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 -