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Applications in Plant Sciences

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
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
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
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
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
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
Phillip C Klahs, Timothy J Gallaher, Lynn G Clark
Premise of the Study: A refined procedure is described for modeling small, intricate plant structures using computer-aided design software. The procedure facilitates the study of wind pollination in the family Poaceae and provides virtual biological illustrations for public outreach. Methods and Results: Spikelets were fixed in gFAA, dehydrated using ethanol and xylene, embedded in paraffin wax, and then sectioned with a rotary microtome. Images of serial sections were used as a reference for modeling the shape of bracts with splines in a computer-aided design program...
August 2018: Applications in Plant Sciences
Bin-Bin Du, Ya Zhan, Jiao-Kun Li, Ying-Zhuo Chen, Lu-Lu Tang
Premise of the Study: Microsatellite primers were developed for the gynodioecious Chinese endemic Thalictrum smithii (Ranunculaceae). Methods and Results: Thirty-nine microsatellite primers were developed using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) method. Thirteen microsatellite loci were found to be highly polymorphic after screening 114 specimens (60 hermaphrodite and 54 female) from three T. smithii populations. The number of alleles per locus ranged from three to 13, and the levels of observed and expected heterozygosity per locus ranged from 0...
August 2018: Applications in Plant Sciences
Chiun-Jr Huang, Fang-Hua Chu, Shau-Chian Liu, Yu-Hsin Tseng, Yi-Shiang Huang, Li-Ting Ma, Chieh-Ting Wang, Ya Ting You, Shuo-Yu Hsu, Hsiang-Chih Hsieh, Chi-Tsong Chen, Chi-Hsiang Chao
Premise of the Study: Simple sequence repeat (SSR) and expressed sequence tag (EST)-SSR markers were developed as tools for marker-assisted selection of Chamaecyparis formosensis and for the molecular differentiation of cypress species. Methods and Results: Based on the SSR-enriched genomic libraries and transcriptome data of C. formosensis , 300 primer pairs were selected for initial confirmation, of which 19 polymorphic SSR and eight polymorphic EST-SSR loci were chosen after testing in 92 individuals...
August 2018: Applications in Plant Sciences
Sorrasak Yodphaka, Kansri Boonpragob, H Thorsten Lumbsch, Ekaphan Kraichak
Premise of the Study: Studies on the diversity of epiphyllous bryophytes have been limited because of minute and incomplete specimens and a lack of taxonomic expertise. The recent development of the DNA barcoding approach has allowed taxon identification and species discovery of many obscure groups of organisms. Methods: With DNA extractions from 99 samples of 16 species, we compared the efficiencies of six DNA markers ( rbcL , matK , trnL-F , psbA , ITS1, and ITS2) in their ability to amplify, using a standard set of primers, as well as their discriminatory power, using distance-based and tree-based approaches with nucleotide data...
August 2018: Applications in Plant Sciences
Yi Yang, Sixin Huang, Yanling Wang, Lingjian Gui, Yiran Liu, Xiaomei Huang, Guoqingzi Chen, Fengxiao Tan, Jianwu Wang
Premise of the Study: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for Pluchea indica , a traditional medicinal species widespread along the tropical coastlines of Asia and northern Australia. Methods and Results: Based on transcriptome data for P. indica , a total of 40 primer pairs were initially designed and tested, of which 17 were successfully amplified and showed clear polymorphism. For these SSR loci, one to nine alleles per locus were identified...
August 2018: Applications in Plant Sciences
Yves Cuenot, José M Gómez, Adela González-Megias, John R Pannell, Rubén Torices
Premise of the Study: Polymorphic microsatellite markers were developed to study population structure and mating patterns of the monocarpic herb Moricandia moricandioides (Brassicaceae). Methods and Results: Illumina MiSeq sequencing was used to develop a panel of 15 polymorphic microsatellite markers that were tested across 77 individuals from three populations on the Iberian Peninsula. All markers were polymorphic in at least two studied populations, and the number of alleles ranged from one to 11 per locus...
August 2018: Applications in Plant Sciences
David Gutiérrez-Larruscain, Teresa Malvar Ferreras, M Montserrat Martínez-Ortega, Enrique Rico, Santiago Andrés-Sánchez
Premise of the Study: Microsatellite primers were developed for the first time in the genus Filago (Gnaphalieae: Asteraceae). These markers will facilitate low-scale phylogenetic, phylogeographic, and population genetic studies within the genus Filago . Methods and Results: Ten pairs of polymorphic microsatellite primers (as well as five pairs of monomorphic primers) were identified and optimized on two species of Filago ( F. gaditana and F. carpetana ) using a microsatellite-enrichment library method and 454 GS-FLX technique...
August 2018: Applications in Plant Sciences
Jong-Won Park, In-Su Choi, Byoung-Hee Choi
Premise of the Study: Vicia hirticalycina (Fabaceae) is a narrowly endemic species restricted to mountain valleys of southern Korea. To investigate its fine-scale genetic diversity and differentiation in Korea, we developed polymorphic microsatellite markers. Methods and Results: Sixteen polymorphic microsatellite markers were developed from Illumina MiSeq data. In 74 individual plants from four populations, one to seven alleles were expressed for each locus. The levels of observed and expected heterozygosity ranged from 0...
June 2018: Applications in Plant Sciences
Xiongfang Liu, Hong Ma, Taiqiang Li, Zhenghong Li, Youming Wan, Xiuxian Liu, Liyong Fu
Premise of the Study: A novel set of EST-SSR markers was developed for Phyllanthus emblica (Phyllanthaceae) to investigate the genetic structure and gene flow, identify novel genes of interest, and develop markers for assisted breeding. Methods and Results: Based on the transcriptome data of P. emblica , 83 EST-SSR primer pairs were designed; 52 primer pairs were successfully amplified, with 20 showing polymorphisms in 90 individuals from three populations of P...
June 2018: Applications in Plant Sciences
Hui Wang, Han Yang, Pei-Liang Liu, Chun Su, Liang Xiao, Zhao-Yang Chang
Premise of the Study: Microsatellite primers were developed for a perennial legume from northern China, Oxytropis diversifolia (Fabaceae), to investigate population genetic structure of this taxon, as well as potential hybridization events with closely related taxa in this genus. Methods and Results: One hundred and five primer pairs were designed from Illumina sequence data and screened for suitability. Fifteen of these primer pairs were polymorphic, and these primers amplified tri-, tetra-, and pentanucleotide repeats with 10-56 alleles per locus...
June 2018: Applications in Plant Sciences
Gillian H Dean, Rani Asmarayani, Marlina Ardiyani, Yessi Santika, Teguh Triono, Sarah Mathews, Campbell O Webb
The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost-effective generation of high-quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data...
June 2018: Applications in Plant Sciences
Hua-Ying Wang, Bai-Ying Wei, Hong-Xing Xiao
Premise of the Study: Acer (Aceraceae) is an important genus in forest ecosystems in the Northern Hemisphere. In China, 151 species have been reported, and approximately 61 species are endemic. Thus, China is considered to host the greatest diversity of Acer , but markers are needed to evaluate the genetic structure and genetic diversity of these populations of wild Acer species. Methods and Results: Using an enriched genomic library, we developed and characterized 15 microsatellite primers for A...
June 2018: Applications in Plant Sciences
Ezgi Ogutcen, Larissa Ramsay, Eric Bishop von Wettberg, Kirstin E Bett
Premise of the Study: Lentil is an important legume crop with reduced genetic diversity caused by domestication bottlenecks. Due to its large and complex genome, tools for reduced representation sequencing are needed. We developed an exome capture array for use in various genetic diversity studies. Methods: Based on the CDC Redberry draft genome, we developed an exome capture array using multiple sources of transcript resources. The probes were designed to target not only the cultivated lentil, but also wild species...
June 2018: Applications in Plant Sciences
Tyler William Smith, Paul Kron, Sara L Martin
Premise of the Study: Despite advantages in terms of reproducibility, histogram analysis based on nonlinear regression is rarely used in genome size assessments in plant biology. This is due in part to the lack of a freely available program to implement the procedure. We have developed such a program, the R package flowPloidy. Methods and Results: flowPloidy builds on the existing statistical tools provided with the R environment. This base provides tools for importing flow cytometry data, fitting nonlinear regressions, and interactively visualizing data...
June 2018: Applications in Plant Sciences
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