the naming scheme for the relevant file seems to just be gensp + collection identifier + gff3.gz, e.g.:
/Glycine/max/markers/FiskebyIII.gnm1.mrk.SoySNP50K/glyma.FiskebyIII.gnm1.mrk.SoySNP50K.gff3.gz
(presumably this would use the glyma.FiskebyIII.gnm1 genome as target)
the naming scheme for the relevant file seems to just be gensp + collection identifier + gff3.gz, e.g.: /Glycine/max/markers/FiskebyIII.gnm1.mrk.SoySNP50K/glyma.FiskebyIII.gnm1.mrk.SoySNP50K.gff3.gz
(presumably this would use the glyma.FiskebyIII.gnm1 genome as target)