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CerealsDB home WheatBP home FAQs Contact us
Wheat evolution Wheat development Wheat farming Milling Baking and brewing Wheat research SNPs SNP discovery
Our publications Related Web-sites
Homoeologous vs varietal SNPs
Diagrammatic representation of the SNP nomeclature used in our laboratory.
- a) A homoeologous SNP exist if there is a difference between the three homoeologous genomes (A, B and D) in a single individual; here, both varieties 1 and 2 possess the same homoeologous SNP. Homoeologous SNPs make no reference to a second variety or individual, they are a characteristic of a single individual.
- b) A varietal SNP exists where individuals from two different wheat varieties differ in the nucleotides they possess at any particular locus. In the diagram shown here, there is a homozygous TT in the D genome of Variety 1 and a homozygous AA in the D genome of Variety 2. Different types of varietal SNP are describe below.
- a) Co-dominant SNPs: homozygous calls for all varieties studies (panel (a)), e.g., A:A and T:T.
- b) Partially co-dominant SNP: heterozygous and both homozygous calls detected (panel (b)), e.g., A:T as wll as A:A and T:T.
- c) Dominant SNPs: heterozygotes and only one type of homozygote detected (panel (c)), e.g., A:T and T:T.
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Varietal SNPs
Varietal SNPs may been divided into three categories.
When a SNP is amplified from just a single homoeologous genome the assay is capable of differentiating between homozygotes (call ratio of 2:0) and heterozygotes (call ration of 1:1). The detection of heterozygous SNPs in hexaploid wheat is dependent on the ability of the assay to accurately discriminate between different call ratios: for 'dominant' SNP assays, which amplify from all three homoeologous chromosomes, it is often difficult to distinguish homozygotes (call ratio of 4:2) from heterozygotes (call ratio of 5:1). See the article by Allen et al. for further details of this terminology.
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