Calculates QTL effects in single-environment trials (M.P. Boer, M. Malosetti, S.J. Welham & J.T.N.M. Thissen).
Options
PRINT = string tokens |
What to print (summary, model, components, effects, means, stratumvariances, monitoring, vcovariance, deviance, Waldtests, missingvalues, covariancemodels); default summ |
|---|---|
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL, BCxSy, CP); must be set |
NGENERATIONS = scalar |
Number of generations of selfing for a RIL population |
NBACKCROSSES = scalar |
Number of backcrosses for a BCxSy population |
NSELFINGS = scalar |
Number of selfings for a BCxSy population |
FIXED = formula |
Defines extra fixed effects |
UNITFACTOR = factor |
Saves the units factor required to define the random model when UNITERROR is to be used |
MVINCLUDE = string tokens |
Whether to include units with missing values in the explanatory factors and variates and/or the y-variates (explanatory, yvariate); default expl, yvar |
MAXCYCLE = scalar |
Limit on the number of iterations; default 100 |
WORKSPACE = scalar |
Number of blocks of internal memory to be set up for use by the REML algorithm; default 100 |
Parameters
TRAIT = variates |
Quantitative trait to be analysed; must be set |
|---|---|
GENOTYPES = factors |
Genotype factor; must be set |
UNITERROR = variates |
Uncertainty on trait means (derived from individual unit or plot error) to be included in QTL analysis; default * i.e. omitted |
ADDITIVEPREDICTORS = pointers |
Additive genetic predictors; must be set |
ADD2PREDICTORS = pointers |
Second (paternal) set of additive genetic predictors |
DOMINANCEPREDICTORS = pointers |
Dominance genetic predictors |
CHROMOSOMES = factors |
Chromosomes corresponding to the additive genetic predictors; must be set |
POSITIONS = variates |
Positions on the chromosomes corresponding to the additive genetic predictors; must be set |
IDLOCI = texts |
Labels for the loci |
MKLOCI = variates |
Logical variate containing the value 1 if the locus is a marker, otherwise 0; must be set |
IDMGENOTYPES = texts |
Labels for the genotypes corresponding to the the additive genetic predictors |
IDPARENTS = texts |
Labels to identify the parents |
QTLSELECTED = variates |
Index numbers of the selected QTLs; must be set |
DOMSELECTED = variates |
Logical variate indicating whether the dominance predictor of each selected QTL must be present (1) or absent (0) in the model |
RESIDUALS = variates |
Residuals from the analysis |
FITTEDVALUES = variates |
Fitted values from the analysis |
WALDSTATISTICS = variates |
Saves the Wald test statistics |
PRWALD = variates |
Saves the associated Wald probabilities |
QEFFECTS = pointers |
Saves the estimated QTL effects |
QSE = pointers |
Saves the standard errors of the QTL effects |
OUTFILENAME = texts |
Name of the Genstat workbook file (*.gwb) to be created |
QSAVE = pointers |
Saves a pointer with information and results for the significant effects |
SAVE = REML save structures |
Save the details of each REML analysis for use in subsequent VDISPLAY and VKEEP directives |
Description
QSESTIMATE fits a final QTL model to estimate QTL effects in single-environment trials. It uses single observations per genotype as phenotypic data. The response variable must be specified by the TRAIT parameter, and the genotypes by the GENOTYPES parameter.The POPULATIONTYPE option must be set to specify the population from which the genotypes are derived. For recombinant inbred lines (POPULATIONTYPE = RIL), the NGENERATIONS option, must be set to supply the number of generations. For backcross inbred lines (POPULATIONTYPE = BCxSy), the NBACKCROSSES and NSELFINGS options must be set to define the number of backcrosses to the first parent and the number of selfings, respectively.
Molecular information must be provided in the form of additive genetic predictors stored in variates and supplied, in a pointer, by the ADDITIVEPREDICTORS parameter. Non-additive effects can be included in the model by specifying dominance genetic predictors using the DOMINANCEPREDICTORS parameter (e.g. in a F2 population). In the case of segregating F1 populations (outbreeders) two sets of additive genetic predictors must be specified, the maternal ones by the ADDITIVEPREDICTORS parameter, and the paternal ones by the ADD2PREDICTORS parameter. The corresponding map information for the genetic predictors must be given by the CHROMOSOMES and POSITIONS parameters. The labels for the loci can be supplied by the IDLOCI parameter, and the labels for the genotypes in the marker data can be supplied by the IDMGENOTYPES parameter. If IDMGENOTYPES is set, the match between the genotypes in the phenotypic and in the marker data will be checked. The IDPARENTS parameter can supply labels to identify the parents.
The QTL model assumes genotypes as random and QTLs as fixed effects. Extra fixed effects can be specified using the FIXED option. The QTLSELECTED parameter must specify the set of QTLs, in the form of a variate containing the index number of the positions where the QTLs are located. When the DOMINANCEPREDICTORS parameter is set, the DOMSELECTED parameter supplies a logical variate containing one if the dominance predictor of the corresponding marker must be present in the model, and zero if the dominance predictor of the corresponding marker must be absent in the model. If DOMINANCEPREDICTORS is set but DOMSELECTED is not set, all the dominance predictors are included.
The MVINCLUDE, MAXCYCLE and WORKSPACE options operate in the same way as these options of the REML directive. The UNITERROR parameter allows uncertainty on the trait means (derived from individual unit or plot error) to be specified to include in the random model; by default this is omitted. The UNITFACTOR option allows the factor that is needed to define the unit-error term to be saved (this would be needed, for example, to save information later about the term using VKEEP).
The PRINT option specifies the output to be displayed. The summary setting prints the information about the QTLs retained in the model, and the other settings correspond to those in the PRINT option of the REML directive. To be able to calculate the explained variance in the summary, the option POPULATIONTYPE must be set.
The QTL effects and their standard errors can be saved by the QEFFECTS and QSE parameters, respectively, and the fitted values and residuals can be saved by the FITTEDVALUES and RESIDUALS parameters. These are saved in pointers that contain a single variate if only the ADDITIVEPREDICTORS parameter is specified, or two or three variates if the DOMINANCEPREDICTORS and/or ADD2PREDICTORS parameters are also specified. The Wald statistics, degrees of freedom and probabilities can be saved by the parameters WALDSTATISTICS, DFWALD and PRWALD, respectively.
The OUTFILENAME parameter can be used to save the Wald statistics and the QEFFECTS and QSE structures in a Genstat work book file in a sheet named STATISTICS. This parameter should not contain an extension as the extension is defined automatically as .gwb.
The QSAVE parameter can be used to save a pointer containing information and results for the significant QTLs. The elements of the pointer are labelled as follows to simplify their subsequent use:
'procedure' |
stores the string ‘QSESTIMATE’ to indicate the source of the results, |
|---|---|
'trait' |
trait name, |
'markernames' |
marker names, |
'chromosomes' |
chromosomes, |
'positions' |
positions, |
'envnames' |
stores the string ‘Experiment’, |
'waldstatistics' |
wald statistics, |
'prwald' |
probability values of wald statistics, |
'dfwald' |
degrees of freedom of the wald statistics, |
'qeffects' |
QTL effects, |
'qse' |
standard errors of the QTL effects, |
'%vexplained' |
percentage explained variance, |
'lowerci' |
lower bound of confidence interval of estimated QTL position, |
'upperci' |
upper bound of confidence interval of estimated QTL position, |
'posmin' |
position of left flanking marker, |
'posmax' |
position of right flanking marker, |
'idlfm' |
marker name of left flanking marker, |
'idrfm' |
marker name of right flanking marker, |
'posminci' |
position of left flanking marker outside confidence interval, |
'posmaxci' |
position of right flanking marker outside confidence interval, |
'idlfmci' |
marker name of left flanking marker outside confidence interval, |
'idrfmci' |
marker name of right flanking marker outside confidence interval, |
'locus' |
index numbers of the significant QTLs, and |
'neff' |
number of additive and dominance predictors in the model. |
The elements 'procedure', 'trait', 'markernames', 'chromosomes', 'envnames', 'idlfm', 'idrfm', 'idlfmci' and 'idrfmci' are text structures; 'positions', 'waldstatistics', 'prwald', 'dfwald', 'lowerci', 'upperci', 'posmin', 'posmax', 'posminci, 'posmaxci', 'vexplained' and 'locus' are variates; 'qeffects' and 'qse' are pointers (see parameters QEFFECTS and QSE); and 'neff' is a scalar.
The SAVE parameter can be used to save the REML save structure from the analysis for use with subsequent VKEEP and VDISPLAY directives.
Options: PRINT, POPULATIONTYPE, NGENERATIONS, NBACKCROSSES, NSELFINGS, FIXED, UNITFACTOR, MVINCLUDE, MAXCYCLE, WORKSPACE.
Parameters: TRAIT, GENOTYPES, UNITERROR, ADDITIVEPREDICTORS, ADD2PREDICTORS, DOMINANCEPREDICTORS, CHROMOSOMES, POSITIONS, IDLOCI, MKLOCI, IDMGENOTYPES, IDPARENTS, QTLSELECTED, RESIDUALS, FITTEDVALUES, WALDSTATISTICS, PRWALD, QEFFECTS, QSE, OUTFILENAME, QSAVE, SAVE.
Method
QSESTIMATE fits the following models which include a set L of QTLs:
1) yi = μ + Σl∈L xiladd αladd + Gi
if only ADDITIVEPREDICTORS are specified
2) yi = μ + Σl∈L ( xiladd αladd + xildom αldom ) + Gi
if DOMINANCEPREDICTORS are also specified
3) yi = μ + Σl∈L ( xiladd αladd + xiladd2 αladd2 + xildom αldom ) + Gi
if both ADD2PREDICTORS and DOMINANCEPREDICTORS are specified (for population type CP)
where yi is the trait value of genotype i, xiladd are the additive genetic predictors of genotype i for locus l, and αadd are the associated effects. In models 2 and 3, xildom are the dominance genetic predictors, and αladd are the associated effects. In model 3, xiladd are the additive genetic predictors for maternal genotype i at locus l, xiladd2 are the additive genetic predictors for paternal genotype i, and αadd and αadd2 are the associated effects. Genetic predictors are genotypic covariables that reflect the genotypic composition of a genotype at a specific chromosome location (Lynch & Walsh 1998). Gi is the residual unexplained genetic and environmental variation, which is assumed to follow a Normal distribution with mean 0 and variance σ2.
Action with RESTRICT
Restrictions are not allowed.
Reference
Lynch, M. & Walsh, B. (1998). Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
See also
Procedures: QSBACKSELECT, QSQTLSCAN, QFLAPJACK, QREPORT.
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QSESTIMATE example'; STYLE=meta
SPLOAD [PRINT=*] '%GENDIR%/Examples/F2maize_traits.gsh'
& '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='LOCI'
& '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='ADDPREDICTORS'
& '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='DOMPREDICTORS'
" create single environment "
SUBSET [E.EQ.6] G,yld
" Candidate QTL positions from QSBACKSELECT "
VARIATE [VALUES=19,111,237] Qid
VARIATE [VALUES=0,1,0] Domid
QSESTIMATE [PRINT=summary,model,wald,effects; POPULATIONTYPE=F2]\
TRAIT=yld; GENOTYPES=G; CHROMOSOMES=mkchr; POSITIONS=mkpos;\
IDLOCI=idlocus; MKLOCI=marker;\
ADDITIVEPREDICTORS=addpred; DOMINANCEPREDICTORS=dompred;\
QTLSELECTED=Qid; DOMSELECTED=Domid; QEFFECTS=qeff; QSE=qse;\
QSAVE=Output; OUTFILENAME='F2maize_qsestimate'