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Application of large-scale sequencing to marker discovery in plants

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Abstract

Advances in DNA sequencing provide tools for efficient large-scale discovery of markers for use in plants. Discovery options include large-scale amplicon sequencing, transcriptome sequencing, gene-enriched genome sequencing and whole genome sequencing. Examples of each of these approaches and their potential to generate molecular markers for specific applications have been described. Sequencing the whole genome of parents identifies all the polymorphisms available for analysis in their progeny. Sequencing PCR amplicons of sets of candidate genes from DNA bulks can be used to define the available variation in these genes that might be exploited in a population or germplasm collection. Sequencing of the transcriptomes of genotypes varying for the trait of interest may identify genes with patterns of expression that could explain the phenotypic variation. Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Examples of application of the above-mentioned techniques have been described.

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Acknowledgements

Financial support from the Australian Research Council, Grains Research and Development Corporation, Sugar Research and Development Corporation, and Rural Industries Research and Development Corporation is acknowledged. GKS visit to SCPS was sponsored by the BOYSCAST fellowship of Department of Science and Technology, India.

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Authors and Affiliations

  1. Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia

    Robert J Henry

  2. Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia

    Mark Edwards, Daniel L E Waters, Gopala Krishnan S, Peter Bundock, Ardashir K Masouleh & Catherine J Nock

  3. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110 012, India

    Gopala Krishnan S

  4. Departmant of Forest Sciences, The University of British Columbia, Vancouver, British Columbia,, V6T 1Z4, Canada

    Timothy R Sexton

  5. EH Graham Centre for Agricultural Innovation, School of Agricultural and Wine Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW, 2678, Australia

    Julie Pattemore

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  1. Robert J Henry
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  2. Mark Edwards
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Correspondence to Robert J Henry.

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[Henry RJ, Edwards M, Waters DLE, Gopala Krishnan S, Bundock P, Sexton TR, Masouleh AK, Nock CJ and Pattemore J 2012 Application of large-scale sequencing to marker discovery in plants. J. Biosci. 37 1–13] DOI 10.1007/s12038-012-9253-z

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Henry, R.J., Edwards, M., Waters, D.L.E. et al. Application of large-scale sequencing to marker discovery in plants. J Biosci 37, 829–841 (2012). https://doi.org/10.1007/s12038-012-9253-z

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