Sorts individuals of a segregating population by their genetic similarity with a defined target genotype, using the identity by descent (IBD) information at QTL positions for one or more traits (M. Malosetti & F.A. van Eeuwijk).
Options
PRINT = string tokens |
What to print (summary); default summ |
|---|---|
PLOT = string tokens |
What to plot (haplotypes); default hapl |
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL); default F2 |
IBDWINDOW = scalar |
Size of the window around the QTL position to use to construct the haplotypes; default 10 |
TRAITS = text |
Names of the traits whose QTL information is to be used; default is to use all the traits |
SELECTION = variate |
Indicator variate with values defining whether each trait should be maximized (1), minimized (-1) or remain unchanged (0); if unset, the default is to maximize every trait |
%BESTGENOTYPES = scalar |
Specifies the percentage of the best genotypes to display in the output and plots; default 10 |
Parameters
GENFILENAME = texts |
Name of a Flapjack genotype file |
|---|---|
MAPFILENAME = texts |
Name of a Flapjack map file |
FJQTLFILENAME = texts |
Name of a file to supply the QTL results |
QTRAITS = texts |
Names of the traits affected by each QTL |
QCHROMOSOMES = factors |
Factor defining the linkage group of each QTL |
QPOSITIONS = variates |
Position of each QTL within the linkage group |
QNAMES = texts |
Name of each QTL |
QEFFECTS = variates |
Individual QTL effects |
QBESTSAVE = pointers |
Saves similarities with the target genotype, and their ranks, across and per trait |
Description
QBESTGENOTYPE is a procedure for post processing of QTL mapping results. It uses the identity by descent (IBD) information of genotypes at QTL positions to define genetic similarities with a target genotype. It can deal with QTL information for one or several traits simultaneously.
By default, QBESTGENOTYPE prints the results, but you can suppress this by setting option PRINT=*. It also produces a plot of the best genotypes, and this can be suppressed by setting option PLOT=*. The %BESTGENOTYPES specifies the percentage of genotypes, at the top of the ranking, that are to be displayed or plotted (default 10%).
The POPULATIONTYPE option specifies the population type (default F2), and the IBDWINDOW option defines the size of the window around the QTL position in which IBD probabilities are estimated (default 10 cM). The traits from which QTL information will be used are specified by the TRAITS option. The direction of selection for each trait is defined in a variate supplied by the SELECTION option. This contains the value one if the aim is to increase the trait, minus one if it should be decreased, or zero if it should not change.
The GENFILENAME and MAPFILENAME parameters must supply the names of Flapjack files with the marker scores and map information, respectively. The FJQTLFILENAME parameter can be used to supply the QTL information as a Flapjack QTL file (for example saved by the QFLAPJACK procedure). Alternatively the QTL information can be supplied (in vectors with equal lengths) by the following parameters: QTRAITS (names of the traits), QNAMES (names of the QTLs), QCHROMOSOMES (chromosome locations), QPOSITIONS (positions within the chromosomes) and QEFFECTS (QTL effects).
The QBESTSAVE parameter can save the results of the selection, in a pointer with 3 elements. The first, labelled 'Genotypes', saves the names of the genotypes. The second, labelled 'Ranking', is itself a pointer with an element 'All traits' for the combined ranking, and then an element for each individual trait (labelled by the trait name). The third, labelled 'Similarity', stores the similarities in a pointer like that used for the ranks.
Options: PRINT, PLOT, POPULATIONTYPE, IBDWINDOW, TRAITS, SELECTION, %BESTGENOTYPES.
Parameters: GENFILENAME, MAPFILENAME, FJQTLFILENAME, QTRAITS, QNAMES, QCHROMOSOMES, QPOSITIONS, QEFFECTS, QBESTSAVE.
Method
The QIBDPROBABILITIES procedure is used to calculate IBD probabilities around the QTL positions. A target genotype is defined combining the individual QTL effects and selection objectives per trait. The FSIMILARITY directive is used to estimate a similarity of each genotype to the target per trait, and an overall similarity across traits is obtained as the average similarity across traits (i.e. traits are equally weighted).
Action with RESTRICT
Restrictions are not allowed.
See also
Procedures: QFLAPJACK, QIBDPROBABILITIES, QREPORT.
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QBESTGENOTYPES example'; STYLE=meta
VARIATE [VALUES=-1,1,0,1] objectives
QBESTGENOTYPE [SELECTION=objectives]\
GENFILE='%gendir%/examples/F2maize_geno.txt';\
MAPFILE='%gendir%/examples/F2maize_map.txt';\
FJQTLFILE='%gendir%/examples/FJQTLfile.txt'