Plant Methods最新文献

{"title":"Revisiting superiority and stability metrics of cultivar performances using genomic data: derivations of new estimators.","authors":"Humberto Fanelli Carvalho, Simon Rio, Julian García-Abadillo, Julio Isidro Y Sánchez","doi":"10.1186/s13007-024-01207-1","DOIUrl":"10.1186/s13007-024-01207-1","url":null,"abstract":"<p><p>The selection of highly productive genotypes with stable performance across environments is a major challenge of plant breeding programs due to genotype-by-environment (GE) interactions. Over the years, different metrics have been proposed that aim at characterizing the superiority and/or stability of genotype performance across environments. However, these metrics are traditionally estimated using phenotypic values only and are not well suited to an unbalanced design in which genotypes are not observed in all environments. The objective of this research was to propose and evaluate new estimators of the following GE metrics: Ecovalence, Environmental Variance, Finlay-Wilkinson regression coefficient, and Lin-Binns superiority measure. Drawing from a multi-environment genomic prediction model, we derived the best linear unbiased prediction for each GE metric. These derivations included both a squared expectation and a variance term. To assess the effectiveness of our new estimators, we conducted simulations that varied in traits and environment parameters. In our results, new estimators consistently outperformed traditional phenotype-based estimators in terms of accuracy. By incorporating a variance term into our new estimators, in addition to the squared expectation term, we were able to improve the precision of our estimates, particularly for Ecovalence in situations where heritability was low and/or sparseness was high. All methods are implemented in a new R-package: GEmetrics. These genomic-based estimators enable estimating GE metrics in unbalanced designs and predicting GE metrics for new genotypes, which should help improve the selection efficiency of high-performance and stable genotypes across environments.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"85"},"PeriodicalIF":4.7,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141284458","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":"Mapping the membrane orientation of auxin homeostasis regulators PIN5 and PIN8 in Arabidopsis thaliana root cells reveals their divergent topology.","authors":"Yewubnesh Wendimu Seifu, Vendula Pukyšová, Nikola Rýdza, Veronika Bilanovičová, Marta Zwiewka, Marek Sedláček, Tomasz Nodzyński","doi":"10.1186/s13007-024-01182-7","DOIUrl":"10.1186/s13007-024-01182-7","url":null,"abstract":"<p><p>PIN proteins establish the auxin concentration gradient, which coordinates plant growth. PIN1-4 and 7 localized at the plasma membrane (PM) and facilitate polar auxin transport while the endoplasmic reticulum (ER) localized PIN5 and PIN8 maintain the intracellular auxin homeostasis. Although an antagonistic activity of PIN5 and PIN8 proteins in regulating the intracellular auxin homeostasis and other developmental events have been reported, the membrane topology of these proteins, which might be a basis for their antagonistic function, is poorly understood. In this study we optimized digitonin based PM-permeabilizing protocols coupled with immunocytochemistry labeling to map the membrane topology of PIN5 and PIN8 in Arabidopsis thaliana root cells. Our results indicate that, except for the similarities in the orientation of the N-terminus, PIN5 and PIN8 have an opposite orientation of the central hydrophilic loop and the C-terminus, as well as an unequal number of transmembrane domains (TMDs). PIN8 has ten TMDs with groups of five alpha-helices separated by the central hydrophilic loop (HL) residing in the ER lumen, and its N- and C-terminals are positioned in the cytoplasm. However, the topology of PIN5 comprises nine TMDs. Its N-terminal end and the central HL face the cytoplasm while its C-terminus resides in the ER lumen. Overall, this study shows that PIN5 and PIN8 proteins have a divergent membrane topology while introducing a toolkit of methods for studying membrane topology of integral proteins including those localized at the ER membrane.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"84"},"PeriodicalIF":5.1,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11145782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199688","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":"Non-wounding contact-based Inoculation of fruits with fungal pathogens in postharvest.","authors":"Adrian O Sbodio, Saskia D Mesquida-Pesci, Nancy Yip, Isabela Alvarez-Rojo, Elia Gutierrez-Baeza, Samantha Tay, Pedro Bello, Luxin Wang, Barbara Blanco-Ulate","doi":"10.1186/s13007-024-01214-2","DOIUrl":"10.1186/s13007-024-01214-2","url":null,"abstract":"<p><strong>Background: </strong>Fungal pathogens significantly impact the quality of fruits and vegetables at different stages of the supply chain, leading to substantial food losses. Understanding how these persistent fungal infections occur and progress in postharvest conditions is essential to developing effective control strategies.</p><p><strong>Results: </strong>In this study, we developed a reliable and consistent inoculation protocol to simulate disease spread from infected fruits to adjacent healthy fruits during postharvest storage. We tested different combinations of relevant fruit commodities, including oranges, tomatoes, and apples, against impactful postharvest pathogens such as Penicillium digitatum, Penicillium italicum, Botrytis cinerea, and Penicillium expansum. We assessed the efficacy of this protocol using fruits treated with various postharvest methods and multiple isolates for each pathogen. We optimized the source of infected tissue and incubation conditions for each fruit-pathogen combination. Disease incidence and severity were quantitatively evaluated to study infection success and progression. At the final evaluation point, 80% or higher disease incidence rates were observed in all trials except for the fungicide-treated oranges inoculated with fungicide-susceptible Penicillium spp. isolates. Although disease incidence was lower in that particular scenario, it is noteworthy that the pathogen was still able to establish itself under unfavorable conditions, indicating the robustness of our methodology. Finally, we used multispectral imaging to detect early P. digitatum infections in oranges before the disease became visible to the naked eye but after the pathogen was established.</p><p><strong>Conclusions: </strong>We developed a non-invasive inoculation strategy that can be used to recreate infections caused by contact or nesting in postharvest. The observed high disease incidence and severity values across fruit commodities and fungal pathogens demonstrate the robustness, efficacy, and reproducibility of the developed methodology. The protocol has the potential to be tailored for other pathosystems. Additionally, this approach can facilitate the study of fruit-pathogen interactions and the assessment of innovative control strategies.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"83"},"PeriodicalIF":5.1,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11145807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199689","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":"Optimizing PGRs for in vitro shoot proliferation of pomegranate with bayesian-tuned ensemble stacking regression and NSGA-II: a comparative evaluation of machine learning models.","authors":"Saeedeh Zarbakhsh, Ali Reza Shahsavar, Mohammad Soltani","doi":"10.1186/s13007-024-01211-5","DOIUrl":"10.1186/s13007-024-01211-5","url":null,"abstract":"<p><strong>Background: </strong>The process of optimizing in vitro shoot proliferation is a complicated task, as it is influenced by interactions of many factors as well as genotype. This study investigated the role of various concentrations of plant growth regulators (zeatin and gibberellic acid) in the successful in vitro shoot proliferation of three Punica granatum cultivars ('Faroogh', 'Atabaki' and 'Shirineshahvar'). Also, the utility of five Machine Learning (ML) algorithms-Support Vector Regression (SVR), Random Forest (RF), Extreme Gradient Boosting (XGB), Ensemble Stacking Regression (ESR) and Elastic Net Multivariate Linear Regression (ENMLR)-as modeling tools were evaluated on in vitro multiplication of pomegranate. A new automatic hyperparameter optimization method named Adaptive Tree Pazen Estimator (ATPE) was developed to tune the hyperparameters. The performance of the models was evaluated and compared using statistical indicators (MAE, RMSE, RRMSE, MAPE, R and R²), while a specific Global Performance Indicator (GPI) was introduced to rank the models based on a single parameter. Moreover, Non‑dominated Sorting Genetic Algorithm‑II (NSGA‑II) was employed to optimize the selected prediction model.</p><p><strong>Results: </strong>The results demonstrated that the ESR algorithm exhibited higher predictive accuracy in comparison to other ML algorithms. The ESR model was subsequently introduced for optimization by NSGA‑II. ESR-NSGA‑II revealed that the highest proliferation rate (3.47, 3.84, and 3.22), shoot length (2.74, 3.32, and 1.86 cm), leave number (18.18, 19.76, and 18.77), and explant survival (84.21%, 85.49%, and 56.39%) could be achieved with a medium containing 0.750, 0.654, and 0.705 mg/L zeatin, and 0.50, 0.329, and 0.347 mg/L gibberellic acid in the 'Atabaki', 'Faroogh', and 'Shirineshahvar' cultivars, respectively.</p><p><strong>Conclusions: </strong>This study demonstrates that the 'Shirineshahvar' cultivar exhibited lower shoot proliferation success compared to the other cultivars. The results indicated the good performance of ESR-NSGA-II in modeling and optimizing in vitro propagation. ESR-NSGA-II can be applied as an up-to-date and reliable computational tool for future studies in plant in vitro culture.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"82"},"PeriodicalIF":5.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11143642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186466","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":"ScAnalyzer: an image processing tool to monitor plant disease symptoms and pathogen spread in Arabidopsis thaliana leaves.","authors":"Misha Paauw, Gerrit Hardeman, Nanne W Taks, Lennart Lambalk, Jeroen A Berg, Sebastian Pfeilmeier, Harrold A van den Burg","doi":"10.1186/s13007-024-01213-3","DOIUrl":"10.1186/s13007-024-01213-3","url":null,"abstract":"<p><strong>Background: </strong>Plants are known to be infected by a wide range of pathogenic microbes. To study plant diseases caused by microbes, it is imperative to be able to monitor disease symptoms and microbial colonization in a quantitative and objective manner. In contrast to more traditional measures that use manual assignments of disease categories, image processing provides a more accurate and objective quantification of plant disease symptoms. Besides monitoring disease symptoms, computational image processing provides additional information on the spatial localization of pathogenic microbes in different plant tissues.</p><p><strong>Results: </strong>Here we report on an image analysis tool called ScAnalyzer to monitor disease symptoms and bacterial spread in Arabidopsis thaliana leaves. Thereto, detached leaves are assembled in a grid and scanned, which enables automated separation of individual samples. A pixel color threshold is used to segment healthy (green) from chlorotic (yellow) leaf areas. The spread of luminescence-tagged bacteria is monitored via light-sensitive films, which are processed in a similar manner as the leaf scans. We show that this tool is able to capture previously identified differences in susceptibility of the model plant A. thaliana to the bacterial pathogen Xanthomonas campestris pv. campestris. Moreover, we show that the ScAnalyzer pipeline provides a more detailed assessment of bacterial spread within plant leaves than previously used methods. Finally, by combining the disease symptom values with bacterial spread values from the same leaves, we show that bacterial spread precedes visual disease symptoms.</p><p><strong>Conclusion: </strong>Taken together, we present an automated script to monitor plant disease symptoms and microbial spread in A. thaliana leaves. The freely available software ( https://github.com/MolPlantPathology/ScAnalyzer ) has the potential to standardize the analysis of disease assays between different groups.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"80"},"PeriodicalIF":5.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11141064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141184462","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 comprehensive review of in planta stable transformation strategies.","authors":"Jérôme Gélinas Bélanger, Tanya Rose Copley, Valerio Hoyos-Villegas, Jean-Benoit Charron, Louise O'Donoughue","doi":"10.1186/s13007-024-01200-8","DOIUrl":"10.1186/s13007-024-01200-8","url":null,"abstract":"<p><p>Plant transformation remains a major bottleneck to the improvement of plant science, both on fundamental and practical levels. The recalcitrant nature of most commercial and minor crops to genetic transformation slows scientific progress for a large range of crops that are essential for food security on a global scale. Over the years, novel stable transformation strategies loosely grouped under the term \"in planta\" have been proposed and validated in a large number of model (e.g. Arabidopsis and rice), major (e.g. wheat and soybean) and minor (e.g. chickpea and lablab bean) species. The in planta approach is revolutionary as it is considered genotype-independent, technically simple (i.e. devoid of or with minimal tissue culture steps), affordable, and easy to implement in a broad range of experimental settings. In this article, we reviewed and categorized over 300 research articles, patents, theses, and videos demonstrating the applicability of different in planta transformation strategies in 105 different genera across 139 plant species. To support this review process, we propose a classification system for the in planta techniques based on five categories and a new nomenclature for more than 30 different in planta techniques. In complement to this, we clarified some grey areas regarding the in planta conceptual framework and provided insights regarding the past, current, and future scientific impacts of these techniques. To support the diffusion of this concept across the community, this review article will serve as an introductory point for an online compendium about in planta transformation strategies that will be available to all scientists. By expanding our knowledge about in planta transformation, we can find innovative approaches to unlock the full potential of plants, support the growth of scientific knowledge, and stimulate an equitable development of plant research in all countries and institutions.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"79"},"PeriodicalIF":4.7,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11140912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186453","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":"Rapid identification of medicinal plants via visual feature-based deep learning.","authors":"Chaoqun Tan, Long Tian, Chunjie Wu, Ke Li","doi":"10.1186/s13007-024-01202-6","DOIUrl":"10.1186/s13007-024-01202-6","url":null,"abstract":"<p><strong>Background: </strong>Traditional Chinese Medicinal Plants (CMPs) hold a significant and core status for the healthcare system and cultural heritage in China. It has been practiced and refined with a history of exceeding thousands of years for health-protective affection and clinical treatment in China. It plays an indispensable role in the traditional health landscape and modern medical care. It is important to accurately identify CMPs for avoiding the affected clinical safety and medication efficacy by the different processed conditions and cultivation environment confusion.</p><p><strong>Results: </strong>In this study, we utilize a self-developed device to obtain high-resolution data. Furthermore, we constructed a visual multi-varieties CMPs image dataset. Firstly, a random local data enhancement preprocessing method is proposed to enrich the feature representation for imbalanced data by random cropping and random shadowing. Then, a novel hybrid supervised pre-training network is proposed to expand the integration of global features within Masked Autoencoders (MAE) by incorporating a parallel classification branch. It can effectively enhance the feature capture capabilities by integrating global features and local details. Besides, the newly designed losses are proposed to strengthen the training efficiency and improve the learning capacity, based on reconstruction loss and classification loss.</p><p><strong>Conclusions: </strong>Extensive experiments are performed on our dataset as well as the public dataset. Experimental results demonstrate that our method achieves the best performance among the state-of-the-art methods, highlighting the advantages of efficient implementation of plant technology and having good prospects for real-world applications.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"81"},"PeriodicalIF":5.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11140858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186469","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":"High-throughput color determination of red raspberry puree and correlation of color parameters with total anthocyanins.","authors":"Claudia Baldassi, Clover Lee, Michael Dossett, Simone D Castellarin","doi":"10.1186/s13007-024-01197-0","DOIUrl":"10.1186/s13007-024-01197-0","url":null,"abstract":"<p><strong>Background: </strong>Red raspberry fruit color is a key driver of consumer preference and a major target of breeding programs worldwide. Screening for fruit color typically involves the determination of anthocyanin content and/or the assessment of color through a colorimeter. However, both procedures are time-consuming when the analyses involve hundreds or thousands of samples. The objectives of this study were to develop a high-throughput method for red raspberry puree color measurement and to test the correlations between color parameters and total anthocyanin content. Color coordinates were collected with a colorimeter on 126 puree samples contained in Petri dishes and with the Tomato Analyzer Color Test (TACT) module to assess the same samples prepared in Petri dishes and in 96-well plates. An additional 425 samples were analyzed using only 96-well plates. Total anthocyanins were extracted from all 551 samples.</p><p><strong>Results: </strong>Regression models for L*, a*, b* measured with the colorimeter and TACT using Petri dishes were all significant (p < 0.001), but very consistent only for L* (R² = 0.94). Significant (p < 0.001) and very consistent regressions (R² = 0.94 for L* and b*, R² = 0.93 for a*) were obtained for color parameters measured with TACT using Petri dishes and TACT using plates. Of the color parameters measured with the colorimeter, only L*, a*/b*, and hue significantly correlated with total anthocyanins (p < 0.05), but, except for L* (R = - 0.79), the correlations were weak (R = - 0.23 for a*/b* and R = 0.22 for hue). Conversely, all correlations with total anthocyanins and color parameters measured with TACT were significant (p < 0.001) and moderately strong (e.g., R = - 0.69 for L* and R = 0.55 for a*/b*). These values were indicative of darker colors as total anthocyanin content increased.</p><p><strong>Conclusions: </strong>While the colorimeter and TACT-based methods were not fully interchangeable, TACT better captured color differences among raspberry genotypes than the colorimeter. The correlations between color parameters measured with TACT and total anthocyanins were not strong enough to develop prediction models, yet the use of TACT with 96-well plates instead of Petri dishes would enable the high-throughput measurement of red raspberry puree color.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"78"},"PeriodicalIF":5.1,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11137939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141175737","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 prediction model of rubber content in the dried root of Taraxacum kok-saghyz Rodin based on near-infrared spectroscopy","authors":"Runfeng Chen, Qingqing Yan, Tuhanguli Tuoheti, Lin Xu, Qiang Gao, Yan Zhang, Hailong Ren, Lipeng Zheng, Feng Wang, Ya Liu","doi":"10.1186/s13007-024-01183-6","DOIUrl":"https://doi.org/10.1186/s13007-024-01183-6","url":null,"abstract":"Taraxacum kok-saghyz Rodin (TKS) is a highly potential source of natural rubber (NR) due to its wide range of suitable planting areas, strong adaptability, and suitability for mechanized planting and harvesting. However, current methods for detecting NR content are relatively cumbersome, necessitating the development of a rapid detection model. This study used near-infrared spectroscopy technology to establish a rapid detection model for NR content in TKS root segments and powder samples. The K445 strain at different growth stages within a year and 129 TKS samples hybridized with dandelion were used to obtain their near-infrared spectral data. The rubber content in the root of the samples was detected using the alkaline boiling method. The Monte Carlo sampling method (MCS) was used to filter abnormal data from the root segments of TKS and powder samples, respectively. The SPXY algorithm was used to divide the training set and validation set in a 3:1 ratio. The original spectrum was preprocessed using moving window smoothing (MWS), standard normalized variate (SNV), multiplicative scatter correction (MSC), and first derivative (FD) algorithms. The competitive adaptive reweighted sampling (CARS) algorithm and the corresponding chemical characteristic bands of NR were used to screen the bands. Partial least squares (PLS), random forest (RF), Lightweight gradient augmentation machine (LightGBM), and convolutional neural network (CNN) algorithms were employed to establish a model using the optimal spectral processing method for three different bands: full band, CARS algorithm, and chemical characteristic bands corresponding to NR. The model with the best predictive performance for high rubber content intervals (rubber content > 15%) was identified. The results indicated that the optimal rubber content prediction models for TKS root segments and powder samples were MWS–FD CASR–RF and MWS–FD chemical characteristic band RF, respectively. Their respective $${text{R}}_{{text{P}}}^{2}$$ , RMSEP, and RPDP values were 0.951, 0.979, 1.814, 1.133, 4.498, and 6.845. In the high rubber content range, the model based on the LightGBM algorithm had the best prediction performance, with the RMSEP of the root segments and powder samples being 0.752 and 0.918, respectively. This research indicates that dried TKS root powder samples are more appropriate for constructing a rubber content prediction model than segmented samples, and the predictive capability of root powder samples is superior to that of root segmented samples. Especially in the elevated rubber content range, the model formulated using the LightGBM algorithm has superior predictive performance, which could offer a theoretical basis for the rapid detection technology of TKS content in the future.","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"42 1","pages":""},"PeriodicalIF":5.1,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141153463","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":"Efficient isolated microspore culture protocol for callus induction and plantlet regeneration in japonica rice (Oryza sativa L.).","authors":"Runhong Gao, Yingjie Zong, Shuwei Zhang, Guimei Guo, Wenqi Zhang, Zhiwei Chen, Ruiju Lu, Chenghong Liu, Yifei Wang, Yingbo Li","doi":"10.1186/s13007-024-01189-0","DOIUrl":"10.1186/s13007-024-01189-0","url":null,"abstract":"<p><strong>Background: </strong>Isolated microspore culture is a useful biotechnological technique applied in modern plant breeding programs as it can produce doubled haploid (DH) plants and accelerate the development of new varieties. Furthermore, as a single-cell culture technique, the isolated microspore culture provides an excellent platform for studying microspore embryogenesis. However, the reports on isolated microspore culture are rather limited in rice due to the low callus induction rate, poor regeneration capability, and high genotypic dependency. The present study developed an effective isolated microspore culture protocol for high-frequency androgenesis in four japonica rice genotypes. Several factors affecting the isolated microspore culture were studied to evaluate their effects on callus induction and plantlet regeneration.</p><p><strong>Results: </strong>Low-temperature pre-treatment at 4 ℃ for 10-15 days could effectively promote microspore embryogenesis in japonica rice. A simple and efficient method was proposed for identifying the microspore developmental stage. The anthers in yellow-green florets located on the second type of primary branch on the rice panicle were found to be the optimal stage for isolated microspore culture. The most effective induction media for callus induction were IM2 and IM3, depending on the genotype. The optimal concentration of 2, 4-D in the medium for callus induction was 1 mg/L. Callus induction was negatively affected by a high concentration of KT over 1.5 mg/L. The differentiation medium suitable for japonica rice microspore callus comprised 1/2 MS, 2 mg/L 6-BA, 0.5 mg/L NAA, 30 g/L sucrose, and 6 g/L agar. The regeneration frequency of the four genotypes ranged from 61-211 green plantlets per 100 mg calli, with Chongxiangjing showing the highest regeneration frequency.</p><p><strong>Conclusions: </strong>This study presented an efficient protocol for improved callus induction and green plantlet regeneration in japonica rice via isolated microspore culture, which could provide valuable support for rice breeding and genetic research.</p>","PeriodicalId":20100,"journal":{"name":"Plant Methods","volume":"20 1","pages":"76"},"PeriodicalIF":5.1,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11127448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141093822","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}