Frontiers in Plant Science最新文献

{"title":"Classification of field wheat varieties based on a lightweight G-PPW-VGG11 model","authors":"Yu Pan, Xun Yu, Jihua Dong, Yonghang Zhao, Shuanming Li, Xiuliang Jin","doi":"10.3389/fpls.2024.1375245","DOIUrl":"https://doi.org/10.3389/fpls.2024.1375245","url":null,"abstract":"In agriculture, especially wheat cultivation, farmers often use multi-variety planting strategies to reduce monoculture-related harvest risks. However, the subtle morphological differences among wheat varieties make accurate discrimination technically challenging. Traditional variety classification methods, reliant on expert knowledge, are inefficient for modern intelligent agricultural management. Numerous existing classification models are computationally complex, memory-intensive, and difficult to deploy on mobile devices effectively. This study introduces G-PPW-VGG11, an innovative lightweight convolutional neural network model, to address these issues.G-PPW-VGG11 ingeniously combines partial convolution (PConv) and partially mixed depthwise separable convolution (PMConv), reducing computational complexity and feature redundancy. Simultaneously, incorporating ECANet, an efficient channel attention mechanism, enables precise leaf information capture and effective background noise suppression. Additionally, G-PPW-VGG11 replaces traditional VGG11’s fully connected layers with two pointwise convolutional layers and a global average pooling layer, significantly reducing memory footprint and enhancing nonlinear expressiveness and training efficiency.Rigorous testing showed G-PPW-VGG11's superior performance, with an impressive 93.52% classification accuracy and only 1.79MB memory usage. Compared to VGG11, G-PPW-VGG11 showed a 5.89% increase in accuracy, 35.44% faster inference, and a 99.64% reduction in memory usage. G-PPW-VGG11 also surpasses traditional lightweight networks in classification accuracy and inference speed. Notably, G-PPW-VGG11 was successfully deployed on Android and its performance evaluated in real-world settings. The results showed an 84.67% classification accuracy with an average time of 291.04ms per image.This validates the model's feasibility for practical agricultural wheat variety classification, establishing a foundation for intelligent management. For future research, the trained model and complete dataset are made publicly available.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"89 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140978468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of the mitochondrial genome of Rehmannia glutinosa: insights into repeat-mediated recombinations and RNA editing-induced stop codon acquisition","authors":"Tiexin Zeng, Y. Ni, Jingling Li, Haimei Chen, Qianqi Lu, Mei Jiang, Lijia Xu, Chang Liu, Peigen Xiao","doi":"10.3389/fpls.2024.1326387","DOIUrl":"https://doi.org/10.3389/fpls.2024.1326387","url":null,"abstract":"Rehmannia glutinosa is an economically significant medicinal plant. Yet, the structure and sequence of its mitochondrial genome has not been published, which plays a crucial role in evolutionary analysis and regulating respiratory-related macromolecule synthesis. In this study, the R. glutinosa mitogenome was sequenced employing a combination of Illumina short reads and Nanopore long reads, with subsequent assembly using a hybrid strategy. We found that the predominant configuration of the R. glutinosa mitogenome comprises two circular chromosomes. The primary structure of the mitogenome encompasses two mitochondrial chromosomes corresponding to the two major configurations, Mac1-1 and Mac1-2. The R. glutinosa mitogenome encoded an angiosperm-typical set of 24 core genes, nine variable genes, three rRNA genes, and 15 tRNA genes. A phylogenetic analysis using the 16 shared protein-coding genes (PCG) yielded a tree consistent with the phylogeny of Lamiales species and two outgroup taxa. Mapping RNA-seq data to the coding sequences (CDS) of the PCGs revealed 507 C-to-U RNA editing sites across 31 PCGs of the R. glutinosa mitogenome. Furthermore, one start codon (nad4L) and two stop codons (rpl10 and atp6) were identified as products of RNA editing events in the R. glutinosa mitogenome.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"26 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140980328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Changes induced by parental neighboring untouched in the clonal plant Glechoma longituba depend on the light environment","authors":"Linya Xing, Jiaxin Quan, Shuqi Zhang, Xiao Liu, Hua Bai, Ming Yue","doi":"10.3389/fpls.2024.1358924","DOIUrl":"https://doi.org/10.3389/fpls.2024.1358924","url":null,"abstract":"Touch by neighboring plants is a common but overlooked environmental variable for plants, especially in dense vegetation. In addition, shade is inevitable for understory plants. The growth performance of clonal plant to the interaction between thigmomorphogenesis and shade response, and their impact on light adaptability is still unknown.At the present study, parental ramets of Glechoma longituba were exposed to two conditions (neighboring touch and shade), and their offspring ramets were in ambient or shaded environment. The phenotype and growth of parental and offspring ramets were analyzed. The results showed that neighboring touch of parental ramets regulated the performance of offspring ramets, while the effect depended on the light environment. The parental neighboring touch occurring in ambient environment suppressed the expansion of leaf organ, showed as a shorter petiole and smaller leaf area. Moreover, G. longituba exhibited both shade avoidance and shade tolerance characters to shaded environment, such as increased leaf area ratio and leaf mass ratio, longer specific petiole length and specific stolon length. It was notable that these characters of shade response could be promoted by parental neighboring touch to some extent. Additionally, parental light environment plays an important role in offspring growth, parent with ambient light always had well-grown offspring whatever the light condition of offspring, but the growth of offspring whose parent in shaded environment was inhibited. Finally, for the offspring with shaded environment, the touch between parental ramets in shade environment showed a disadvantage on their growth, but the influence of the touch between parental ramets in ambient environment was slight. Overall, the interaction of parental neighboring touch and shade environment complicate the growth of understory plants, the performance of plants is the integrated effect of both. These findings are conducive to an in-depth understanding of the environmental adaptation of plants.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"41 19","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140981448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IAA-producing plant growth promoting rhizobacteria from Ceanothus velutinus enhance cutting propagation efficiency and Arabidopsis biomass","authors":"J. Ganesh, Katherine Hewitt, A. R. Devkota, Ty Wilson, A. Kaundal","doi":"10.3389/fpls.2024.1374877","DOIUrl":"https://doi.org/10.3389/fpls.2024.1374877","url":null,"abstract":"Climate-induced drought impacts plant growth and development. Recurring droughts increase the demand for water for food production and landscaping. Native plants in the Intermountain West region of the US are of keen interest in low water use landscaping as they are acclimatized to dry and cold environments. These native plants do very well at their native locations but are difficult to propagate in landscape. One of the possible reasons is the lack of associated microbiome in the landscaping. Microbiome in the soil contributes to soil health and impacts plant growth and development. Here, we used the bulk soil from the native plant Ceanothus velutinus (snowbrush ceanothus) as inoculant to enhance its propagation. Snowbrush ceanothus is an ornamental plant for low-water landscaping that is hard to propagate asexually. Using 50% native bulk soil as inoculant in the potting mix significantly improved the survival rate of the cuttings compared to no-treated cuttings. Twenty-four plant growth-promoting rhizobacteria (PGPR) producing indole acetic acid (IAA) were isolated from the rhizosphere and roots of the survived snowbrush. Seventeen isolates had more than 10µg/mL of IAA were shortlisted and tested for seven different plant growth-promoting (PGP) traits; 76% showed nitrogen-fixing ability on Norris Glucose Nitrogen free media,70% showed phosphate solubilization activity, 76% showed siderophore production, 36% showed protease activity, 94% showed ACC deaminase activity on DF-ACC media, 76% produced catalase and all of isolates produced ammonia. Eight of seventeen isolates, CK-6, CK-22, CK-41, CK-44, CK-47, CK-50, CK-53, and CK-55, showed an increase in shoot biomass in Arabidopsis thaliana. Seven out of eight isolates were identified as Pseudomonas, except CK-55, identified as Sphingobium based on 16S rRNA gene sequencing. The shortlisted isolates are being tested on different grain and vegetable crops to mitigate drought stress and promote plant growth.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"14 17","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140980721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatial and temporal variation of net primary productivity of herbaceous marshes and its climatic drivers in China","authors":"Liyuan Wu, Xiangjin Shen, Jiaqi Zhang, Yiwen Liu, Chen Ding, Rong Ma, Xianguo Lu, Ming Jiang","doi":"10.3389/fpls.2024.1380081","DOIUrl":"https://doi.org/10.3389/fpls.2024.1380081","url":null,"abstract":"Herbaceous marshes are widely distributed in China and are vital to regional ecological security and sustainable development. Vegetation net primary productivity (NPP) is a vital indicator of vegetation growth. Climatic change can significantly affect NPP, but variations in NPP of herbaceous marsh and their responses to climate change in China remain unclear. Using meteorological data and MODIS NPP data during 2000-2020, this study analyzed the spatial and temporal variations of NPP and their responses to climate change in Chinese herbaceous marshes. We found that the annual NPP of herbaceous marshes in China increased significantly at a rate of 3.34 g C/m2/a from 2000 to 2020, with an average value of 336.60 g C/m2. The increased annual total precipitation enhanced the national average NPP, whereas annual mean temperature had no significant effect on the national average NPP. Regionally, precipitation had a significant positive effect on the NPP in temperate semi-arid and arid and temperate semi-humid and humid marsh regions. For the first time, we discovered asymmetry effects of daytime and nighttime temperatures on NPP in herbaceous marshes of China. In temperate humid and semi-humid marsh regions, increased summer daytime temperature decreased the NPP while increased summer nighttime temperature increased the NPP. In the Tibetan Plateau, increased autumn daytime temperature, as well as summer daytime and nighttime temperatures could increase the NPP of herbaceous marshes. This study highlights the different influences of seasonal climate change on the NPP of herbaceous marshes in China and indicates that the differential effects of daytime and nighttime temperatures should be considering in simulating the NPP of herbaceous marshes in terrestrial ecosystem models, especially under the background of global asymmetric diurnal warming.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"32 17","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140981251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review on blueberry drought tolerance from the perspective of cultivar improvement","authors":"Sushan Ru, Alvaro Sanz-Saez, Courtney P. Leisner, Tanzeel Rehman, Savannah Busby","doi":"10.3389/fpls.2024.1352768","DOIUrl":"https://doi.org/10.3389/fpls.2024.1352768","url":null,"abstract":"Blueberry (Vaccinium spp.) is an increasingly popular fruit around the world for their attractive taste, appearance, and most importantly their many health benefits. Global blueberry production was valued at $2.31 billion with the United States alone producing $1.02 billion of cultivated blueberries in 2021. The sustainability of blueberry production is increasingly threatened by more frequent and extreme drought events caused by climate change. Blueberry is especially prone to adverse effects from drought events due to their superficial root system and lack of root hairs, which limit blueberry’s ability to intake water and nutrients from the soil especially under drought stress conditions. The goal of this paper is to review previous studies on blueberry drought tolerance focusing on physiological, biochemical, and molecular drought tolerance mechanisms, as well as genetic variability present in cultivated blueberries. We also discuss limitations of previous studies and potential directions for future efforts to develop drought-tolerant blueberry cultivars. Our review showed that the following areas are lacking in blueberry drought tolerance research: studies of root and fruit traits related to drought tolerance, large-scale cultivar screening, efforts to understand the genetic architecture of drought tolerance, tools for molecular-assisted drought tolerance improvement, and high-throughput phenotyping capability for efficient cultivar screening. Future research should be devoted to following areas: (1) drought tolerance evaluation to include a broader range of traits, such as root architecture and fruit-related performance under drought stress, to establish stronger association between physiological and molecular signals with drought tolerance mechanisms; (2) large-scale drought tolerance screening across diverse blueberry germplasm to uncover various drought tolerance mechanisms and valuable genetic resources; (3) high-throughput phenotyping tools for drought-related traits to enhance the efficiency and affordability of drought phenotyping; (4) identification of genetic architecture of drought tolerance using various mapping technologies and transcriptome analysis; (5) tools for molecular-assisted breeding for drought tolerance, such as marker-assisted selection and genomic selection, and (6) investigation of the interactions between drought and other stresses such as heat to develop stress resilient genotypes.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"72 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140978897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: The impact of abiotic stresses on agriculture: mitigation through climate smart strategies","authors":"D. Moulick, S. Choudhury, M. Brestic, Akbar Hossain","doi":"10.3389/fpls.2024.1391051","DOIUrl":"https://doi.org/10.3389/fpls.2024.1391051","url":null,"abstract":"","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"86 19","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140978241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Longitudinal genome-wide association study reveals early QTL that predict biomass accumulation under cold stress in sorghum","authors":"Erica Agnew, Greg Ziegler, Scott Lee, Cesar Lizarraga, N. Fahlgren, Ivan Baxter, Todd C. Mockler, N. Shakoor","doi":"10.3389/fpls.2024.1278802","DOIUrl":"https://doi.org/10.3389/fpls.2024.1278802","url":null,"abstract":"Sorghum bicolor is a promising cellulosic feedstock crop for bioenergy due to its high biomass yields. However, early growth phases of sorghum are sensitive to cold stress, limiting its planting in temperate environments. Cold adaptability is crucial for cultivating bioenergy and grain sorghum at higher latitudes and elevations, or for extending the growing season. Identifying genes and alleles that enhance biomass accumulation under early cold stress can lead to improved sorghum varieties through breeding or genetic engineering.We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP includes diverse accessions with dense genotyping and varied racial, geographical, and phenotypic backgrounds. Daily, non-destructive imaging allowed temporal analysis of growth-related traits and water use efficiency (WUE). A genome-wide association study (GWAS) was performed to identify genomic intervals and genes associated with cold stress response.The GWAS identified transient quantitative trait loci (QTL) strongly associated with growth-related traits, enabling an exploration of the genetic basis of cold stress response at different developmental stages. This analysis of daily growth traits, rather than endpoint traits, revealed early transient QTL predictive of final phenotypes. The study identified both known and novel candidate genes associated with growth-related traits and temporal responses to cold stress.The identified QTL and candidate genes contribute to understanding the genetic mechanisms underlying sorghum's response to cold stress. These findings can inform breeding and genetic engineering strategies to develop sorghum varieties with improved biomass yields and resilience to cold, facilitating earlier planting, extended growing seasons, and cultivation at higher latitudes and elevations.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"23 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140979795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tackling unbalanced datasets for yellow and brown rust detection in wheat","authors":"Carmen Cuenca-Romero, O. E. Apolo-Apolo, Jaime Nolasco Rodríguez Vázquez, Gregorio Egea, M. Pérez-Ruiz","doi":"10.3389/fpls.2024.1392409","DOIUrl":"https://doi.org/10.3389/fpls.2024.1392409","url":null,"abstract":"This study evaluates the efficacy of hyperspectral data for detecting yellow and brown rust in wheat, employing machine learning models and the SMOTE (Synthetic Minority Oversampling Technique) augmentation technique to tackle unbalanced datasets. Artificial Neural Network (ANN), Support Vector Machine (SVM), Random Forest (RF), and Gaussian Naïve Bayes (GNB) models were assessed. Overall, SVM and RF models showed higher accuracies, particularly when utilizing SMOTE-enhanced datasets. The RF model achieved 70% accuracy in detecting yellow rust without data alteration. Conversely, for brown rust, the SVM model outperformed others, reaching 63% accuracy with SMOTE applied to the training set. This study highlights the potential of spectral data and machine learning (ML) techniques in plant disease detection. It emphasizes the need for further research in data processing methodologies, particularly in exploring the impact of techniques like SMOTE on model performance.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"20 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140980535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deacclimation and reacclimation processes in winter wheat: novel perspectives from time-series transcriptome analysis","authors":"Gabija Vaitkevičiūtė, A. Aleliūnas, G. Brazauskas, R. Armonienė","doi":"10.3389/fpls.2024.1395830","DOIUrl":"https://doi.org/10.3389/fpls.2024.1395830","url":null,"abstract":"Winter wheat achieves freezing tolerance (FT) through cold acclimation (CA) – a process which is induced by low positive temperatures in autumn. The increasing occurrences of temperature fluctuations in winter lead to deacclimation (DEA), causing premature loss of FT, and the cultivars capable of reacclimation (REA) are more likely to survive the subsequent cold spells. The genetic mechanisms of DEA and REA remain poorly understood, necessitating further research to bolster climate resilience in winter wheat. Here, we selected two winter wheat genotypes with contrasting levels of FT and conducted a ten-week-long experiment imitating low-temperature fluctuations after CA under controlled conditions. Crown and leaf tissue samples for RNA-sequencing were collected at CA, DEA, and REA time-points. It is the first transcriptomic study covering both short- and long-term responses to DEA and REA in winter wheat. The study provides novel knowledge regarding CA, DEA, and REA and discusses the gene expression patterns conferring FT under temperature fluctuations. The freezing-tolerant genotype “Lakaja DS” showed elevated photosynthetic activity in leaf tissue and upregulated cryoprotective protein-encoding genes in crowns after CA when compared to the freezing-susceptible “KWS Ferrum”. “Lakaja DS” also expressed cold acclimation-associated transcripts at a significantly higher level after 1 week of DEA. Following REA, “Lakaja DS” continued to upregulate dehydrin-related genes in crowns and exhibited significantly higher expression of chitinase transcripts in leaves, when compared to “KWS Ferrum”. The findings of this study shed light on the genetic mechanisms governing DEA and REA in winter wheat, thus addressing the gaps in knowledge regarding FT under low-temperature fluctuations. The identified genes should be further examined as potential molecular markers for breeding strategies focused on developing freezing-tolerant winter-type crops. Publicly available datasets generated in this study are valuable resources for further research into DEA and REA, contributing towards the enhancement of winter wheat under global climate change.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"11 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140979997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}