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Evaluation of Genome-Wide Markers and Orthologous Markers in Brachypodium distachyon

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Brachypodium Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1667))

Abstract

Molecular markers play an important role in identifying the species variation, characterizing the genic diversity, and also linking the identified markers to trait of interest. Genome- and transcriptome-derived molecular markers have been widely used to understand the geographical diversity and have also played a major role in the development of high-density linkage maps. In the present protocol, we present a detailed protocol on bioinformatics approaches towards the whole-genome and transcriptome-assisted simple sequence repeats (SSRs) marker mining in Brachypodium distachyon and identification of orthologus SSRs and their validation in Brachypodium ecotypes. We also present a protocol for the validation of the identified markers.

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Author information

Authors and Affiliations

  1. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, IASMA, 380010, Italy

    Gaurav Sablok

  2. Centre for Bioinformatics Research (CBR), SRKR Engineering College, Chinna Amiram, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India

    Suresh B. Mudunuri, Kranthi Chennamsetti & G. P. Saradhi Varma

  3. Department of Genetics, University of Silesia in Katowice, 40-032, Katowice, Poland

    Korneliya Gudys & Miroslaw Kwasniewski

  4. Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia

    Gaurav Sablok

Authors
  1. Gaurav Sablok
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  2. Suresh B. Mudunuri
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  3. Korneliya Gudys
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  4. Kranthi Chennamsetti
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  5. G. P. Saradhi Varma
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  6. Miroslaw Kwasniewski
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Corresponding author

Correspondence to Gaurav Sablok .

Editor information

Editors and Affiliations

  1. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach IASMA, Trentino, Italy

    Gaurav Sablok

  2. Sabanci University, Istanbul, Turkey

    Hikmet Budak

  3. Climate Change Cluster (C3), University of Technology Sydney, Sydney, New South Wales, Australia

    Peter J. Ralph

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Sablok, G., Mudunuri, S.B., Gudys, K., Chennamsetti, K., Varma, G.P.S., Kwasniewski, M. (2018). Evaluation of Genome-Wide Markers and Orthologous Markers in Brachypodium distachyon . In: Sablok, G., Budak, H., Ralph, P. (eds) Brachypodium Genomics. Methods in Molecular Biology, vol 1667. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7278-4_15

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  • DOI: https://doi.org/10.1007/978-1-4939-7278-4_15

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7276-0

  • Online ISBN: 978-1-4939-7278-4

  • eBook Packages: Springer Protocols

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