Datensatz

Zusammenfassung

In order to reveal the molecular cause of observed phenotypic variation, geneticists
map the responsible locus in segregating populations using genetic
markers. The mapping of laboratory induced mutations has usually been
done between standard laboratory strains like Columbia and Landsberg erecta
and by now there are many markers between these two strains available.
Studies of natural variation, however, aim at finding different alleles at one
locus (or many loci at once) between different accessions (ecotypes), which
are usually not very well characterized. Thus, mapping the genetic cause
of phenotypic differences between any two accessions first requires the
development of markers.
We were in the particular need to develop markers to genotype 5 sets of
Recombinant Imbred Lines (RILs) our laboratory has constructed (http://naturalvariation.
org). For all parents of our RIL-sets sequencing information is publicly
available (1) and we developed software to detect SNP-markers using
that information. Our software requires the input of DNA sequences of the
same locus from (many) different accessions and it will return SNP markers
between any subsets of accessions the user specifies. The output is organized
such, that it can directly be used to design the SNP detection assay. Our
programs are written in Perl and make use of the emboss-package (2).
As of now, we mined 854 fragments (600-700 bp in length) and detected
173 SNP markers, that can theoretically be used to genotype our 5 RIL sets.
54 of these markers have already been tested by genotyping 192 lines of our
est-1 x col-0 RIL-set and 92 lines of our nd-1 x col-0 RIL-set and all markers
worked.