Applications in Plant Sciences最新文献

{"title":"Embryo excision in Compositae, with implications for combating biodiversity loss","authors":"Bruce G. Baldwin,&nbsp;Susan Fawcett,&nbsp;Dustin Wolkis","doi":"10.1002/aps3.11608","DOIUrl":"10.1002/aps3.11608","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Embryo excision is an effective, under-described means of promoting germination in the sunflower family and may help to ensure the survival of endangered taxa or lineages with limited seed availability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We describe and illustrate a detailed method of embryo excision used successfully to stimulate germination in a diversity of composites and that requires minimal materials and expense, using <i>Layia platyglossa</i> as an example. We show how this procedure greatly increases germination compared to control treatments in <i>Madia elegans</i>, a close relative of Hawaiian silverswords that exhibits physiological dormancy.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This technique can be learned quickly and is highly effective. Embryo excision can aid conservation efforts dependent on minimal seed resources by enhancing germination and allowing evaluation of seed quality before or after storage, as well as synchronizing seedling development, thereby allowing for refinement of ex situ seed bank conditions and efficient use of horticultural resources.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11608","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142199633","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}

{"title":"Data-driven guidelines for phylogenomic analyses using SNP data","authors":"Jacob S. Suissa,&nbsp;Gisel Y. De La Cerda,&nbsp;Leland C. Graber,&nbsp;Chloe Jelley,&nbsp;David Wickell,&nbsp;Heather R. Phillips,&nbsp;Ayress D. Grinage,&nbsp;Corrie S. Moreau,&nbsp;Chelsea D. Specht,&nbsp;Jeff J. Doyle,&nbsp;Jacob B. Landis","doi":"10.1002/aps3.11611","DOIUrl":"10.1002/aps3.11611","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full “locus”) in phylogenomic analyses and subsequent comparative methods.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using genotyping-by-sequencing data from 22 <i>Glycine</i> species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90–100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11611","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921682","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}

{"title":"The impact of extraction method and pollen concentration on community composition for pollen metabarcoding","authors":"Arne Devriese,&nbsp;Gerrit Peeters,&nbsp;Rein Brys,&nbsp;Hans Jacquemyn","doi":"10.1002/aps3.11601","DOIUrl":"10.1002/aps3.11601","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plants and pollinators closely interact with each other to form complex networks of species interactions. Metabarcoding of pollen collections has recently been proposed as an advantageous method for the construction of such networks, but the extent to which diversity and community analyses depend on the extraction method and pollen concentration used remains unclear.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In this study, we used a dilution series of two pollen mixtures (a mock community and pooled natural pollen loads from bumblebees) to assess the effect of mechanical homogenization and two DNA extraction kits (spin column DNA extraction kit and magnetic bead DNA extraction kit) on the detected pollen richness and community composition.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>All species were successfully detected using the three methods, even in the most dilute samples. However, the extraction method had a significant effect on the detected pollen richness and community composition, with simple mechanical homogenization introducing an extraction bias.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our findings suggest that all three methods are effective for detecting plant species in the pollen loads on insects, even in cases of very low pollen loads. However, our results also indicate that extraction methods can have a profound impact on the ability to correctly assess the community composition of the pollen loads on insects. The choice of extraction methodology should therefore be carefully considered to ensure reliable and unbiased results in pollen diversity and community analyses.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11601","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141932620","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}

{"title":"Guidelines for quantifying leaf chlorophyll content via non-destructive spectrometry","authors":"Giancarlo M. Chiarenza,&nbsp;Eve Slavich,&nbsp;Angela T. Moles","doi":"10.1002/aps3.11610","DOIUrl":"10.1002/aps3.11610","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf chlorophyll is a fundamental bioindicator used in several fields; however, we lack clear guidelines for optimizing sampling efforts and producing comparable studies.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We estimated the leaf chlorophyll content of 10 plant species using nondestructive spectrometry methods. We stored half of the leaves at 4°C and half at room temperature under similar light levels to assess the role of storage in the chlorophyll degradation rate.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The chilled mature leaves maintained a chlorophyll content within 5% of the original value for ~1.5 d, while the chlorophyll content of unrefrigerated mature leaves decreased rapidly, indicating that their chlorophyll content should be measured within 4 h. When refrigerated, the chlorophyll content of the expanding leaves remained within 5% of the original level for at least 5 d, but we suggest analyzing them within 3 d. In mature leaves, 73% of the variation in chlorophyll content is at the species level, 15% is between individuals, and the variation within leaves is negligible (&lt;1%). Measuring one mature leaf from eight individuals was sufficient to provide a species chlorophyll estimate within 5% of the true value at least 80% of the time.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We advise researchers to prioritize sampling more individuals rather than repeating measures within leaves or individuals. Our findings will help researchers to optimize their time and research efforts, and to obtain more robust ecological data.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11610","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141932621","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}

{"title":"expowo: An R package for mining global plant diversity and distribution data","authors":"Débora C. Zuanny,&nbsp;Bruno Vilela,&nbsp;Peter W. Moonlight,&nbsp;Tiina E. Särkinen,&nbsp;Domingos Cardoso","doi":"10.1002/aps3.11609","DOIUrl":"10.1002/aps3.11609","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open-source package that facilitates extracting and using botanical data from POWO.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species-discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy-to-handle outputs, we also show empirical examples from a set of biodiverse countries and representative species-rich and ecologically important angiosperm families.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141870157","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}

{"title":"A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal lineages","authors":"Camilo Patarroyo,&nbsp;Stéphane Dupas,&nbsp;Silvia Restrepo","doi":"10.1002/aps3.11603","DOIUrl":"10.1002/aps3.11603","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The prompt categorization of <i>Phytophthora infestans</i> isolates into described clonal lineages is a key tool for the management of its associated disease, potato late blight. New isolates of this pathogen are currently classified by comparing their microsatellite genotypes with characterized clonal lineages, but an automated classification tool would greatly improve this process. Here, we developed a flexible machine learning–based classifier for <i>P. infestans</i> genotypes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The performance of different machine learning algorithms in classifying <i>P. infestans</i> genotypes into its clonal lineages was preliminarily evaluated with decreasing amounts of training data. The four best algorithms were then evaluated using all collected genotypes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>mlpML, cforest, nnet, and AdaBag performed best in the preliminary test, correctly classifying almost 100% of the genotypes. AdaBag performed significantly better than the others when tested using the complete data set (Tukey HSD <i>P</i> &lt; 0.001). This algorithm was then implemented in a web application for the automated classification of <i>P. infestans</i> genotypes, which is freely available at https://github.com/cpatarroyo/genotypeclas.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We developed a gradient boosting–based tool to automatically classify <i>P. infestans</i> genotypes into its clonal lineages. This could become a valuable resource for the prompt identification of clonal lineages spreading into new regions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11603","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141778214","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}

{"title":"Variant calling in polyploids for population and quantitative genetics","authors":"Alyssa R. Phillips","doi":"10.1002/aps3.11607","DOIUrl":"10.1002/aps3.11607","url":null,"abstract":"<p>Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11607","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141738604","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}

{"title":"Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology","authors":"Robert L. Baker,&nbsp;Grace L. Brock,&nbsp;Eastyn L. Newsome,&nbsp;Meixia Zhao","doi":"10.1002/aps3.11605","DOIUrl":"10.1002/aps3.11605","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Most traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We apply network modeling, a common gene co-expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus <i>Brassica</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure–function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Phenotypic network analysis may provide important insights into the effects of selection on non-target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11605","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141738603","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}

{"title":"nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity","authors":"Michelle L. Gaynor,&nbsp;Jacob B. Landis,&nbsp;Timothy K. O'Connor,&nbsp;Robert G. Laport,&nbsp;Jeff J. Doyle,&nbsp;Douglas E. Soltis,&nbsp;José Miguel Ponciano,&nbsp;Pamela S. Soltis","doi":"10.1002/aps3.11606","DOIUrl":"10.1002/aps3.11606","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11606","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141721618","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}

{"title":"Bringing genomics to the field: An integrative approach to seed sourcing for forest restoration","authors":"Anoob Prakash,&nbsp;Thibaut Capblancq,&nbsp;Kathryn Shallows,&nbsp;David Saville,&nbsp;Deborah Landau,&nbsp;Chad Landress,&nbsp;Tal Jacobs,&nbsp;Stephen Keller","doi":"10.1002/aps3.11600","DOIUrl":"https://doi.org/10.1002/aps3.11600","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Global anthropogenic change threatens the health and productivity of forest ecosystems. Assisted migration and reforestation are tools to help mitigate these impacts. However, questions remain about how to approach sourcing seeds to ensure high establishment and future adaptability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using exome-capture sequencing, we demonstrate a computational approach to finding the best <i>n</i>-sets from a candidate list of seed sources that collectively achieve high genetic diversity (GD) and minimal genetic load (GL), while also increasing evolvability in quantitative traits. The benefits of this three-part strategy (diversity-load-evolvability) are to increase near-term establishment success while also boosting evolutionary potential to respond to future stressors. Members of The Nature Conservancy and the Central Appalachian Spruce Restoration Initiative planted 58,000 seedlings across 255 acres. A subset of seedlings was monitored for establishment success and variation in growth.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The results show gains in GD relative to GL and increases in quantitative genetic variation in seedling growth for pooled vs. single-source restoration. No single “super source” was observed across planting sites; rather, monitoring results demonstrate that pooling of multiple sources helps achieve higher GD:GL and evolvability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our study shows the potential for integrating genomics into local-scale restoration and the importance of building partnerships between academic researchers and applied conservation managers.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11600","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441384","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}