• Open Access

Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species

Authors

  • Sukhjiwan Kaur,

    1. Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Victoria, Australia
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  • Michael G. Francki,

    1. Department of Agriculture and Food Western Australia, South Perth, WA, and State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
    2. Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
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  • John W. Forster

    Corresponding author
    1. Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Victoria, Australia
    2. Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
    3. Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
    4. La Trobe University, Bundoora, Victoria, Australia
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(Tel +61-3-9032-7054; fax +61-3-9032-7158; email john.forster@dpi.vic.gov.au)

Summary

An understanding of nature and extent of nucleotide sequence variation is required for programmes of discovery and characterization of single nucleotide polymorphisms (SNPs), which provide the most versatile class of molecular genetic marker. A majority of higher plant species are polyploids, and allopolyploidy, because of hybrid formation between closely related taxa, is very common. Mutational variation may arise both between allelic (homologous) sequences within individual subgenomes and between homoeologous sequences among subgenomes, in addition to paralogous variation between duplicated gene copies. Successful SNP validation in allopolyploids depends on differentiation of the sequence variation classes. A number of biological factors influence the feasibility of discrimination, including degree of gene family complexity, inbreeding or outbreeding reproductive habit, and the level of knowledge concerning progenitor diploid species. In addition, developments in high-throughput DNA sequencing and associated computational analysis provide general solutions for the genetic analysis of allopolyploids. These issues are explored in the context of experience from a range of allopolyploid species, representing grain (wheat and canola), forage (pasture legumes and grasses), and horticultural (strawberry) crop. Following SNP discovery, detection in routine genotyping applications also presents challenges for allopolyploids. Strategies based on either design of subgenome-specific SNP assays through homoeolocus-targeted polymerase chain reaction (PCR) amplification, or detection of incremental changes in nucleotide variant dosage, are described.

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