RAPD PCR method

Thu Jul 30 10:44:00 EST 1992

Phillip Lowrey asked about RAPD as a means of obtaining markers
for genetic mapping studies. Our group (Forest Biotechnology Group
at North Carolina State University) has used RAPD markers extensively
in genetic mapping in pines, which are particularly well suited to
the use of dominant markers because haploid tissue can be obtained
from the megagametophyte in the seeds. We generated a map with 191
markers covering a total of 1687 cM in twelve linkage groups using
60 open-pollinated seed in about two months (which strikes me as
fairly high efficiency). Other experiments in the lab have shown
RAPDs are most useful on species with high levels of genetic variability,
such as populations of forest trees. A student using RAPDs to map in
a horticultural species has had to look through more primers to find
markers segregating in his crosses. RAPDs are definitely easier and
faster to screen for than virtually any other molecular marker, though,
so this is not a devastating criticism. We have found reproducibility
to be good (98%), as long as you're careful in choosing which bands
to score as markers. The thing to remember about RAPD is that what you
see on the gel is a _phenotype_, not a genotype. There is a lot
of variation on the gels, and not all of it is due to genetic
variation between the individuals sampled. Choose markers that
segregate in Mendelian ratios and reproducibility is very good.
Ross Whetten

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