RAPD mapping

Ross Whetten rosswhet at forbt2.nrrc.ncsu.edu
Fri Oct 2 13:53:59 EST 1992

In article <1ad34kINN4np at overload.lbl.gov>, Claire Williams writes:
|> [This message is from Claire Williams _not_ Brad Sherman.]
|> In article <1992Sep28.144722.666 at ncsu.edu> rosswhet at forbt2.nrrc.ncsu.edu (Ross Whetten) writes:
|> > The short answer to the above question is likely to be "No, RFLPS
|> > are not worth the effort for QTL mapping for practical tree breeding
|> > purposes", because of the linkage equilibrium problem.
|> Practical tree breeding in tropical and subtropical conifers is into
|> the third breeding cycle using extremely small heterozygous lines.
|> Could one really argue that linkage equilibrium is present in the
|> domesticated population? It may not always be necessary to genotype
|> an entire population, But if genotyping an entire population is
|> necessary then genotyping a small population is not an arduous task.
|> RFLP and RAPD markers would take the same amount of time.
|>    --Claire Williams

For the benefit of observers of this exchange: Claire Williams is a geneticist with
Weyerhaeuser Corporation, and is participating in an RFLP mapping project with loblolly pine.

I would contend that linkage equilibrium is at a 
minimum between individuals from different inbred lines, 
and that it increases over time once those individuals 
or lines are crossed. Charlie Stuber has experimentally 
tested this in maize, and (I think) five generations after 
the initial cross between inbred lines, the population 
reached linkage equilibrium again. This being the case, if 
one begins _not_ with completely homozygous inbred lines but 
with highly heterozygous outbred populations, it seems unlikely that the population
will spontaneously move away from linkage equilibrium. Inbreeding
is the best way of introducing linkage _dis_equilibrium, and most
tree breeding programs have worked hard to avoid inbreeding.

Regarding the second point: I said in the first posting that 
"I am not arguing against the use of RFLPs in crop plants in which 
the markers have already been identified ...". The current RFLP project underway 
in loblolly pine is yielding useful data, and the probes from that
work will be very helpful in mapping other conifer genomes. Pines then
become another crop plant in which mapping is routine. Either RAPDs or
RFLPs could be used to genotype a population; RAPDs are better-suited for
scoring many markers on relatively few individuals, while RFLPs are well-
suited to scoring a few markers on many individuals.

The major point I wished to make was that RAPDs are much more
suitable than RFLPs for beginning a mapping project in a plant
species on which little molecular biology has been done. A plant breeder
need not have access to genomic or cDNA libraries to obtain probes, and the RAPD
technique is more accessible to non-molecular biologists than Southern
blotting and hybridization. 

Ross Whetten, Research Assistant Professor of Forestry
Forest Biotechnology Group
North Carolina State University
Raleigh, North Carolina 27695-8008  USA
telephone or fax (919)515-7801

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