Journal article
Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species
Plant Biotechnology Journal, Vol.10(2), pp.125-138
2011
Abstract
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.
Details
- Title
- Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species
- Authors/Creators
- S. Kaur (Author/Creator) - La Trobe UniversityM.G. Francki (Author/Creator) - Murdoch UniversityJ.W. Forster (Author/Creator) - La Trobe University
- Publication Details
- Plant Biotechnology Journal, Vol.10(2), pp.125-138
- Publisher
- Blackwell Publishing Inc.
- Identifiers
- 991005543631007891
- Copyright
- © 2011 Victorian Department of Primary Industries
- Murdoch Affiliation
- State Agricultural Biotechnology Centre
- Language
- English
- Resource Type
- Journal article
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Source: InCites
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- Collaboration types
- Domestic collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science