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      Development of simple sequence repeat markers for Chamerion angustifolium (Onagraceae)

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          Abstract

          Premise

          Rosebay willowherb, or fireweed ( Chamerion angustifolium: Onagraceae), has diploid, tetraploid, and hexaploid cytotypes. There are known physiological and ecological differences among the three cytotypes, but genetic differences remain undetermined. We developed simple sequence repeat (SSR) markers for this species.

          Methods and Results

          Leaf samples were collected from three hexaploid C. angustifolium populations. We successfully amplified 16 SSR loci, which were found to be highly polymorphic. The number of alleles, the observed heterozygosity levels, and the expected heterozygosity levels ranged from four to 13, 0.286–0.899, and 0.372–0.871, respectively. Most primers could also be amplified successfully in C. conspersum and the closely related species Epilobium palustre.

          Conclusions

          The 16 polymorphic SSR markers developed here will be useful for genetic studies in C. angustifolium and related species.

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          Most cited references16

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          Primer Premier 5

          S. Lalitha (2000)
          Article 0 comments Cited 191 times – based on 0 reviews     Review now
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            Maximum likelihood estimation of the frequency of null alleles at microsatellite loci

            Steven Kalinowski, Mark Taper (2006)
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              Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids

              Oliver Serang, Marcelo Mollinari, Antonio Garcia (2012)
              The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical Bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species.
              Article 0 comments Cited 51 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Kang Huang:
                ORCID: https://orcid.org/0000-0002-8357-117X
                huangkang@nwu.edu.cn
                Journal
                Journal ID (nlm-ta): Appl Plant Sci
                Journal ID (iso-abbrev): Appl Plant Sci
                Journal ID (doi): 10.1002/(ISSN)2168-0450
                Journal ID (publisher-id): APS3
                Title: Applications in Plant Sciences
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Electronic): 2168-0450
                Publication date (Electronic): 08 May 2019
                Publication date Collection: May 2019
                Volume: 7
                Issue: 5 ( doiID: 10.1002/aps3.2019.7.issue-5 )
                Electronic Location Identifier: e01244
                Affiliations
                [ 1 ] Shaanxi Key Laboratory for Animal Conservation College of Life Sciences Northwest University Xi'an 710069 People's Republic of China
                [ 2 ] Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223 People's Republic of China
                Author notes
                [*] [* ]Author for correspondence: huangkang@ 123456nwu.edu.cn
                Author information
                https://orcid.org/0000-0001-5909-1224
                https://orcid.org/0000-0002-8357-117X
                https://orcid.org/0000-0001-7430-3889
                Article
                Publisher ID: APS31244
                DOI: 10.1002/aps3.1244
                PMC ID: 6526638
                SO-VID: 4adc95f7-7bea-49f8-93e7-3f0555a04af9
                Copyright © © 2019 Mi et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America
                License:

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                Date received : 02 December 2018
                Date accepted : 09 January 2019
                Page count
                Figures: 0, Tables: 3, Pages: 4, Words: 4083
                Funding
                Funded by: Chinese Academy of Sciences
                Award ID: XDB31020302
                Funded by: National Natural Science Foundation of China
                Award ID: 31770411
                Funded by: CAST
                Award ID: 2017QNRC001
                Funded by: National Key Programme of Research and Development
                Funded by: Ministry of Science and Technology of China
                Award ID: 2016YFC0503202
                Funded by: Natural Science Basic Research Plan in Shaanxi Province of China
                Award ID: 2018JM3024
                Categories
                Subject: Primer Note
                Subject: Primer Notes
                Custom metadata
                source-schema-version-number 2.0
                component-id aps31244
                cover-date May 2019
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.3 mode:remove_FC converted:20.05.2019

                Keywords: allelic phenotypes,chamerion angustifolium,onagraceae,polyploidy,simple sequence repeats
                Data availability:
                Keywords: allelic phenotypes, chamerion angustifolium, onagraceae, polyploidy, simple sequence repeats

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