Most of the QTL reported in soybean were identified by ANOVA at the markers, not by using interval mapping. Typically the authors only report the tested marker with the highest correlation to the measured phenotype while the flanking markers with lower correlations were not reported. Because of these inexact data, the authors actually only know that the underlying gene is (perhaps only loosely) linked to the reported marker.
To accommodate these inexact data and to avoid showing the QTL as a point in the SoyBase genetic maps, we arbitrarily made the QTL ends equal to the marker position +/- 1 cM. Very importantly, since the gene underlying the QTL may be only loosely linked to the marker tested it could be anywhere +/- 0-30 cM in either direction from the QTL position shown on the genetic map.
Given this uncertainty, QTL in SoyBase are shown only on the genetic maps as the genetic position is all that was reported. However, since it is often useful to be able to identify the corresponding region in the genome sequence, we have developed a tool that presents the VERY APPROXIMATE region of the genome that is near the QTL. This tool works by finding the closest flanking genetic markers to the QTL that are also on the sequence map and identifying them in the SoyBase genome browser.
This QTL-related genomic region should be considered VERY APPROXIMATE as
Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA | ||