GOBii QTL Format


The information on this page refers to an as yet unreleased version of Flapjack.

In addition to the Flapjack’s standard QTL format (described on Projects & Data Formats) it also supports an extended QTL format that was developed in colloboration with the GOBii project.

As with all Flapjack input files, the formatting is tab-delimited and looks as follows:

# fjFile = QTL-GOBii
marker_group_name   germplasm_group   marker_name   platform   fav_allele   unfav_allele   trait_allele_name_ref   priority_marker   breeding_value   model     substitution_effect   relative_weight
QGpc.cd1-2B.1                         QGpc.cd1-2B.1 KASP       A                           +                       YES               YES              Additive  2.1                   0.4
QGpc.cd1-7B.2                         QGpc.cd1-7B.2 KASP       G                           +                       YES               YES              Dominant  1.3                   0.4
Sb3                                   gwp2334       KASP       T                           +                       NO                YES              Additive  -1.4                  0.2
Sb3                                   gwp2343       KASP       G                           +                       YES               YES              Additive  -1.4                  0.2
Sb3                                   gwp1223       KASP       C                           +                       NO                YES              Additive  -1.4                  0.2
Lr68                                  gwp45542      KASP       C                           +                       YES               NO               NA        NA                    NA
Lr68                                  gwp44341      KASP       T                           +                       NO                NO               NA        NA                    NA
Yr7                                   gwp45565      KASP       G                           Yr7                     YES               NO               NA        NA                    NA

There are three required columns:

  • marker_group_name - the name of the QTL being defined
  • marker_name - the name of a marker whose position information (chromosome location) will be used to define the QTL’s range (haplotype)
  • fav_allele - (or favorable_alleles) defines the favourable allele for this marker

All other columns are optional, but if provided, can be used as input parameters for an Indexed Forward Breeding (IFB) Analysis.

  • germplasm_group - currently unused by Flapjack, defines the germplasm group this marker belongs to
  • platform - currently unused by Flapjack, defines the technology used to create this marker
  • unfav_allele - (or unfavorable_alleles)
  • trait_allele_name_ref -
  • priority_marker - identifies the priority marker for a given QTL/haplotype, whose properties will be used in preference of those from other markers when there is no consensus between markers during an IFB analysis
  • breeding_value -
  • model -
  • substitution_effect -
  • relative_weight -