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Integrating Genetics and Genomics to Advance Soybean Research


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

  • the gene underlying the QTL may not lie between the nearest flanking markers
  • recombination is not uniform across the chromosome and hot/cold spots of recombination expand/contract the two representations of the genome relative to each other
  • the genetic map SoyBase presents is a hand-constructed composite of many different published maps; among other things this means the exact order of closely linked markers in the genetic map is not necessarily correct
  • the current Wm82 genome sequence assembly is known to have a number of both large and small scale errors; see the sequence <> genetic map comparisons at http:// -> Genetic and Sequence Maps Comparison
The nearest genetically mapped markers chosen will be highlighted in ORANGE in the map verion 4.0 track of the genomic viewer

Nearest sequence-based genetic marker 3' to Salt tolerance 3-2
     name: Sat_304
     position: Gm03:39088673

Nearest sequence-based genetic marker 5' to Salt tolerance 3-2
     name: Sat_304
     position: Gm03:39088673

Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA
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