strong>Results: </strong>The results revealed the following: (1) The AGB of cotton at the bud stage was highest under the W₁N₂ gradient. At the flowering stage, the highest AGB was observed under the W₃N₂ gradient. At the boll stage, the highest AGB was under the W₃N₀ gradient. (2) The optimal spectral model based on SVM for cotton AGB identification had higher R² values and lower RMSE values at the boll stage, with R² = 0.76, RMSE = 0.35 g and RPD = 17.59. The optimal spectral model based on RT had higher R² values and lower RMSE values at the bud stage, with R² = 0.79, RMSE = 0.24 g and RPD = 16.18. The optimal spectral model based on CNN also had higher R² values and lower RMSE values at the bud stage, with R² = 0.70, RMSE = 0.42 g and RPD = 4.50. These results indicated that the inversion effect at the bud stage was better than at other stages.</p><p><strong>Conclusions: </strong>In terms of model testing, the RT model was found to be the most accurate for estimating cotton AGB, outperforming SVM and CNN.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"34"},"PeriodicalIF":4.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143615987","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":"DWTFormer: a frequency-spatial features fusion model for tomato leaf disease identification.","authors":"Yuyun Xiang, Shuang Gao, Xiaopeng Li, Shuqin Li","doi":"10.1186/s13007-025-01349-w","DOIUrl":"10.1186/s13007-025-01349-w","url":null,"abstract":"<p><p>Remarkable inter-class similarity and intra-class variability of tomato leaf diseases seriously affect the accuracy of identification models. A novel tomato leaf disease identification model, DWTFormer, based on frequency-spatial feature fusion, was proposed to address this issue. Firstly, a Bneck-DSM module was designed to extract shallow features, laying the groundwork for deep feature extraction. Then, a dual-branch feature mapping network (DFMM) was proposed to extract multi-scale disease features from frequency and spatial domain information. In the frequency branch, a 2D discrete wavelet transform feature decomposition module effectively captured the rich frequency information in the disease image, compensating for spatial domain information. In the spatial branch, a multi-scale convolution and PVT (Pyramid Vision Transformer)-based module was developed to extract the global and local spatial features, enabling comprehensive spatial representation. Finally, a dual-domain features fusion model based on dynamic cross-attention was proposed to fuse the frequency-spatial features. Experimental results on the tomato leaf disease dataset demonstrated that DWTFormer achieved 99.28% identification accuracy, outperforming most existing mainstream models. Furthermore, 96.18% and 99.89% identification accuracies have been obtained on the AI Challenger 2018 and PlantVillage datasets. In-field experiments demonstrated that DWTFormer achieved an identification accuracy of 97.22% and an average inference time of 0.028 seconds in real plant environments. This work has effectively reduced the impact of inter-class similarity and intra-class variability on tomato leaf disease identification. It provides a scalable model reference for fast and accurate disease identification.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"33"},"PeriodicalIF":4.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597565","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":"The genetic puzzle of multicopy genes: challenges and troubleshooting.","authors":"Vania Gabriela Sedano Partida, Henrique Moura Dias, Maria Teresa Portes, Marie-Anne Van Sluys","doi":"10.1186/s13007-025-01329-0","DOIUrl":"10.1186/s13007-025-01329-0","url":null,"abstract":"<p><strong>Background: </strong>Studies of multicopy genes impose challenges related to gene redundancy and sequence similarity among copies. However, recent advances in molecular biology and genomics tools associated with dedicated databases facilitate their study. Thus, the present work emphasizes the need for rigorous methodologies and standardized approaches to interpret RT-qPCR results accurately.</p><p><strong>Results: </strong>Data from Physcomitrium patens provides a comprehensive five-step protocol, using thiamine thiazole synthase (THI1) and sucrose 6-phosphate phosphohydrolase (S6PP) genes as proof of concept to showcase a systematic workflow for studying multicopy genes. Beyond examining genes of interest, we highlight the critical role of choosing appropriate internal controls in the analytical process for interpreting gene expression patterns accurately. We emphasize the importance of identifying the relevant orthologous gene, recognizing the inherent challenges in determining the most functional copy for subsequent studies. Our objective is to enhance comprehension of gene redundancy by dissecting multicopy genes' genomic landscape and its characteristics. Furthermore, we address the decision-making process surrounding the expression level quantification of multicopy genes.</p><p><strong>Conclusions: </strong>The study of multicopy genes discloses early events for functional adaptation. Here, we discuss the significance of multicopy genes in plant biology and provide an experimental protocol to analyze them. As plant systems are strongly influenced by light/dark cycles, challenges inherent to circadian processes are also acknowledged. Therefore, our comprehensive approach aims to advance the understanding of multicopy gene dynamics, offering practical methodologies and contributing with valuable insights to the scientific community.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"32"},"PeriodicalIF":4.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586690","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":"Benefiting from the past: establishing in vitro culture of European beech (Fagus sylvatica L.) from provenance trial trees and seedlings.","authors":"Virginia Zahn, Alexander Fendel, Alice-Jeannine Sievers, Matthias Fladung, Tobias Bruegmann","doi":"10.1186/s13007-025-01350-3","DOIUrl":"10.1186/s13007-025-01350-3","url":null,"abstract":"<p><strong>Background: </strong>European beech (Fagus sylvatica L.) is distributed across diverse climate conditions throughout Europe. Local adaptations, such as drought tolerance, could become crucial for maintaining beech populations facing climate change. In vitro culture offers a promising tool for preserving and propagating valuable genotypes and provides a basis for biotechnological research, although establishing and propagating recalcitrant beech in vitro is difficult. To the best of our knowledge, this study is the first to use beeches from a provenance trial to establish in vitro cultures, aiming to capture a wide genetic spectrum and investigate provenance-specific suitability for in vitro cultivation. In addition, a high-throughput method using seedlings has been developed to increase the success of establishing in vitro cultures of a provenance.</p><p><strong>Results: </strong>Actively growing shoots from 22 field-grown provenances were obtained for in vitro establishment. After 12 weeks, shoot formation on shoot tips and nodal segments was induced in 13 provenances (57%), with success rates ranging from 3 to 80%, significantly influenced by the provenance and sampling date of the branches. Combining one harvest each in February and May resulted in the highest shoot formation rate (18%). However, after two years, stable micropropagation was achieved for a single genotype. In the second approach, whole shoots or shoot tips from seedlings were used for in vitro establishment, achieving shoot formation rates between 38 and 94%. Bacterial contamination during establishment was controlled through antibiotic application. Using culture medium without phytohormones improved initial leaf flush on shoot tips within the first 8 weeks of in vitro culture. Phytohormone-supplemented media were needed for shoot multiplication and prolonged in vitro culture. Cultures of 25 genotypes were maintained for up to two years. The viability of in vitro shoots was maintained by supplementing the medium with FeNaEDTA, MgSO₄, and glucose. Some genotypes showed enhanced performance on sugar-free media with increased light intensity, which reduced bacterial outgrowth.</p><p><strong>Conclusion: </strong>With the technical approaches presented here, we provide starting points for the establishment of beech cultures from various types of starting material, as well as for further method improvement for establishment and long-term cultivation.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"31"},"PeriodicalIF":4.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11887157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586674","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":"Swin-Unet++: a study on phenotypic parameter analysis of cabbage seedling roots.","authors":"Hongda Li, Yue Zhao, Zeyang Bi, Peng Hao, Huarui Wu, Chunjiang Zhao","doi":"10.1186/s13007-025-01340-5","DOIUrl":"10.1186/s13007-025-01340-5","url":null,"abstract":"<p><strong>Background: </strong>As an important economic crop, the growth status of the root system of cabbage directly affects its overall health and yield. To monitor the root growth status of cabbage seedlings during their growth period, this study proposes a new network architecture called Swin-Unet++. This architecture integrates the Swin-Transformer module and residual networks and uses attention mechanisms to replace traditional convolution operations for feature extraction. It also adopts the residual concept to fuse contextual information from different levels, addressing the issue of insufficient feature extraction for the thin and mesh-like roots of cabbage seedlings.</p><p><strong>Results: </strong>Compared with other backbone high-precision semantic segmentation networks, SwinUnet + + achieves superior segmentation results. The results show that the accuracy of Swin-Unet + + in root system segmentation tasks reached as high as 98.19%, with a model parameter of 60 M and an average response time of 29.5 ms. Compared with the classic Unet network, the mIoU increased by 1.08%, verifying that the Swin-Transformer and residual networks can accurately extract the fine-grained features of roots. Furthermore, when images after different semantic segmentations are compared to locate the root position through contours, Swin-Unet + + has the best positioning effect. On the basis of the root pixels obtained from semantic segmentation, the calculated maximum root length, extension width, and root thickness are compared with actual measurements. The resulting goodness of fit R² values are 94.82%, 94.43%, and 86.45%, respectively. Verifying the effectiveness of this network in extracting the phenotypic traits of cabbage seedling roots.</p><p><strong>Conclusions: </strong>The Swin-Unet + + framework developed in this study provides a new technique for the monitoring and analysis of cabbage root systems, ultimately leading to the development of an automated analysis platform that offers technical support for intelligent agriculture and efficient planting practices.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"30"},"PeriodicalIF":4.7,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11874442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542783","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":"Rootrainertrons: a novel root phenotyping method used to identify genotypic variation in lettuce rooting.","authors":"Cara Wharton, Andrew Beacham, Miriam L Gifford, James Monaghan","doi":"10.1186/s13007-025-01348-x","DOIUrl":"10.1186/s13007-025-01348-x","url":null,"abstract":"<p><strong>Background: </strong>There is much interest in how roots can be manipulated to improve crop performance in a changing climate, yet root research is made difficult by the challenges of visualising the root system accurately, particularly when grown in natural environments such as soil. Scientists often resort to use of agar- or paper-based assays, which provide unnatural growing media, with the roots often exposed to light. Alternatives include rhizotrons or x-ray computed tomography, which require specialist and expensive pieces of equipment, not accessible to those in developing countries most affected by climate change. Another option is excavation of roots, however, this is time-consuming and near impossible to achieve without some degree of root damage. Therefore, new, affordable but reliable alternatives for root phenotyping are necessary.</p><p><strong>Results: </strong>This study reports a novel, low cost, Rootrainer-based system for root phenotyping. Rootrainers were tilted at an angle, in a rhizotron-like set-up. This encouraged root growth on the bottom plane of the Rootrainers, and since Rootrainers open (in a book-like fashion), root growth can be easily observed. This new technique was successfully used to uncover significant genotypic variance in rooting traits for a selection of lettuce (L. sativa) varieties across multiple timepoints.</p><p><strong>Conclusion: </strong>This novel Rootrainertron method has many advantages over existing methods of phenotyping seedling roots. Rootrainers are cheap, and readily available from garden centres, unlike rhizotrons which are expensive and only available from specialist suppliers. Rootrainers allow the roots to grow in substrate medium, providing a significant advantage over agar and paper assays.This approach offers an affordable and relevant root phenotyping option and makes root phenotyping more accessible and applicable for researchers.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"21 1","pages":"29"},"PeriodicalIF":4.7,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537552","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}