RIs and hets

scolnipa at esvax.dnet.dupont.com scolnipa at esvax.dnet.dupont.com
Mon Oct 4 15:38:30 EST 1993


Regarding Phil McLean's questions:

Most RI collections have a very low (<5%) level of heterozygosity.  I 
don't know whether these residual hets are due to a random failure to 
fix a locus or there is actually selection for heterozygosity (enforced 
heterozygosity) in certain areas of the genome.  In any case, the 
seriousness of the problem depends on your objectives.

Dominant markers are not as effective as codominants for repulsion-phase 
linkage (see Fig. 5 in PNAS 89, pp. 1477-1481, 1992).  For molecular 
markers, scoring a het as homozygous will result in distorted distances.  
To spot these errors, it's very useful to look for events that could 
result from double recombinations over short distances (see NAR 21, 
2697-2702, 1993).  However, if you are just trying to place a marker in 
a general region of the genome, I don't believe heterozygosity is going 
to be problem with RIs.  After reading your message, we conducted a 
"real life" simulation.  We selected a RFLP marker that shows 5 hets in 
117 RIs.  If we had used dominant markers, we would have scored these 
het loci as homozygous for parental alleles.  So we replaced these five 
"missings" with either As or Bs (A and B being parental alleles).  The A 
replacement resulted in the same map location, but the distances to 
flanking markers and the LOD scores were affected.  The B replacement 
also placed the marker in the same area of the genome, but now the order 
of the subject locus and one flaking marker was reversed.  So our 
assumption was correct, we were still able to place the marker in the 
map, but with less confidence as to order and distances.  Three of the 
five "errors" were easy to spot by looking at the flanking markers.  If 
you're planning to use the marker for fine structure mapping, I 
recommend you switch to co-dominance (various ways of doing this).

Regarding dominant phenotypic markers such as disease resistance, the 
best strategy is to map them by phenotypic pooling or BSA (same NAR 
reference).  In this case, it's easy to select sensitive individuals.  
Forming a pool of resistant plants requires progeny testing.  Two 
dominant genes is a problem only if you can't distinguish them.

Hope this helps.

Pablo A. Scolnik



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