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Whole Genome Wide SSR Markers Identification Based on ddRADseq Data

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Plant Genotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2638))

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Abstract

The advent of advanced NGS technologies have led to the generation of enormous amount of sequence data which further aid in the discovery of the various type of markers such as SSRs, SNPs, InDels, etc. Among all these markers, microsatellite SSR markers can be mined from the ddRADseq data as certain properties of SSR markers make them ideal markers for study. These assist researchers and breeders in diversity analysis and producing new varieties with desired traits. To extract the markers, first, the ddRADseq data is assembled into consensus sequences using STACKS program which are further assembled for mining microsatellites using QDD along with MISA tool.

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Authors and Affiliations

  1. Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India

    Gitanjali Tandon, Sarika Jaiswal, Mir Asif Iquebal, Anil Rai & Dinesh Kumar

  2. Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India

    Dinesh Kumar

Authors
  1. Gitanjali Tandon
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  2. Sarika Jaiswal
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  3. Mir Asif Iquebal
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  4. Anil Rai
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  5. Dinesh Kumar
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Corresponding author

Correspondence to Mir Asif Iquebal .

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Editors and Affiliations

  1. College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia

    Yuri Shavrukov

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Tandon, G., Jaiswal, S., Iquebal, M.A., Rai, A., Kumar, D. (2023). Whole Genome Wide SSR Markers Identification Based on ddRADseq Data. In: Shavrukov, Y. (eds) Plant Genotyping. Methods in Molecular Biology, vol 2638. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3024-2_5

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  • DOI: https://doi.org/10.1007/978-1-0716-3024-2_5

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3023-5

  • Online ISBN: 978-1-0716-3024-2

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