Types of variable sites in the tetraploid wheat genome. (a) At genome-specific sites (GSSs) nucleotide variants represent fixed mutations that differentiate the diploid ancestors of the wheat A and B genomes brought together by interspecies hybridization resulting in origin of allotetraploid wheat. SNP sites originate due to a mutation in one of the wheat genomes (in this example, in the A genome of Ld). Intra-species variable sites (IVSs) are highlighted in grey. (b) An example of CNV due to the deletion of a homoeologous copy of a gene. Deletion of a gene in the A genome of Td resulted in the disappearance of three bases, T, A and A, in the alignment.
Saintenac et al. Genome Biology 2011 12:R88 doi:10.1186/gb-2011-12-9-r88