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      Development, characterization, and cross-amplification of 16 microsatellite primers for Atriplex tatarica (Amaranthaceae) 1

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          Abstract

          Premise of the study:

          Microsatellite primers were developed to characterize the genetic diversity and structure of the annual herb Atriplex tatarica (Amaranthaceae) and to facilitate ecological and evolutionary studies of A. tatarica and its relatives.

          Methods and Results:

          Sixteen novel microsatellite primers were developed for A. tatarica based on high-throughput sequencing of enriched libraries. All markers were polymorphic, with the number of alleles per locus ranging from three to 25 and observed and expected heterozygosity ranging from 0.08 to 0.74 and 0.10 to 0.87, respectively. In addition, some of these loci were successfully amplified and showed polymorphisms in four Atriplex and seven Chenopodium species.

          Conclusions:

          The microsatellite markers published here will be useful in assessing genetic diversity, structure, and gene flow within and across populations of A. tatarica, as well as in other species of Atriplex and the related genus Chenopodium.

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          Most cited references9

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          QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.

          Emese Meglécz, Caroline Costedoat, Vincent Dubut … (2010)
          QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input. The following tasks are completed by QDD: tag sorting, adapter/vector removal, elimination of redundant sequences, detection of possible genomic multicopies (duplicated loci or transposable elements), stringent selection of target microsatellites and customizable primer design. It can treat up to one million sequences of a few hundred base pairs in the tag-sorting step, and up to 50,000 sequences in a single input file for the steps involving estimation of sequence similarity. QDD is freely available under the GPL licence for Windows and Linux from the following web site: http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html. Supplementary data are available at Bioinformatics online.
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            High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries.

            Christophe Délye, Stéphanie Duthoy, Philippe Castagnone-Sereno … (2011)
            Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11,497 to 34,483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms. © 2011 Blackwell Publishing Ltd.
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              MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data

              C. Van Oosterhout, WF Hutchison, DPM Wills … (2004)
              Article 0 comments Cited 32 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Appl Plant Sci
                Journal ID (iso-abbrev): Appl Plant Sci
                Journal ID (publisher-id): apps
                Title: Applications in Plant Sciences
                Publisher: Botanical Society of America
                ISSN (Electronic): 2168-0450
                Publication date Collection: November 2017
                Publication date (Electronic): 17 November 2017
                Volume: 5
                Issue: 11
                Electronic Location Identifier: apps.1700094
                Affiliations
                [2 ]Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, CZ-165 21 Czech Republic
                [3 ]Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
                Author notes
                [1]

                This research was supported by grant no. 15-06632S from the Grant Agency of the Czech Republic and by the long-term research development project RVO 67985939. The authors thank Lucia Marková and Martina Slavíčková for their help in the laboratory and Fred Rooks for help with English editing.

                [4 ]Author for correspondence: mandak@ 123456fzp.czu.cz
                Article
                Publisher ID: apps1700094
                DOI: 10.3732/apps.1700094
                PMC ID: 5703183
                SO-VID: d64eb831-bfa2-4437-999c-3b9414ddf012
                Copyright © © 2017 Kondrysová et al. Published by the Botanical Society of America
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( CC-BY-NC-SA 4.0), which permits unrestricted noncommercial use and redistribution provided that the original author and source are credited and the new work is distributed under the same license as the original.

                History
                Date received : 25 August 2017
                Date accepted : 25 September 2017
                Categories
                Subject: Primer Note

                Keywords: amaranthaceae,atriplex,chenopodium,cross-amplification,microsatellites
                Data availability:
                Keywords: amaranthaceae, atriplex, chenopodium, cross-amplification, microsatellites

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