Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species
Article first published online: 10 AUG 2011
© 2011 Victorian Department of Primary Industries. Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd
Plant Biotechnology Journal
Volume 10, Issue 2, pages 125–138, February 2012
How to Cite
Kaur, S., Francki, M. G. and Forster, J. W. (2012), Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species. Plant Biotechnology Journal, 10: 125–138. doi: 10.1111/j.1467-7652.2011.00644.x
- Issue published online: 2 JAN 2012
- Article first published online: 10 AUG 2011
- Received 8 April 2011; revised 5 June 2011; accepted 12 June 2011.
- single-nucleotide polymorphism;
- forage plant;
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.