Read by QxMD icon Read

Applications in Plant Sciences

Si-Qian Jiao, Yan-Qiang Sun, Dong-Xu Zhang, Qiong Gao, Yuqing Jin, Hui Liu, Yongpeng Ma, Yong Yang, Ilga Porth, Jian-Feng Mao
Premise of the Study: Ephedra sinica (Ephedraceae) is a gymnosperm shrub with a wide distribution across Central and Eastern Asia. It is widely cultivated as a medicinal plant, but its wild populations are monitored to determine whether protection is needed. Methods and Results: Thirty-six microsatellite markers, including 11 polymorphic markers, were developed from E. distachya RNA-Seq data deposited in the National Center for Biotechology Information dbEST database...
January 2019: Applications in Plant Sciences
Alireza Pour-Aboughadareh, Mohsen Yousefian, Hoda Moradkhani, Peter Poczai, Kadambot H M Siddique
Premise of the Study: Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype-by-environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non-parametric models...
January 2019: Applications in Plant Sciences
Chandra N Jack, Shawna L Rowe, Stephanie S Porter, Maren L Friesen
Premise of the Study: Current methods for quantifying herbivore-induced alterations in plant biochemistry are often unusable by researchers due to practical constraints. We present a cost-effective, high-throughput protocol to quantify multiple biochemical responses from small plant tissue samples using spectrophotometric techniques. Methods and Results: Using Solanum lycopersicum and Medicago polymorpha leaves pre- and post-herbivory, we demonstrate that our protocol quantifies common plant defense responses: peroxidase production, polyphenol oxidase production, reactive oxygen species production, total protein production, and trypsin-like protease inhibition activity...
January 2019: Applications in Plant Sciences
Lele Liu, Jingwen Wang, Meiqi Yin, Xiao Guo, Yunfei Cai, Ning Du, Xiaona Yu, Weihua Guo
Premise of the Study: Vitex negundo var. heterophylla (Lamiaceae) is a dominant shrub in the warm temperate zone of northern China. Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed to investigate its genetic diversity and structure. Methods and Results: We detected 12,075 SSRs in V. negundo var. heterophylla using transcriptome sequencing. Primer pairs for 100 SSR loci were designed and amplified in three populations of V. negundo var...
January 2019: Applications in Plant Sciences
Xinjia Wang, Li Zhong, Zhikun Wu, Huaying Sun, Hong Wang, Dezhu Li, Spencer C H Barrett, Wei Zhou
Premise of the Study: Microsatellite markers were developed for Primula sinolisteri , a perennial distylous herb belonging to section Obconicolisteri (Primulaceae), to facilitate future investigations of the population genetics and mating patterns of populations in this species. Methods and Results: We developed 30 microsatellite markers for P. sinolisteri using HiSeq X-Ten sequencing and measured polymorphism and genetic diversity in a sample of 36 individuals from three natural populations...
January 2019: Applications in Plant Sciences
Rodrigo Rivero, Emily B Sessa, Rosana Zenil-Ferguson
Premise of the Study: Chromosome count data are available for hundreds of plant species and can be explored in text-only format at the Chromosome Counts Database ( CCDBcurator and EyeChrom are an R package and a web application, respectively, that first curate and then visualize these data graphically, so that intra- and interspecific variation of chromosome numbers can be easily summarized and displayed for a given genus. Methods and Results: We developed R code to clean, summarize, and display in several formats the chromosome count data for a selected genus or set of species present in the Chromosome Counts Database...
January 2019: Applications in Plant Sciences
Rui-Guang Shang, Pu Yang, Bing-Yi Wang, Zun-Ling Zhao
Premise of the Study: Maca ( Lepidium meyenii ; Brassicaceae) has been cultivated by Andeans for thousands of years as a food source and has been used for medicinal purposes. However, little is known about the mechanism underlying material accumulation during plant growth. Methods: RNA-Seq technology was used to compare the transcriptome of black maca root at three developmental stages. Gene Ontology term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied for the identification of pathways in which differentially expressed genes were significantly enriched...
December 2018: Applications in Plant Sciences
Peng-Fei Wang, Yong Li, Zhi-Hao Qian, Jia-Xin Li, Xue-Jun Ge
Premise of the Study: Microsatellite markers of Pterocarya stenoptera (Juglandaceae) were developed for future studies on the population genetic diversity and spatial genetic structure of the species. Methods and Results: Based on Illumina sequencing of the transcriptome of P. stenoptera , a total of 2452 microsatellites were identified from 83,674 assembled unigenes. One hundred microsatellites were randomly selected to design amplification primer pairs. Of these, 15 were successfully amplified and displayed polymorphism...
December 2018: Applications in Plant Sciences
Asher Wishkerman, Paul B Hamilton
Premise of the Study: Studies of plant cell and organ outline using shape analysis for taxonomic and morphological research have increased in the past decade. However, there are a limited number of available modern, intuitive, and easy software tools to conduct this work. Methods: We developed a tool for shape outline extraction using MATLAB accompanied with R scripts to perform elliptic Fourier analysis. To demonstrate the shape tool, we applied the software and scripts for genera and species shape determinations of diatom (single cell) species with x-, y-, and x- + y-shape symmetries...
December 2018: Applications in Plant Sciences
Hailee B Leimbach-Maus, Syndell R Parks, Charlyn G Partridge
Premise of the Study: Gypsophila paniculata (baby's breath; Caryophyllaceae) is a herbaceous perennial that has invaded much of northern and western United States and Canada, outcompeting and crowding out native and endemic species. Microsatellite primers were developed to analyze the genetic structure of invasive populations. Methods and Results: We identified 16 polymorphic nuclear microsatellite loci for G. paniculata out of 73 loci that successfully amplified from a primer library created using Illumina sequencing technology...
December 2018: Applications in Plant Sciences
Jian-Wen Li, Xin Yin, You-Jie Zhao, Shu-Jiao Yang, Lu-Min Vaario, Xue-Fei Yang
Premise of the Study: Novel and cost-effective microsatellite markers were developed to explore the population genetics, biogeographic structure, and evolutionary history of the prized Euro-Asian wild edible ectomycorrhizal fungus Tricholoma matsutake (Tricholomataceae). Methods and results: Eighteen new polymorphic simple sequence repeat loci, detected from a microsatellite-enriched genomic library, were used to characterize 131 individuals from eight T. matsutake populations...
December 2018: Applications in Plant Sciences
Juan Viruel, Anne Haguenauer, Marianick Juin, Fatma Mirleau, Delphine Bouteiller, Magda Boudagher-Kharrat, Lahcen Ouahmane, Stefano La Malfa, Frédéric Médail, Hervé Sanguin, Gonzalo Nieto Feliner, Alex Baumel
Premise of the Study: Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. Methods: In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua ...
December 2018: Applications in Plant Sciences
Bo-Yun Kim, Soo-Rang Lee, Yong-In Kim, Dae-Hyun Kang, Young-Dong Kim
Premise of the Study: Plagiorhegma dubium (Berberidaceae) has been listed as an endangered species in Korea due to extensive collection and destruction of natural habitats. In this study, 30 microsatellite loci, including 25 polymorphic loci, were developed for P. dubium for use in population-level genetic analyses. Methods and Results: We carried out transcriptome sequencing and isolated a total of 30 expressed sequence tag-simple sequence repeat markers from P...
December 2018: Applications in Plant Sciences
Ai-Li Zhang, Ya-Fang Gao, Guo-Dong Li, Zi-Gang Qian
Premise of the Study: Psammosilene tunicoides (Caryophyllaceae) is a narrowly distributed and endemic plant species in southwestern China. The overexploitation of natural P. tunicoides has led to the destruction of many populations. Population and genetic studies will provide crucial data for the protection and management of P. tunicoides . In this study, we develop simple sequence repeat markers of P. tunicoides to analyze population diversity. Methods and Results: Microsatellite loci of P...
December 2018: Applications in Plant Sciences
I-Ju Chen, Chou-Tou Shii, Tsu-Liang Chang, Kae-Kang Hwu
Premise of the Study: Lycoris is an ornamental and medicinal plant. We developed microsatellite markers for L. aurea and L. radiata simultaneously by using a hybrid between these two species. Methods and Results: Ion Torrent next-generation sequencing produced 1,784,504 reads. Testing 64 primer sets allowed for the development of 17 novel microsatellite markers: 16 for L. aurea , 10 for L. radiata , and nine common markers. Lycoris aurea had one to 12 alleles per locus and observed and expected heterozygosity levels of 0-0...
November 2018: Applications in Plant Sciences
Aparna Krishnamurthy, Robert J Ferl, Anna-Lisa Paul
Premise of the Study: The root apex is an important region involved in environmental sensing, but comprises a very small part of the root. Obtaining root apex transcriptomes is therefore challenging when the samples are limited. The feasibility of using tiny root sections for transcriptome analysis was examined, comparing RNA sequencing (RNA-Seq) to microarrays in characterizing genes that are relevant to spaceflight. Methods: Arabidopsis thaliana Columbia ecotype (Col-0) roots were sectioned into Zone 1 (0...
November 2018: Applications in Plant Sciences
Joel Nichols, Gabriel C Conroy, Naga Kasinadhuni, Robert W Lamont, Steven M Ogbourne
Premise of the Study: Alectryon ramiflorus (Sapindaceae) is an endangered rainforest tree known from only two populations. In this study, we identified polymorphic microsatellites, in silico, improving the effectiveness and efficiency of microsatellite development of nonmodel species. The development of genetic markers will support future conservation management of the species. Methods and Results: We used next-generation sequencing and bioinformatics to detect polymorphic microsatellites, in silico, reducing both the time and cost of marker development...
November 2018: Applications in Plant Sciences
Vishnupriya Kasireddy, Erika Mitchell, Zack E Murrell, Emily L Gillespie
Premise of the Study: Microsatellite markers were developed for Polypodium appalachianum (Polypodiaceae) to facilitate investigation of species boundaries between P. appalachianum and its putative hybrid, P. virginianum , and potentially among other members of the Miocene-age P. vulgare species complex. Methods and Results: Forty-eight primer pairs were designed from Illumina data and screened for successful amplification. Sixteen pairs were genotyped and evaluated for variability within and among three populations in North Carolina, Vermont, and New Hampshire...
November 2018: Applications in Plant Sciences
Juan M Cevallos-Cevallos, Cristina Jines, María G Maridueña-Zavala, María J Molina-Miranda, Daniel E Ochoa, José A Flores-Cedeno
Premise of the Study: The production of banana ( Musa spp.; Musaceae) plants is affected by various types of somaclonal variations (SV), including dwarfism. However, methods for specific detection of SV are still scarce. To overcome this, a metabolite-based method for detection of dwarf variants was evaluated. Methods: The gas chromatography-mass spectrometry (GC-MS) metabolite profile of dwarf banana variants was investigated and compared to that of normal-healthy (N) and cucumber mosaic virus (CMV)-infected plants using principal components analysis and partial least squares discriminant analysis (PLS-DA)...
November 2018: Applications in Plant Sciences
J Mason Heberling, Bonnie L Isaac
Premise of the Study: Innovative approaches to specimen collection and curation are needed to maximize the utility of natural history collections in a new era of data use. Associated data, such as digital images from the field, are routinely collected with recent herbarium specimens. However, these data often remain inaccessible and are rarely curated alongside the associated physical specimens, which limits future data use. Methods and Results: We leveraged the widely used citizen science platform, iNaturalist, to permanently associate field-collected data to herbarium specimens, including information not well preserved in traditional specimens...
November 2018: Applications in Plant Sciences
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"