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From Genes to Markers: Exploiting Gene Sequence Information to Develop Tools for Plant Breeding

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Crop Breeding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1145))

Abstract

Once the sequence is known for a gene of interest, it is usually possible to design markers to detect polymorphisms within the gene. Such markers can be particularly useful in plant breeding, especially if they detect the causal polymorphism within the gene and are diagnostic of the phenotype. In this chapter, we (1) discuss how gene sequences are obtained and aligned and how polymorphic sites can be identified or predicted; (2) explain the principles of PCR primer design and PCR amplification and provide guidelines for their application in the design and testing of markers; (3) discuss detection methods for presence/absence (dominant) polymorphisms, length polymorphisms and single nucleotide polymorphisms (SNPs); and (4) outline some of the factors that affect the utility of markers in plant breeding and explain how markers can be evaluated (validated) for use in plant breeding.

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Author information

Authors and Affiliations

  1. Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Urrbrae, Glen Osmond, SA, Australia

    Melissa Garcia

  2. School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, Australia

    Diane E. Mather

Authors
  1. Melissa Garcia
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  2. Diane E. Mather
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Corresponding author

Correspondence to Melissa Garcia .

Editor information

Editors and Affiliations

  1. University of Adelaide, Australian Centre for Plant Functional Genomics (ACPFG), Urrbrae, South Australia, Australia

    Delphine Fleury

  2. University of Adelaide, Australian Centre for Plant Functional Genomics (ACPFG), Urrbrae, South Australia, Australia

    Ryan Whitford

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Garcia, M., Mather, D.E. (2014). From Genes to Markers: Exploiting Gene Sequence Information to Develop Tools for Plant Breeding. In: Fleury, D., Whitford, R. (eds) Crop Breeding. Methods in Molecular Biology, vol 1145. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0446-4_2

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  • DOI: https://doi.org/10.1007/978-1-4939-0446-4_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0445-7

  • Online ISBN: 978-1-4939-0446-4

  • eBook Packages: Springer Protocols

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