Applications in Plant Sciences最新文献

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Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems Compositae-ParaLoss-1272:向日葵特异性互补探针集可在复杂系统的系统发生组分析中减少旁系亲属的数量
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2024-01-27 DOI: 10.1002/aps3.11568
Erika R. Moore-Pollard, Daniel S. Jones, Jennifer R. Mandel
{"title":"Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems","authors":"Erika R. Moore-Pollard,&nbsp;Daniel S. Jones,&nbsp;Jennifer R. Mandel","doi":"10.1002/aps3.11568","DOIUrl":"10.1002/aps3.11568","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus <i>Packera</i>. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 <i>Packera</i> taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11568","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139587590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An updated and extended version of the Melastomataceae probe set for target capture 用于目标捕获的最新扩展版 Melastomataceae 探针集
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2024-01-18 DOI: 10.1002/aps3.11564
Léo-Paul M. J. Dagallier, Fabián A. Michelangeli
{"title":"An updated and extended version of the Melastomataceae probe set for target capture","authors":"Léo-Paul M. J. Dagallier,&nbsp;Fabián A. Michelangeli","doi":"10.1002/aps3.11564","DOIUrl":"10.1002/aps3.11564","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant-targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11564","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139495487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
FloraTraiter: Automated parsing of traits from descriptive biodiversity literature FloraTraiter:从描述性生物多样性文献中自动解析特征
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2024-01-18 DOI: 10.1002/aps3.11563
Ryan A. Folk, Robert P. Guralnick, Raphael T. LaFrance
{"title":"FloraTraiter: Automated parsing of traits from descriptive biodiversity literature","authors":"Ryan A. Folk,&nbsp;Robert P. Guralnick,&nbsp;Raphael T. LaFrance","doi":"10.1002/aps3.11563","DOIUrl":"10.1002/aps3.11563","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule-based natural language processing (NLP) to parse computable trait data from biodiversity literature.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>FloraTraiter was implemented through collaborative work between programmers and botanical experts and customized for both online floras and scanned literature. We report a strategy spanning optical character recognition, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Over 95% of treatment content was successfully parsed for traits with &lt;1% error. Data for more than 700 taxa are reported, including a demonstration of common downstream uses.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait data sets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139495519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Toward an open-source 3D-printable laboratory 打造开源可三维打印实验室
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2024-01-18 DOI: 10.1002/aps3.11562
Mason C. McNair, Sebastian C. Cocioba, Peter Pietrzyk, Trevor W. Rife
{"title":"Toward an open-source 3D-printable laboratory","authors":"Mason C. McNair,&nbsp;Sebastian C. Cocioba,&nbsp;Peter Pietrzyk,&nbsp;Trevor W. Rife","doi":"10.1002/aps3.11562","DOIUrl":"10.1002/aps3.11562","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Low-cost, repairable lab equipment is rare within the biological sciences. By lowering the costs of entry using 3D printing and open-source hardware, our goal is to empower both amateur and professional scientists to conduct research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a modular system of 3D-printable designs called COBLE (Collection of Bespoke Laboratory Equipment), including novel and remixed 3D-printable lab equipment that can be inexpensively printed, assembled, and repaired for a fraction of the cost of retail equivalents.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Here we present novel tools that utilize 3D printing to enable a wide range of scientific experiments. We include additional resources for scientists and labs that are interested in utilizing 3D printing for their research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>By describing the broad potential that 3D-printed designs can have in the biological sciences, we hope to inspire others to implement and improve upon these designs, improving accessibility and enabling science for all.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11562","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139515161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks 人类在循环中:社区科学与机器学习协同克服标本馆数字化瓶颈
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2024-01-03 DOI: 10.1002/aps3.11560
Robert Guralnick, Raphael LaFrance, Michael Denslow, Samantha Blickhan, Mark Bouslog, Sean Miller, Jenn Yost, Jason Best, Deborah L. Paul, Elizabeth Ellwood, Edward Gilbert, Julie Allen
{"title":"Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks","authors":"Robert Guralnick,&nbsp;Raphael LaFrance,&nbsp;Michael Denslow,&nbsp;Samantha Blickhan,&nbsp;Mark Bouslog,&nbsp;Sean Miller,&nbsp;Jenn Yost,&nbsp;Jason Best,&nbsp;Deborah L. Paul,&nbsp;Elizabeth Ellwood,&nbsp;Edward Gilbert,&nbsp;Julie Allen","doi":"10.1002/aps3.11560","DOIUrl":"10.1002/aps3.11560","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Among the slowest steps in the digitization of natural history collections is converting imaged labels into digital text. We present here a working solution to overcome this long-recognized efficiency bottleneck that leverages synergies between community science efforts and machine learning approaches.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We present two new semi-automated services. The first detects and classifies typewritten, handwritten, or mixed labels from herbarium sheets. The second uses a workflow tuned for specimen labels to label text using optical character recognition (OCR). The label finder and classifier was built via humans-in-the-loop processes that utilize the community science Notes from Nature platform to develop training and validation data sets to feed into a machine learning pipeline.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our results showcase a &gt;93% success rate for finding and classifying main labels. The OCR pipeline optimizes pre-processing, multiple OCR engines, and post-processing steps, including an alignment approach borrowed from molecular systematics. This pipeline yields &gt;4-fold reductions in errors compared to off-the-shelf open-source solutions. The OCR workflow also allows human validation using a custom Notes from Nature tool.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our work showcases a usable set of tools for herbarium digitization including a custom-built web application that is freely accessible. Further work to better integrate these services into existing toolkits can support broad community use.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11560","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139372778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computer vision for plant pathology: A review with examples from cocoa agriculture 植物病理学计算机视觉:以可可农业为例进行综述
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-12-19 DOI: 10.1002/aps3.11559
Jamie R. Sykes, Katherine J. Denby, Daniel W. Franks
{"title":"Computer vision for plant pathology: A review with examples from cocoa agriculture","authors":"Jamie R. Sykes,&nbsp;Katherine J. Denby,&nbsp;Daniel W. Franks","doi":"10.1002/aps3.11559","DOIUrl":"10.1002/aps3.11559","url":null,"abstract":"<p>Plant pathogens can decimate crops and render the local cultivation of a species unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital in treating crop diseases, and the use of computer vision for precise disease detection and timing of pesticide application is gaining popularity. Computer vision can reduce labour costs, prevent misdiagnosis of disease, and prevent misapplication of pesticides. Pesticide misapplication is both financially costly and can exacerbate pesticide resistance and pollution. Here, we review the application and development of computer vision and machine learning methods for the detection of plant disease. This review goes beyond the scope of previous works to discuss important technical concepts and considerations when applying computer vision to plant pathology. We present new case studies on adapting standard computer vision methods and review techniques for acquiring training data, the use of diagnostic tools from biology, and the inspection of informative features. In addition to an in-depth discussion of convolutional neural networks (CNNs) and transformers, we also highlight the strengths of methods such as support vector machines and evolved neural networks. We discuss the benefits of carefully curating training data and consider situations where less computationally expensive techniques are advantageous. This includes a comparison of popular model architectures and a guide to their implementation.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11559","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction to Development and characterization of microsatellite primers in the federally endangered Astragalus bibullatus (Fabaceae) 联邦濒危植物黄芪(豆科)微卫星引物的发育与鉴定的修正
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-12-05 DOI: 10.1002/aps3.11555
{"title":"Correction to Development and characterization of microsatellite primers in the federally endangered Astragalus bibullatus (Fabaceae)","authors":"","doi":"10.1002/aps3.11555","DOIUrl":"10.1002/aps3.11555","url":null,"abstract":"<p>Morris, A. B., C. Scalf, A. Burleyson, L. T. Johnson, and K. Trostel. 2016. Development and characterization of microsatellite primers in the federally endangered <i>Astragalus bibullatus</i> (Fabaceae). <i>Applications in Plant Sciences</i> 4(4): e1500126.</p><p>In Table 1, the reverse primer sequences for loci Abib051, Abib156, and Abib170 were incorrect. Table 1 is provided here with the corrected sequences shown in boldface.</p><p>We apologize for this error.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11555","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138526675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Calceolariaceae809: A bait set for targeted sequencing of nuclear loci calceolariace809:一种用于核位点靶向测序的诱饵
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-12-02 DOI: 10.1002/aps3.11557
Nicolas Medina, David C. Tank, Anahí Espíndola
{"title":"Calceolariaceae809: A bait set for targeted sequencing of nuclear loci","authors":"Nicolas Medina,&nbsp;David C. Tank,&nbsp;Anahí Espíndola","doi":"10.1002/aps3.11557","DOIUrl":"10.1002/aps3.11557","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The genus <i>Calceolaria</i> (Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless and many offer floral oils as a pollination reward collected by specialist bees. Despite their evolutionary and ecological significance, obtaining a resolved phylogeny for the group has proved difficult. To address this challenge, we present a new bait set for targeted sequencing of nuclear loci in Calceolariaceae and close relatives.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a bioinformatic workflow to use incomplete, low-coverage genomes of 10 <i>Calceolaria</i> species to identify single-copy loci suitable for phylogenetic studies and design baits for targeted sequencing.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our approach resulted in the identification of 809 single-copy loci (733 noncoding and 76 coding regions) and the development of 39,937 baits, which we validated in silico (10 specimens) and in vitro (29 Calceolariaceae and six outgroups). In both cases, the data allowed us to recover robust phylogenetic estimates.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our results demonstrate the appropriateness of the bait set for sequencing recent and historic specimens of Calceolariaceae and close relatives, and open new doors for further investigation of the evolutionary history of this hyperdiverse genus.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11557","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138526691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Candidate pathway association and genome-wide association approaches reveal alternative genetic architectures of carotenoid content in cultivated sunflower (Helianthus annuus) 候选途径关联和全基因组关联方法揭示了栽培向日葵类胡萝卜素含量的不同遗传结构
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-12-02 DOI: 10.1002/aps3.11558
Jordan A. Dowell, Chase Mason
{"title":"Candidate pathway association and genome-wide association approaches reveal alternative genetic architectures of carotenoid content in cultivated sunflower (Helianthus annuus)","authors":"Jordan A. Dowell,&nbsp;Chase Mason","doi":"10.1002/aps3.11558","DOIUrl":"10.1002/aps3.11558","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The explosion of available genomic data poses significant opportunities and challenges for genome-wide association studies. Current approaches via linear mixed models (LMM) are straightforward but prevent flexible assumptions of an a priori genomic architecture, while Bayesian sparse LMMs (BSLMMs) allow this flexibility. Complex traits, such as specialized metabolites, are subject to various hierarchical effects, including gene regulation, enzyme efficiency, and the availability of reactants.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>To identify alternative genetic architectures, we examined the genetic architecture underlying the carotenoid content of an association mapping panel of <i>Helianthus annuus</i> individuals using multiple BSLMM and LMM frameworks.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The LMMs of genome-wide single-nucleotide polymorphisms (SNPs) identified a single transcription factor responsible for the observed variations in the carotenoid content; however, a BSLMM of the SNPs with the bottom 1% of effect sizes from the results of the LMM identified multiple biologically relevant quantitative trait loci (QTLs) for carotenoid content external to the known (annotated) carotenoid pathway. A candidate pathway analysis (CPA) suggested a β-carotene isomerase to be the enzyme with the highest impact on the observed carotenoid content within the carotenoid pathway.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>While traditional LMM approaches suggested a single unknown transcription factor associated with carotenoid content variation in sunflower petals, BSLMM proposed several QTLs with interpretable biological relevance to this trait. In addition, the CPA allowed for the dissection of the regulatory vs. biosynthetic genetic architectures underlying this metabolic trait.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11558","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138526693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Review of the cellulose acetate peel method and the physical and digital curation of coal balls 醋酸纤维素剥离法及煤球的物理和数字管理综述
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-11-29 DOI: 10.1002/aps3.11556
Scott R. Lakeram, Scott Elrick, Surangi W. Punyasena
{"title":"Review of the cellulose acetate peel method and the physical and digital curation of coal balls","authors":"Scott R. Lakeram,&nbsp;Scott Elrick,&nbsp;Surangi W. Punyasena","doi":"10.1002/aps3.11556","DOIUrl":"10.1002/aps3.11556","url":null,"abstract":"<p>Coal balls, in which fossil plants are preserved in permineralized peat deposits, have widely been described from coal deposits representing the tropical forest of the Carboniferous. Coal ball preparation techniques have evolved over the past century, with the cellulose acetate peel method becoming the standard in the 1950s. While coal ball research is not as active as it has been in the past, large collections of coal balls and their respective peels still form a large part of many museum and university collections. This contribution aims to review coal ball preparation methods, curation, and the digital archiving of peels to create a cohesive guide for researchers working with coal balls and other petrified plant material. The physical and digital curation of cellulose acetate peels and other types of coal ball specimens is critical for long-term preservation and accessibility. Physical curation involves embedding coal balls in media to slow pyrite deterioration. Digital curation creates high-resolution scans of peels, which can be shared and accessed online. Cellulose acetate peels and their digital curation are a valuable and accessible technique for the analysis of coal balls, and physical and digital curation ensures long-term preservation.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11556","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138526695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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