674 results match your criteria Applications In Plant Sciences[Journal]


A basic ddRADseq two-enzyme protocol performs well with herbarium and silica-dried tissues across four genera.

Appl Plant Sci 2020 Apr 23;8(4):e11344. Epub 2020 Apr 23.

University Herbaria and Department of Integrative Biology University of California Berkeley 3040 Valley Life Sciences Building Berkeley California 94720 USA.

Premise: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site-associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue.

Methods: DNAs from , , , and were processed with a ddRADseq protocol. Read More

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http://dx.doi.org/10.1002/aps3.11344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186894PMC

Low-cost FloPump for regulated air sampling of volatile organic compounds.

Appl Plant Sci 2020 Apr 26;8(4):e11343. Epub 2020 Apr 26.

Department of Biological Sciences Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal Madhya Pradesh 462066 India.

Premise: We present a low-cost, battery-operated, portable pump, "FloPump," which allows regulated air sampling for the study of volatile organic compounds (VOCs). VOCs are routinely investigated in applications such as atmospheric chemistry, agriculture, and fragrance biology.

Methods And Results: We compared the performance of FloPump with the Supelco pump in collecting VOCs using two test samples: guava fruit () and a perfume. Read More

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http://dx.doi.org/10.1002/aps3.11343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186897PMC

Using clear plastic CD cases as low-cost mini-rhizotrons to phenotype root traits.

Appl Plant Sci 2020 Apr 19;8(4):e11340. Epub 2020 Apr 19.

Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA.

Premise: We developed a novel low-cost method to visually phenotype belowground structures in the plant rhizosphere. We devised the method introduced here to address the difficulties encountered growing plants in seed germination pouches for long-term experiments and the high cost of other mini-rhizotron alternatives.

Methods And Results: The method described here took inspiration from homemade ant farms commonly used as an educational tool in elementary schools. Read More

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http://dx.doi.org/10.1002/aps3.11340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186896PMC

Inferring the impacts of evolutionary history and ecological constraints on spore size and shape in the ferns.

Appl Plant Sci 2020 Apr 20;8(4):e11339. Epub 2020 Apr 20.

Pringle Herbarium University of Vermont 111 Jeffords Hall Burlington Vermont 05405-1737 USA.

Premise: In the ferns, cell size has been explored with spores, which are largely uniform within species, produced in abundance, and durable. However, spore size and shape have been variously defined, and the relationship of these traits to genome size has not been well established. Here, we explore the variation in fern spore size and shape by ploidy level and genome size. Read More

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http://dx.doi.org/10.1002/aps3.11339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186895PMC

Low-cost observations and experiments return a high value in plant phenology research.

Appl Plant Sci 2020 Apr 25;8(4):e11338. Epub 2020 Apr 25.

Biology Department Boston University 5 Cummington Mall Boston Massachusetts 02215 USA.

Plant ecologists in the Anthropocene are tasked with documenting, interpreting, and predicting how plants respond to environmental change. Phenology, the timing of seasonal biological events including leaf-out, flowering, fruiting, and leaf senescence, is among the most visible and oft-recorded facets of plant ecology. Climate-driven shifts in plant phenology can alter reproductive success, interspecific competition, and trophic interactions. Read More

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http://dx.doi.org/10.1002/aps3.11338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186900PMC

Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants.

Appl Plant Sci 2020 Apr 14;8(4):e11337. Epub 2020 Apr 14.

Department of Biological Sciences Texas Tech University Lubbock Texas 79409 USA.

The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects. Read More

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http://dx.doi.org/10.1002/aps3.11337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186906PMC

Using a portable hydrogen cyanide gas meter to uncover a dynamic phytochemical landscape.

Appl Plant Sci 2020 Apr 19;8(4):e11336. Epub 2020 Apr 19.

Department of Integrative Biology Graduate Program in Ecology, Evolution and Behavior The University of Texas at Austin Austin Texas USA.

Premise: Over 3000 species of plants and animals release toxic hydrogen cyanide (HCN) gas when their tissues are crushed. To investigate the role of cyanogenesis in -herbivore interactions, we developed an inexpensive, rapid, sensitive method for measuring HCN emissions from crushed tissues.

Methods: The method includes crushed tissue confinement in a closed chamber, where cyanogenesis reactions occur, followed by evacuation of gas to a portable HCN meter. Read More

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http://dx.doi.org/10.1002/aps3.11336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186902PMC

An efficient low-cost xylem sap isolation method for bacterial wilt assays in tomato.

Appl Plant Sci 2020 Apr 19;8(4):e11335. Epub 2020 Apr 19.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg New Delhi 110067 India.

Premise: A portable, simple, yet efficient method was developed for the rapid extraction of xylem sap from the stems and petioles of tomato plants for diagnostic and quantification assays of the xylem-colonizing wilt bacterium .

Methods And Results: Xylem saps were extracted from tomato stem sections using negative pressure generated from handheld needleless syringes. The samples were collected from plants grown under different soil moisture levels at four days after inoculation with the pathogen. Read More

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http://dx.doi.org/10.1002/aps3.11335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186903PMC

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi.

Appl Plant Sci 2020 Apr 15;8(4):e11334. Epub 2020 Apr 15.

Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del Valle Calle 13 #100-00, Building E20 760032 Cali, Valle del Cauca Colombia.

High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). Read More

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http://dx.doi.org/10.1002/aps3.11334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186905PMC

A simple, non-toxic method for separating seeds based on density, and its application in isolating seed oil mutants.

Appl Plant Sci 2020 Apr 20;8(4):e11332. Epub 2020 Apr 20.

Department of Botany University of British Columbia 6270 University Boulevard Vancouver V6T 1Z4 Canada.

Premise: Seed oil is an economically important trait in oilseed crops. A novel method was developed to isolate seeds with altered oil content.

Methods And Results: In , seed oil content is correlated with seed density, with high-oil seeds being less dense than wild type and tending to float in solution, and low-oil seeds being denser and tending to sink. Read More

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http://dx.doi.org/10.1002/aps3.11332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186901PMC

Extraction of high-quality, high-molecular-weight DNA depends heavily on cell homogenization methods in green microalgae.

Appl Plant Sci 2020 Mar 10;8(3):e11333. Epub 2020 Mar 10.

Ecosystems Center Marine Biological Laboratory 7 MBL Street Woods Hole Massachusetts 02543 USA.

Premise: New sequencing technologies have facilitated genomic studies in green microalgae; however, extracting high-quality DNA is often a bottleneck for long-read sequencing.

Methods And Results: Here, we present a low-cost, highly transferrable method for the extraction of high-molecular-weight (HMW), high-purity DNA from microalgae. We first determined the effect of sample preparation on DNA quality using three homogenization methods: manual grinding using a mini-pestle, automatic grinding using a vortex adapter, and grinding in liquid nitrogen. Read More

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http://dx.doi.org/10.1002/aps3.11333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073325PMC

Enabling automated herbarium sheet image post-processing using neural network models for color reference chart detection.

Appl Plant Sci 2020 Mar 2;8(3):e11331. Epub 2020 Mar 2.

Department of Computer Science and Engineering University of Tennessee at Chattanooga Chattanooga Tennessee USA.

Premise: Large-scale efforts to digitize herbaria have resulted in more than 18 million publicly available Plantae images on sites such as iDigBio. The automation of image post-processing will lead to time savings in the digitization of biological specimens, as well as improvements in data quality. Here, new and modified neural network methodologies were developed to automatically detect color reference charts (CRC), enabling the future automation of various post-processing tasks. Read More

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http://dx.doi.org/10.1002/aps3.11331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073326PMC

Combining rare alleles and grouped pollen donors to assign paternity in pollen dispersal studies.

Appl Plant Sci 2020 Mar 4;8(3):e11330. Epub 2020 Mar 4.

Louis Calder Center, Biological Field Station Fordham University 31 Whippoorwill Road Armonk New York 10504 USA.

Premise: Pollen dispersal plays a critical role in gene flow of seed plants. Most often, pollen dispersal is measured using paternity assignment. However, this approach can be time-consuming because it typically entails genotyping all pollen donors, receptors, and offspring at several molecular markers. Read More

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http://dx.doi.org/10.1002/aps3.11330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073328PMC

Development and characterization of 17 microsatellite markers for .

Appl Plant Sci 2020 Mar 24;8(3):e11329. Epub 2020 Feb 24.

Department of Biological Sciences Sungkyunkwan University 2066 Seobu-ro Suwon 16419 Republic of Korea.

Premise: The common sowthistle, (Asteraceae), is a globally invasive weedy species. In order to investigate its genetic diversity, population genetic structure, and evolutionary history, we developed and characterized nuclear simple sequence repeat markers (SSRs or microsatellites).

Methods And Results: Seventeen microsatellite primer pairs were developed based on the Illumina sequence data. Read More

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http://dx.doi.org/10.1002/aps3.11329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073324PMC

Development of 32 novel microsatellite loci in using genomic data.

Appl Plant Sci 2020 Mar 27;8(3):e11328. Epub 2020 Feb 27.

Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 Yunnan China.

Premise: A novel set of microsatellite markers was developed for (Juglandaceae), an endemic walnut species in southwestern China, to facilitate cultivar identification and future investigations into the genetic structure and domestication history of this species and its close relatives.

Methods And Results: We developed 32 microsatellite loci for using genomic data and used them to examine 60 individuals from three natural populations. A high level of polymorphism was detected by these primers, with up to eight alleles observed per locus, and an average of four alleles across populations. Read More

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http://dx.doi.org/10.1002/aps3.11328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073327PMC

Development of microsatellite markers for the perennial plant .

Appl Plant Sci 2020 Mar 13;8(3):e11327. Epub 2020 Mar 13.

Faculty of Science Department of Botany Charles University Benátská 2 Prague 12801 Czech Republic.

Premise: Polymorphic microsatellite markers were developed to study genetic diversity and genetic structure of populations of the locally endangered species (Tofieldiaceae).

Methods And Results: Nineteen polymorphic microsatellite loci were developed using DNA-enriched libraries sequenced by Ilumina technology and were then used to genotype 101 individuals from five populations from Austria, Slovakia, Poland, and the Czech Republic. Of the markers tested, 68% were polymorphic in four of the five investigated populations, with one marker polymorphic in all populations. Read More

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http://dx.doi.org/10.1002/aps3.11327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073322PMC

A fishing expedition to discover the pollinators of several subtropical Apocynaceae.

Appl Plant Sci 2020 Feb 13;8(2):e11326. Epub 2020 Feb 13.

Department of Biological Sciences and International Center for Tropical Botany Florida International University Miami Florida 33199 USA.

Premise: Flowers of the Apocynaceae (milkweed family) have complex structures and pollination mechanisms. Pollen removal and deposition in , , and are similar, with anthers releasing pollen onto the sterile style head. The mid-style head excretes a glue that coats the mouthparts of vistors to aid in the transfer of pollen. Read More

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http://dx.doi.org/10.1002/aps3.11326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035433PMC
February 2020

Inexpensive throughfall exclusion experiment for single large trees.

Appl Plant Sci 2020 Feb 14;8(2):e11325. Epub 2020 Feb 14.

School of Biological Sciences The University of Auckland Private Bag 92019 Auckland Mail Center Auckland 1142 New Zealand.

Premise: Drought-induced tree mortality is an emergent threat to forests worldwide, particularly to large trees. Drought-manipulation experiments involving throughfall exclusion (TFE) tend to focus on large plots that can be expensive to establish and maintain and may be unsuitable for large trees or indigenous forests. We set out to establish a relatively inexpensive TFE method in a natural forest with large trees. Read More

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http://dx.doi.org/10.1002/aps3.11325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035431PMC
February 2020

Microsatellite markers for : Development, characterization, and cross-species amplification.

Appl Plant Sci 2020 Feb 14;8(2):e11323. Epub 2020 Feb 14.

Faculty of Environmental Sciences Czech University of Life Sciences Prague Kamýcká 129 Praha 6-Suchdol CZ-165 00 Czech Republic.

Premise: A set of polymorphic nuclear microsatellite loci was developed and tested for use in population genetic analyses of (Agavaceae) and related species.

Methods And Results: Sequences of 110 primers were extracted in silico from Illumina MiSeq genome skimming data. The degree of polymorphism of 19 loci was tested in four . Read More

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http://dx.doi.org/10.1002/aps3.11323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035427PMC
February 2020

cRacle: R tools for estimating climate from vegetation.

Appl Plant Sci 2020 Feb 13;8(2):e11322. Epub 2020 Feb 13.

Department of Biology Stonehill College 320 Washington Street North Easton Massachusetts 02357 USA.

Premise: The Climate Reconstruction Analysis using Coexistence Likelihood Estimation (CRACLE) method utilizes a robust set of modeling tools for estimating climate and paleoclimate from vegetation using large repositories of biodiversity data and open access R software.

Methods: Here, we implement a new R package for the estimation of climate from extant and fossil vegetation. The 'cRacle' package implements functions for data access, aggregation, and modeling to estimate climate from plant community compositions. Read More

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http://dx.doi.org/10.1002/aps3.11322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035432PMC
February 2020

Development and characterization of novel SSR markers in the endangered endemic species .

Appl Plant Sci 2020 Feb 11;8(2):e11321. Epub 2020 Feb 11.

Department of Botany University of Debrecen Debrecen Hungary.

Premise: (Apiaceae) is a polycarpic, perennial herb with a very limited range and small populations. It is listed as "endangered" on the IUCN Red List of Threatened Species. Microsatellite markers can contribute to conservation efforts by allowing the study of the genetic structure of its shrinking populations. Read More

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http://dx.doi.org/10.1002/aps3.11321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035428PMC
February 2020

Development and characterization of 20 novel EST-SSR markers for , a relict tree in China.

Appl Plant Sci 2020 Feb 11;8(2):e11320. Epub 2020 Feb 11.

College of Life Sciences Nanjing University Nanjing 210023 People's Republic of China.

Premise: (Ulmaceae), the only species of the genus , is an endangered tree in China. Here, novel expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed to illuminate its genetic diversity for conservation and assisted breeding.

Methods And Results: Based on Illumina transcriptome data from , a total of 70 EST-SSR markers were initially designed and tested. Read More

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http://dx.doi.org/10.1002/aps3.11320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035429PMC
February 2020

A new model for efficient, need-driven progress in generating primary biodiversity information resources.

Appl Plant Sci 2020 Jan 19;8(1):e11318. Epub 2020 Jan 19.

Biodiversity Institute, and Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas USA.

Premise: The field of biodiversity informatics has developed rapidly in recent years, with broad availability of large-scale information resources. However, online biodiversity information is biased spatially as a result of slow and uneven capture and digitization of existing data resources. The West African Plants Initiative approach to data capture is a prototype of a novel solution to the problems of the traditional model, in which the institutional "owner" of the specimens is responsible for digital capture of associated data. Read More

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http://dx.doi.org/10.1002/aps3.11318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976889PMC
January 2020

Seventeen new microsatellites for and cross-amplification in species.

Appl Plant Sci 2020 Jan 22;8(1):e11317. Epub 2020 Jan 22.

Departamento de Ciencias Ambientales y Recursos Naturales Universidad de Alicante Carretera de San Vicente s/n 03690 San Vicente del Raspeig, Alicante Spain.

Premise: Microsatellite markers were developed for the western Mediterranean tree (Tamaricaceae) as part of a study of its genetic diversity and structure.

Methods And Results: Seventeen microsatellite markers were developed for , 14 of which were polymorphic. These microsatellites have di-, tri-, and tetranucleotide repeats with 1-13 alleles per locus and population. Read More

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http://dx.doi.org/10.1002/aps3.11317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976893PMC
January 2020

Development of 18 microsatellite markers for .

Appl Plant Sci 2020 Jan 22;8(1):e11316. Epub 2020 Jan 22.

Faculty of Environmental Sciences Czech University of Life Sciences in Prague Kamýcká 129 CZ-16521 Czech Republic.

Premise: Microsatellite markers were developed for the perennial herb (Lamiaceae), a species representative of European dry grasslands. The development of microsatellite markers is needed for genetic and phylogeographical studies of species from the genus .

Methods And Results: We used low-coverage Illumina sequencing to identify microsatellite loci. Read More

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http://dx.doi.org/10.1002/aps3.11316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976894PMC
January 2020

Methods for broad-scale plant phenology assessments using citizen scientists' photographs.

Appl Plant Sci 2020 Jan 8;8(1):e11315. Epub 2020 Jan 8.

Florida Museum of Natural History University of Florida Gainesville Florida 32611 USA.

Premise: Citizen science platforms for sharing photographed digital vouchers, such as iNaturalist, are a promising source of phenology data, but methods and best practices for use have not been developed. Here we introduce methods using flowering phenology as a case study, because drivers of phenology are not well understood despite the need to synchronize flowering with obligate pollinators. There is also evidence of recent anomalous winter flowering events, but with unknown spatiotemporal extents. Read More

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http://dx.doi.org/10.1002/aps3.11315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976896PMC
January 2020

Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems.

Appl Plant Sci 2020 Jan 12;8(1):e11314. Epub 2020 Jan 12.

Division of Plant Sciences University of Missouri Columbia Missouri 65211 USA.

The past six years have seen the rapid growth of studies of CRISPR/Cas9 in plant genome editing, a method that enormously facilitates both basic research and practical applications. Most studies have focused on genetic model species, but plant species that are not genetic models may also be economically important or biologically significant, or both. However, developing the CRISPR/Cas9 system in a nongenetic model is challenging. Read More

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http://dx.doi.org/10.1002/aps3.11314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976890PMC
January 2020

Development of chloroplast microsatellite markers for giant ragweed ().

Appl Plant Sci 2020 Jan 22;8(1):e11313. Epub 2020 Jan 22.

Finnish Museum of Natural History (Botany) University of Helsinki P.O. Box 7 Helsinki FI-00014 Finland.

Premise: Plant invasions are increasing globally, and extensive study of the genetic background of the source and invading populations is needed to understand such biological processes. For this reason, chloroplast microsatellite markers were identified to explore the genetic diversity of the noxious weed (Asteraceae).

Methods And Results: The complete chloroplast genome of was mined for microsatellite loci, and 15 novel chloroplast primers were identified to assess the genetic diversity of 49 samples. Read More

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http://dx.doi.org/10.1002/aps3.11313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976888PMC
January 2020

Plot Locator: An app for locating plots in the field.

Appl Plant Sci 2019 Dec 20;7(12):e11311. Epub 2019 Dec 20.

U.S. Geological Survey, Wetland and Aquatic Research Center 700 Cajundome Boulevard Lafayette Louisiana 70506 USA.

Premise: One of the challenges in field biology is locating previously sampled plots. The Plot Locator app was developed to assist field biologists with plot identification and location, with or without GPS or online connectivity.

Methods And Results: The Plot Locator Android app helps users locate field plots by creating a searchable database that stores study area information, such as site/plot names and numbers, distances from landmarks, optional cardinal directions and GPS coordinates, and field notes. Read More

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http://dx.doi.org/10.1002/aps3.11311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923711PMC
December 2019

A data management workflow of biodiversity data from the field to data users.

Appl Plant Sci 2019 Dec 20;7(12):e11310. Epub 2019 Dec 20.

Department of Biology Institute for Great Lakes Research Central Michigan University Bioscience Building 2100, 1455 Calumet Court Mount Pleasant Michigan 48859 USA.

Premise: Heterogeneity of biodiversity data from the collections, research, and management communities presents challenges for data findability, accessibility, interoperability, and reusability. Workflows designed with data collection, standards, dissemination, and reuse in mind will generate better information across geopolitical, administrative, and institutional boundaries. Here, we present our data workflow as a case study of how we collected, shared, and used data from multiple sources. Read More

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http://dx.doi.org/10.1002/aps3.11310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923704PMC
December 2019

Methacrylate: An alternative fixing agent for identifying the botanical origin of propolis.

Appl Plant Sci 2019 Dec 8;7(12):e11309. Epub 2019 Dec 8.

Department of Plant Biology Federal University of Viçosa Av. Peter Henry Rolfs s/n Viçosa Minas Gerais 36571-000 Brazil.

Premise: A new technique was developed to identify the botanical origin of propolis, a resin-like material made by bees by mixing saliva and beeswax with plant buds and exudates, using methacrylate for permanent slide preparation.

Methods And Results: Propolis samples were fixed in methacrylate to produce permanent slides. The anatomical structures of the plant fragments in the methacrylated propolis were compared with propolis slides prepared using conventional techniques that consist of propolis sediment obtained during a series of solvent reactions, filtration, and centrifugations, which cost a similar amount to produce. Read More

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http://dx.doi.org/10.1002/aps3.11309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923709PMC
December 2019

Microsatellite markers for the endangered in Peru.

Appl Plant Sci 2019 Dec 6;7(12):e11308. Epub 2019 Dec 6.

South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 People's Republic of China.

Premise: Microsatellite primers were developed for (Bromeliaceae), an endangered species distributed in the Andean Mountains of Bolivia and Peru.

Methods And Results: Genome skimming of , , and resulted in the selection of 46 pairs of cross-species microsatellite markers. Of these, 12 microsatellite primer pairs produced clear and polymorphic bands in . Read More

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http://dx.doi.org/10.1002/aps3.11308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923705PMC
December 2019

Development, characterization, and cross-amplification of 17 microsatellite markers for .

Appl Plant Sci 2019 Dec 8;7(12):e11307. Epub 2019 Dec 8.

Faculty of Environmental Sciences Czech University of Life Sciences Prague Kamýcká 129 Praha 6-Suchdol CZ-165 00 Czech Republic.

Premise: Polymorphic microsatellite markers were developed as a tool for genetic investigations of (Rosaceae) and related species.

Methods And Results: Seventeen new polymorphic microsatellite markers were developed for using the Illumina MiSeq platform. Polymorphism of the 17 loci was tested in three populations. Read More

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http://dx.doi.org/10.1002/aps3.11307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923706PMC
December 2019

Fourteen polymorphic microsatellite markers for the widespread Labrador tea ().

Appl Plant Sci 2019 Dec 6;7(12):e11306. Epub 2019 Dec 6.

Department of Biological Sciences Butler University 4600 Sunset Avenue Indianapolis Indiana 46208 USA.

Premise: Microsatellite markers were developed for Labrador tea (, Ericaceae) to facilitate downstream genetic investigation of this species and the extremely closely related, circumboreal subsect. .

Methods And Results: Forty-eight primer pairs were designed using Illumina data and screened for excellent amplification. Read More

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http://dx.doi.org/10.1002/aps3.11306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923708PMC
December 2019

Development of 16 single-copy nuclear gene markers for , a perennial herb in China.

Appl Plant Sci 2019 Nov 14;7(11):e11304. Epub 2019 Nov 14.

Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou People's Republic of China.

Premise: We developed single-copy nuclear DNA markers for a perennial herb, (Gesneriaceae), to help infer the evolutionary history of the genus in subtropical China.

Methods And Results: We screened 834 putative single-copy nuclear genes from transcriptomes of 11 species of using the Illumina HiSeq 2000 platform. Based on the screening results, we developed 16 primer sets for accessions of representing three wild populations. Read More

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http://dx.doi.org/10.1002/aps3.11304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858290PMC
November 2019

Characterization of microsatellite loci in and transferability to other genera in the Hawai'ian lobelioid group.

Appl Plant Sci 2019 Nov 11;7(11):e11303. Epub 2019 Nov 11.

Plant Science and Conservation Chicago Botanic Garden 1000 Lake Cook Road Glencoe Illinois 60022 USA.

Premise: Microsatellite markers were developed to measure genetic diversity and relatedness of ex situ collections of (Campanulaceae).

Methods And Results: Potential microsatellite markers were identified from two sources; 28 were developed for and an additional 12 markers from a previously published study of . Primer pairs were tested on 30 individuals of and 24 individuals of to provide measures of genetic diversity and inbreeding. Read More

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http://dx.doi.org/10.1002/aps3.11303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858292PMC
November 2019

Characterization and development of microsatellite markers for and congeneric taxa.

Appl Plant Sci 2019 Nov 8;7(11):e11302. Epub 2019 Nov 8.

Department of Research, Conservations and Collections Desert Botanical Garden 1201 N. Galvin Parkway Phoenix Arizona 85008 USA.

Premise: Microsatellite markers were developed in (Cactaceae) for use in several morphologically similar, closely related taxa within the genus to study genetic structure and diversity within and among individuals and populations.

Methods And Results: Using reads from shallow, whole genome Illumina HiSeq high-throughput sequencing, we developed and characterized 15 microsatellite primer pairs for , var. , var. Read More

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http://dx.doi.org/10.1002/aps3.11302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858291PMC
November 2019

A noninvasive, machine learning-based method for monitoring anthocyanin accumulation in plants using digital color imaging.

Appl Plant Sci 2019 Nov 10;7(11):e11301. Epub 2019 Nov 10.

Horticultural Sciences Department University of Florida Gainesville Florida 32611 USA.

Premise: When plants are exposed to stress conditions, irreversible damage can occur, negatively impacting yields. It is therefore important to detect stress symptoms in plants, such as the accumulation of anthocyanin, as early as possible.

Methods And Results: Twenty-two regression models in five color spaces were trained to develop a prediction model for plant anthocyanin levels from digital color imaging data. Read More

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http://dx.doi.org/10.1002/aps3.11301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858293PMC
November 2019

The genome of : An emerging Andean super grain.

Appl Plant Sci 2019 Nov 8;7(11):e11300. Epub 2019 Nov 8.

Department of Plant and Wildlife Sciences Brigham Young University 5144 LSB Provo Utah 84602 USA.

Premise: Cañahua is a semi-domesticated crop grown in high-altitude regions of the Andes. It is an A-genome diploid (2 = 2 = 18) relative of the allotetraploid (AABB) and shares many of its nutritional benefits. Cañahua seed contains a complete protein, a low glycemic index, and offers a wide variety of nutritionally important vitamins and minerals. Read More

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http://dx.doi.org/10.1002/aps3.11300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858295PMC
November 2019

Optimizing depth and type of high-throughput sequencing data for microsatellite discovery.

Authors:
Mark A Chapman

Appl Plant Sci 2019 Nov 3;7(11):e11298. Epub 2019 Nov 3.

Biological Sciences University of Southampton Life Sciences Building 85, Highfield Campus Southampton SO17 1BJ United Kingdom.

Premise: Simple sequence repeat (SSR) markers (microsatellites) are a mainstay of many labs, especially when working on a limited budget, carrying out preliminary analyses, and in teaching. Whether SSRs mined from plant genomes or transcriptomes are preferred for certain applications, and the depth of sequencing needed to allow efficient SSR discovery, has not been tested.

Methods: I used genome and transcriptome high-throughput sequencing data at a range of sequencing depths to compare efficacy of SSR identification. Read More

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http://dx.doi.org/10.1002/aps3.11298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858294PMC
November 2019

Development of SSR markers for , a vulnerable species from northwestern China.

Appl Plant Sci 2019 Oct 24;7(10):e11297. Epub 2019 Oct 24.

Xinjiang Key Laboratory of Grassland Resources and Ecology and Ministry of Education Key Laboratory for Western Arid Region Grassland Resources and Ecology College of Grassland and Environment Sciences Xinjiang Agricultural University Ürümqi 830052 People's Republic of China.

Premise: (Fabaceae) is a vulnerable species found in the cold deserts of northwestern China. We aimed to characterize polymorphic microsatellite loci for to support future studies of population genetic dynamics and conservation management of the species.

Methods And Results: We used next-generation sequencing to detect polymorphic microsatellites. Read More

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http://dx.doi.org/10.1002/aps3.11297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814180PMC
October 2019

Development of novel microsatellite markers for  by comparative transcriptomics.

Appl Plant Sci 2019 Oct 22;7(10):e11296. Epub 2019 Oct 22.

Center for Health and Bioresources AIT Austrian Institute of Technology GmbH 3430 Tulln Austria.

Premise: (Boraginaceae) is an important medicinal herb with its main distribution across the Mediterranean region. To reveal its genetic variation and population structure, microsatellite markers were developed and validated in four Greek populations.

Methods And Results: RNA-Seq data of the related species and were assembled and mined to identify conserved ortholog sets containing simple sequence repeat motifs. Read More

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http://dx.doi.org/10.1002/aps3.11296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814220PMC
October 2019

An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.

Appl Plant Sci 2019 Oct 25;7(10):e11295. Epub 2019 Oct 25.

Department of Biological Sciences University of Memphis Memphis Tennessee 38152 USA.

Premise: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here.

Methods: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). Read More

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http://dx.doi.org/10.1002/aps3.11295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814182PMC
October 2019

Chloroplast primers for clade-wide phylogenetic studies of .

Appl Plant Sci 2019 Oct 16;7(10):e11294. Epub 2019 Oct 16.

Department of Biological Sciences University of Idaho 875 Perimeter Dr. MS 3051 Moscow Idaho 83844-3051 USA.

Premise: Chloroplast primers were developed for phylogenetic and comparative studies in (Ranunculaceae).

Methods And Results: We assembled and annotated the complete plastome sequence of by combining multiple whole genome sequencing libraries. Using transcriptome-sequencing libraries, we also assembled a partial plastome of the related species . Read More

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http://dx.doi.org/10.1002/aps3.11294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814179PMC
October 2019

Editorial: Growing up and moving forward: Discontinuing Primer Notes.

Authors:
Theresa M Culley

Appl Plant Sci 2019 Oct 8;7(10):e11293. Epub 2019 Oct 8.

Department of Biological Sciences University of Cincinnati 614 Rieveschl Hall Cincinnati Ohio 45221-0006 USA.

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http://dx.doi.org/10.1002/aps3.11293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814178PMC
October 2019

Transcriptome analysis of two radiated species and the subsequent species delimitation of the complex.

Appl Plant Sci 2019 Oct 16;7(10):e11292. Epub 2019 Oct 16.

Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 People's Republic of China.

Premise: is an important gymnosperm genus, and the most diverse of all cycad genera. The complex of species are morphologically similar and difficult to distinguish due to a lack of genomic resources.

Methods: We characterized the transcriptomes of two closely related and endangered species endemic to Hainan, China: and . Read More

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http://dx.doi.org/10.1002/aps3.11292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814181PMC
October 2019

Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae.

Appl Plant Sci 2019 Sep 25;7(9):e11290. Epub 2019 Sep 25.

Department of Systematic and Evolutionary Botany University of Zurich 8008 Zurich Switzerland.

Premise: Information on orthologous groups of genes, their sequence variability, and annotation is required for project design in phylogenetic reconstruction. This resource is unavailable for the flowering plant family Acanthaceae (>4000 species).

Methods: We compared transcriptome sequences spanning the extant diversity of Acanthaceae in order to provide a set of orthologous low-copy nuclear genes and assess their utility for reconstructing phylogenetic relationships within this group of plants. Read More

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http://dx.doi.org/10.1002/aps3.11290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764435PMC
September 2019
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Development and characterization of SSR markers for based on genome skimming.

Appl Plant Sci 2019 Sep 24;7(9):e11289. Epub 2019 Sep 24.

Laboratory of Systematic and Evolutionary Botany and Biodiversity College of Life Sciences Zhejiang University Hangzhou Zhejiang 310058 People's Republic of China.

Premise: Polymorphic nuclear simple sequence repeat (nSSR) markers were developed for (Papaveraceae), a spring ephemeral native to eastern North America.

Methods And Results: Based on the genome skimming data of , a total of 240 nSSR primer pairs were designed for 80 loci from the assembled nuclear contigs. Of these primer pairs, 19 were selected for initial validation in four populations (80 individuals). Read More

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http://dx.doi.org/10.1002/aps3.11289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764431PMC
September 2019
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Morphological Analysis of Size and Shape (MASS): An integrative software program for morphometric analyses of leaves.

Appl Plant Sci 2019 Sep 19;7(9):e11288. Epub 2019 Sep 19.

Department of Physics Kettering University 1700 University Avenue Flint Michigan 48532 USA.

Premise: Morphometric analysis is a common approach for comparing and categorizing botanical samples; however, completing a suite of analyses using existing tools may require a multi-stage, multi-program process. To facilitate streamlined analysis within a single program, Morphological Analysis of Size and Shape (MASS) for leaves was developed. Its utility is demonstrated using exemplar leaf samples from , , and . Read More

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http://dx.doi.org/10.1002/aps3.11288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764432PMC
September 2019
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Development and characterization of microsatellite markers in , a native plant of the Cerrado ecoregions of South America.

Appl Plant Sci 2019 Sep 22;7(9):e11287. Epub 2019 Sep 22.

Faculdade de Ciências Exatas e Tecnologia Universidade Federal da Grande Dourados Dourados Mato Grosso do Sul 79804-970 Brazil.

Premise: A novel set of nuclear microsatellite markers was developed and characterized for (Myrtaceae) and tested for cross-amplification in the related species .

Methods And Results: Forty-one primer pairs were designed for simple sequence repeat loci, of which 36 successfully amplified and were polymorphic. The number of alleles ranged from two to 14, with an average of 8. Read More

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http://dx.doi.org/10.1002/aps3.11287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764490PMC
September 2019
1 Read