GOBii QTL Format¶
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 marker_name germplasm_group platform fav_allele unfav_allele fav_allele_trait_name unfav_allele_trait_name breeding_value model substitution_effect relative_weight QGpc.cd1-2B.1 QGpc.cd1-2B.1 KASP A + YES Additive 2.1 0.4 QGpc.cd1-7B.2 QGpc.cd1-7B.2 KASP G + YES Dominant 1.3 0.4 Sb3 gwp2334 KASP T + NO Additive -1.4 0.2 Sb3 gwp2343 KASP G + YES Recessive 2.4 0.3 Sb3 gwp1223 KASP C + NO Additive -1.4 0.2 Lr68 gwp45542 KASP C + YES NA NA NA Lr68 gwp44341 KASP T + NO NA NA NA Yr7 gwp45565 KASP G Yr7 YES 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 favorable allele for this marker
All other columns are optional, but if provided, can be used as input parameters for an Indexed Forward Breeding 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) -
- fav_allele_trait_name - the name of favorable QTL/gene allele name that will be included in indexed forward breeding output tables for indexed forward breeding analysis. If no favorable allele name is provided, the marker allele name of the first marker in the marker group is used
- unfav_allele_trait_name - the name of unfavorable QTL/gene allele name that will be included in indexed forward breeding output tables for indexed forward breeding analysis. If no unfavorable allele name is provided, the marker allele name of the first marker in the marker group is used
- breeding_value - specifies whether a marker group will be included in calculations of breeding value and weighted breeding value. Accepted values are YES or NO.
- model (required if breeding_value is YES) - the genetic model for favorable alleles in a marker group. Allowed values are “Additive”, “Dominant”, or “Recessive”
- substitution_effect (required if breeding_value is YES) - defines the substitution effect; a change in phenotypic value when one unfavorable allele is substituted with one favorable allele at each QTL
- relative_weight (required if breeding_value is YES) - the weight provided to each QTL. The weight can be anything a breeder wants to use, such as economic or preference to calculate index for a selection. If you don’t want to weight breeding values, values can all be set to 1.
The first marker listed for each qtl will be used as a ‘priority marker’, meaning its values for breeding_value, model, substitution_effect and relative_weight will be used for all Indexed Forward Breeding calculations.