wub

Hi I'm a little puzzled with the following scenario: Two parents 1 & 2 of genotypes (Aa) and (aa) are crossed to producedan F1. Sequencing and assembly is carried out on the genomic dna from two poolsof 1 & 2 progeny. Bioinformatic approaches will establish allelic variants uniquelyassociated with the dominant A allele. Earlier alignment of the parents sequenced genomic DNA to a reference sequence identified polymorphisms between A and a. What I don't understand is why in the scenario above is the identification of polymorphisms only in the dominant A allele. Why is it even necessary to cross to produce F1 progeny (we have already attempted to identify polymorphisms from the using the earlier alignment), is this just to increase the number of plants available for identifying polymorphisms (if we assume there are no other reasons to cross e.g. establishing recombination boundaries of the locus)? Hope you can help!