These plots are a variant of ordinary linkage-map plots, except that each map is specific for one of the individuals in the population and shows its parental genotype at every marker locus. on a chromosome. The original idea for this kind of plot is apparently due to Young and Tanksley who described it in TAG 77: 95-101 (1989) under the name of "graphical genotypes." It is assumed that a marker locus represents a chromosomal segment of the same parental genotype, extending halfway to the next marker locus on either side. The plot can give an idea of the gross genomic composition of a genotype as well as of the genotype of an unseen gene locus lying among marker loci. Viewing the genome of a single individual in both this format and the bit-plot format at the same time on the screen shows the equivalence of the two. Here, cyan (or blank) segments represent missing marker data and the other colors represent the various marker genotypes. The color or pattern legend (QGene 2.30 offers only patterns) appears in response to a mouse-click on a locus name.
QGene 3.04 allows you to export to the Clipboard a chromosome genotype plot for any selected set of individuals, as below. These are editable drawings, not the bitmaps exported by v2.30. This figure illustrates two other new features: the option of displaying centiMorgan distances cumulatively as well as by interval, and the synthesis and display of genotypes with four alleles at a locus. Shown are chromosomes of 22 f2 progeny of a Aa x Cc cross.
Similarity among individuals based on their molecular genotypes is of interest in relationship studies but rarely mentioned in connection with mapping experiments, where the similarity of interest is linkage between markers. What if two or more individuals are genetically identical, as sometimes happens with doubled-haploid populations? At best, one of them is uninformative; in the extreme case of much hidden similarity we could wind up attaching much more significance to the mapping results than the data warrant. The purpose of the Compare genotypes analysis is to give a picture of this internal similarity.
When the dialog is opened from the Analyses menu, individual 1 of the population is the Reference. Against its marker genotypes at all loci (portrayed in the top box) are compared those of all the other individuals. In each comparison, a locus at which neither of the individuals being compared has a missing datapoint (shown in cyan) is called an informative locus, and a mismatch (shown in the third box) is counted if the Reference and Compare individuals (shown in the second box from the top) do not have the same marker genotype at this locus. These mismatches are tallied for all pairwise comparisons against the Reference. Tables of them may be exported and their distribution is shown in the histogram at bottom right. You can find out what loci they represent by dragging the cursor in these boxes.
The population used for this plot was simulated as the F2 of a cross between two outbred diploid parents with different pairs of alleles at 50% of loci; the extra colors represent the third and fourth alleles.
A Jaccard similarity calculation counts as uninformative any loci that have a null phenotype in both compared individuals. This approach is irrelevant in a comparison of two sib progeny of a mapping population generated by a cross of inbred parents. However, in a polymorphism study using dominant markers (like RAPDs) on a panel of cultivars of unknown relationship it might be desirable to exclude double nulls. The Matching nulls uninformative check box tells QGene to do this. For such an analysis you would have coded the population type as dhf1 or ri (even though the entries aren't related in this way), since in a BC type QGene would see no null marker phenotypes (the third symbol, i. e. the aa homozygote) and there would be no difference in the analysis.
You can type an individual's number into the Reference
box and press Return for evaluation of mismatches between
this individual and the population. The comparisons will include
that of the Reference with itself, which will give 0 mismatches,
and the histogram will include this 0 datapoint. The Minimum
mismatches shown under the histogram refers to the next most
similar individual. To find out which this is, scroll the vertical
scroll to its top (the individuals are sorted ascendingly on mismatches)
and then down one line. The information for the individual will
be shown in the text boxes.
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