Effect of heterozygosity on the assembly of the physical map. a| and b| CB Maps of two real contigs of the grape physical map ('a' corresponds to contig number 69 and 'b' to contig number 354) showing the so called 'scissoring effect', one of the main consequences of heterozygosity. On both contigs a polymorphic SNP marker has been physically mapped by BAC-pooling first, followed by PCR determination of the BAC clones containing each of the two alleles. The clones on which one allele maps have been highlighted in red and the ones on which the other allele maps in blue. It is interesting to observe that the two alleles of the same SNP marker map onto different clones which are not overlapping each other. The problem which affects the assembly of these two contigs has been called 'scissoring effect'. Basically, the clones within a contig tend to split apart, with the ones belonging to one allele at one extremity and the ones belonging to the other allele at the other extremity. As a consequence, the affected contigs show an expansion in the CB map size. c| and d| Two plots depicting simulated contigs from the in silico simulation at 42% sequence divergence, where the clones belonging to one allele have been highlighted in orange and the ones belonging to the other allele in blue. In 'c' the 'scissoring effect' is particularly evident on the right extremity, while the other part of the contig shows a more complex situation. Indeed, the scissoring effect can be locally more or less important and this is thought to be related to the variation in the levels of heterozygosity along the contig/chromosome. This situation is particularly consistent with the pictures 'a' and 'b'. The contig displayed in 'd' shows instead a different situation, being made up by clones which belong only to one allele (in orange). This scenario is consistent with the cases of allele testing in which the two alleles hybridize onto separate contigs (see text).
Scalabrin et al. BMC Genomics 2010 11:204 doi:10.1186/1471-2164-11-204