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Applications in Plant Sciences

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https://www.readbyqxmd.com/read/30473944/development-of-17-novel-microsatellite-markers-for-lycoris-aurea-and-l-radiata-amaryllidaceae-using-next-generation-sequencing
#1
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
https://www.readbyqxmd.com/read/30473943/comparing-rna-seq-and-microarray-gene-expression-data-in-two-zones-of-the-arabidopsis-root-apex-relevant-to-spaceflight
#2
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
https://www.readbyqxmd.com/read/30473942/in-silico-detection-of-polymorphic-microsatellites-in-the-endangered-isis-tamarind-alectryon-ramiflorus-sapindaceae
#3
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
https://www.readbyqxmd.com/read/30473941/fifteen-microsatellite-markers-for-the-appalachian-rockcap-fern-polypodium-appalachianum-polypodiaceae-and-its-relatives
#4
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
https://www.readbyqxmd.com/read/30473940/gc-ms-metabolite-profiling-for-specific-detection-of-dwarf-somaclonal-variation-in-banana-plants
#5
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
https://www.readbyqxmd.com/read/30473939/inaturalist-as-a-tool-to-expand-the-research-value-of-museum-specimens
#6
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
https://www.readbyqxmd.com/read/30473938/microsatellite-markers-for-corybas-orchidaceae-species-in-new-zealand
#7
Megan L Van Etten, Carlos A Lehnebach, Sofie M Pearson, Alastair W Robertson, Jennifer A Tate
Premise of the Study: Microsatellite markers were developed for New Zealand species of Corybas (Orchidaceae) to investigate population genetics and species delimitation. Methods and Results: From sequencing a total genomic DNA library (using Illumina MiSeq), we developed 22 microsatellite markers for C. obscurus . The di- and trinucleotide repeat loci were initially trialed on individuals representing seven Corybas taxa ( C . "rimutaka," C. confusus , C...
November 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30386716/tolerance-strategies-revealed-in-tree-peony-paeonia-suffruticosa-paeoniaceae-ecotypes-differentially-adapted-to-desiccation
#8
Lili Guo, Dalong Guo, Weilun Yin, Xiaogai Hou
Premise of the Study: Tree peony ( Paeonia suffruticosa ; Paeoniaceae) is well known for its ornamental value, edible oil, and medicinal properties. However, its growing area has been limited by drought that has been exacerbated by global climate change. Methods: Gene expression profiles of a drought-tolerant cultivar and a drought-sensitive cultivar during dehydration and rehydration were investigated by transcriptome analysis. Expression patterns of unigenes related to drought and recovery response and unrelated to either cultivar were classified by hierarchical clustering and real-time quantitative PCR (qPCR)...
October 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30386715/identification-and-development-of-microsatellite-markers-in-hamamelis-mollis-hamamelidaceae
#9
Qianyi Yin, Cuiying Huang, Yanshuang Huang, Sufang Chen, Huagu Ye, Qiang Fan, Wenbo Liao
Premise of the Study: Hamamelis mollis (Hamamelidaceae) is a Tertiary relict species endemic to southern China. Polymorphic microsatellite markers were developed to reveal the genetic diversity of this species. Methods and Results: The genome of H. mollis was sequenced and de novo assembled into 642,351 contigs. A total of 72,097 paired primers were successfully designed from 80,282 simple sequence repeat (SSR) markers identified in 63,419 contigs. PCR amplification showed that 96 of the 136 synthesized primers could be successfully amplified, and 22 demonstrated polymorphism...
October 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30386714/characterization-of-39-microsatellite-markers-from-nuphar-shimadai-nymphaeaceae-and-cross-amplification-in-two-related-taxa
#10
Hsueh-Yu Lu, Huei-Chuan Shih, Li-Ping Ju, Chao-Ching Hwang, Yu-Chung Chiang
Premise of the Study: Microsatellite loci were developed for Nuphar shimadai (Nymphaeaceae) to evaluate the population genetic dynamics for conservation purposes. The species is an endemic aquatic species in Taiwan that is endangered by anthropogenic activities. Methods and Results: A magnetic bead enrichment protocol was used to identify 72 potential microsatellite loci and develop 39 microsatellite markers from N. shimadai . The number of alleles per locus ranged from one to 10 per locus, with levels of observed heterozygosity ranging from 0 to 1...
October 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30386713/reliability-of-acoustic-tomography-and-ground-penetrating-radar-for-tree-decay-detection
#11
Xi Wu, Guanghui Li, Zhi Jiao, Xiping Wang
Premise of the Study: Various nondestructive testing technologies have been used for detecting and visualizing internal defects in urban trees. The results obtained by using different nondestructive testing tools can be interpreted in different ways, which may result in inaccurate assessment of the true condition of the inspected trees. The main objective of this study was to evaluate the reliability of acoustic tomography and ground-penetrating radar (GPR) technology for detecting internal decay in a number of different tree species...
October 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30386712/utilization-of-single-image-normalized-difference-vegetation-index-si-ndvi-for-early-plant-stress-detection
#12
Nicole S Beisel, Jordan B Callaham, Natasha J Sng, Dylan J Taylor, Anna-Lisa Paul, Robert J Ferl
Premise of the Study: An imaging system was refined to monitor the health of vegetation grown in controlled conditions using spectral reflectance patterns. To measure plant health, the single-image normalized difference vegetation index (SI-NDVI) compares leaf reflectance in visible and near-infrared light spectrums. Methods and Results: The SI-NDVI imaging system was characterized to assess plant responses to stress before visual detection during controlled stress assays...
October 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30386711/development-and-characterization-of-est-ssr-markers-for-carex-angustisquama-cyperaceae-an-extremophyte-in-solfatara-fields
#13
Koki Nagasawa, Hiroaki Setoguchi, Masayuki Maki, Hayato Goto, Keitaro Fukushima, Yuji Isagi, Shota Sakaguchi
Premise of the Study: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for Carex angustisquama  (Cyperaceae) to investigate the evolutionary history of this plant that is endemic to solfatara fields in northern Japan. Methods and Results: Using RNA-Seq data generated by the Illumina HiSeq 2000, 20 EST-SSR markers were developed. Polymorphisms were assessed in C. angustisquama and the closely related species C. doenitzii and C. podogyna ...
October 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30386710/development-characterization-and-transferability-of-ssr-markers-for-vriesea-carinata-bromeliaceae-based-on-rna-sequencing
#14
Cristina C Todeschini, José L B Parizotto, Frank Guzman, Camila M Zanella, Rogério Margis, Márcia Goetze, Gecele M Paggi, Laís M Santana Costa, Camila de Aguiar Melo, Luiza D Hirsch, Fernanda Bered
Premise of the Study: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were isolated for Vriesea carinata , an endemic bromeliad from the Brazilian Atlantic Forest. These SSR loci may be used to investigate the genetic diversity and population structure of this species and related bromeliads. Methods and Results: Based on the transcriptome data of V. carinata , 30 primer pairs were designed and selected for initial validation. Of these primer pairs, 16 generated suitable SSR loci in 69 individuals...
October 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30276031/naoh-low-salt-method-for-chloroplast-isolation-and-highly-pure-cpdna-preparation-from-aeluropus-littoralis
#15
Najmeh Nasiri, Ghorbanali Nematzadeh, Vahid Shariati-Joni, Hamid Najafi-Zarrini
Premise of the Study: High-yield pure chloroplast DNA (cpDNA) is necessary for whole genome sequencing. Chloroplast extraction with traditional high-salt methods causes damage to nuclei and destroys the integrity of organelles, which leads to high genomic contamination from the nucleus and mitochondria. To overcome this issue, we modified a traditional high-salt method to obtain a new approach called the NaOH low-salt method (NLS). Methods and Results: The NLS method is based on the mild alkaline lysis of plant cells, followed by homogenization with ultrasonic waves and fractionation under reduced osmotic pressure...
September 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30276030/regeneration-of-highland-papaya-vasconcellea-pubescens-from-anther-culture
#16
Borys Chong-Pérez, Basilio Carrasco, Herman Silva, Francisca Herrera, Karla Quiroz, Rolando Garcia-Gonzales
Premise of the Study: Vasconcellea pubescens is an important Caricaceae species cultivated in several countries of South America. The objective of this study was to investigate different media compositions and plant growth regulators to induce plant regeneration. Methods: Anthers were cultured in Murashige and Skoog medium with varying concentrations of naphthalene acetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) plus a cytokinin (N-(2-chloro-4-pyridyl)-N'-phenylurea)...
September 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30276029/molecular-markers-for-nassella-trichotoma-poaceae-to-study-genetic-variation-in-new-zealand
#17
Claudia Lange, Dagmar F Goeke, Graeme W Bourdôt, Shona L Lamoureaux, Ana Podolyan, Gary J Houliston
Premise of The Study: Simple sequence repeat (SSR) markers were developed for the study of genetic diversity of New Zealand Nassella trichotoma (Poaceae) and to support future studies in its native range. Methods and Results: Genomic DNA was extracted from N. trichotoma leaf material and subjected to Roche 454 sequencing. From a total of 745 putative SSRs, 48 with di- to pentanucleotide repeats were screened, 32 primer pairs were designed, and 15 polymorphic markers were optimized for multiplex PCR on 105 N...
September 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30276028/development-of-microsatellite-markers-for-the-resin-yielding-non-timber-forest-product-species-boswellia-serrata-burseraceae
#18
Bhavani Shankar Maradani, Ravikanth Gudasalamani, Siddappa Setty, Rajasekaran Chandrasekaran
Premise of the Study: Boswellia serrata (Burseraceae) is an economically important aromatic, gum-resin-yielding, non-timber forest tree species. Microsatellite markers were developed for B. serrata for the first time to study genetic diversity and population structure. Methods and Results: A magnetic bead enrichment method was used to develop 16 microsatellite markers, of which 11 were polymorphic. The number of alleles per locus in the 60 individuals studied ranged from three to 10, and the levels of observed and expected heterozygosity ranged from 0...
September 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30276027/identification-of-sieve-elements-and-companion-cell-protoplasts-by-a-combination-of-brightfield-and-fluorescence-microscopy
#19
Prabhjot Kaur, Pedro Gonzalez, Manjul Dutt, Ed Etxeberria
Premise of the Study: Phloem-limited diseases are becoming increasingly pervasive, threatening the existence of crops worldwide. Studies of phloem diseases are complicated by the inaccessibility of the phloem tissue. Phloem cells are located deep inside the plant body, are interspersed with other cell types, are among the smallest cells in the plant kingdom, and make up a small percentage of the total cell population in a plant. These properties make phloem cells difficult to investigate...
September 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/30276026/development-of-10-single-copy-nuclear-dna-markers-for-euchresta-horsfieldii-fabaceae-a-rare-medicinal-plant
#20
Arief Priyadi, Chao Feng, Ming Kang, Hongwen Huang
Premise of the Study: Euchresta horsfieldii (Fabaceae) is a rare and endangered medicinal plant in Indonesia with restricted distribution. Single-copy nuclear DNA (scnDNA) markers were developed for this species to facilitate further investigation of genetic diversity and population structure. Methods and Results: We performed RNA-Seq and de novo assembly of the transcriptome. Ten primer sets were developed for E. horsfieldii , all of which also amplified in E. japonica and E...
September 2018: Applications in Plant Sciences
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