QTL CartographerQTL Cartographer

A Program Package for finding Quantitative Trait Loci

C. J. Basten

Z.-B. Zeng and B. S. Weir

Experimental DesignExperimental Design

P1 P2

F1

B1 B2F2

Inbred Lines

Three PhasesThree Phases

Phase I: Simulate or Reformat Data Phase II: Analyze Data Phase III: Visualize Results

Data PreparationData Preparation

Simulate a genetic linkage map, genetic model and data set of marker and trait values

Reformat a MAPMAKER data set Reformat your own data set Perform a bootstrap resampling

Reformat MAPMAKER DataReformat MAPMAKER Data

MAPMAKER *.raw file

Create *.maps file with MAPMAKER

Rmap reformats *.maps file

Rcross reformats *.raw file

*.maps *.raw

Rmap Rcross

Rmap.out Rcross.out

Simulate DataSimulate Data

Rmap creates a linkage map

Rqtl creates a genetic model

Rcross creates a data set of marker and trait values

Rmap Rqtl Rcross

Rmap.out Rqtl.out Rcross.out

Resample DataResample Data

Prune allows resampling of data

Permute traits on genotypes

Bootstrap Simulate missing or

dominant markersRcross2.out

Prune

Rmap.out Rcross.out

Transition to AnalysisTransition to Analysis

At this point, we have a genetic linkage map and a data file of the proper format

All analyses will depend on these two files

Call them Rmap.out and Rcross.out

AnalysisAnalysisRmap.out Rcross.out

QstatsLRmapqtlSRmapqtl

ZmapqtlJZmapqtl

Qstats.out LRmapqtl.outSRmapqtl.out

(J)Zmapqtl.out

QstatsQstats

Calculate basic statistics on Trait Produce histogram of Trait Summarize missing data for each

marker and each individual Perform tests for marker segregation

LRmapqtlLRmapqtl

Do simple linear regression of trait on each marker in turn

Trait = Mean + Marker + Error

Estimate model parameters F statistic for Hypothesis of a Linked

QTL

yi =β0 +β1xi +ei

SRmapqtlSRmapqtl

Forward stepwise regression to rank markers

Backward elimination to rank markers Forward addition with a final backward

elimination step: Rank markers, but only add or delete subject to criteria

ZmapqtlZmapqtl

Do interval or composite interval mapping (IM or CIM)

Specify genome walk rate Choose cofactors for CIM Perform tests using the bootstrap,

jacknife or permutation

CIM Model 6CIM Model 6

Markers

Test Site

LFM RFM

Blocked Region

Top markers (as determined by stepwise regression) not in blocked regions used as cofactors

Missing DataMissing Data

Jiang and Zeng method using Markov chain to infer missing markers

Dominant markers can also be used Same algorithms for genotype at test

site in IM and CIM Many experimental designs available

JZmapqtlJZmapqtl

Map multiple traits using IM or CIM Simultaneous estimation of additive and

dominance effects Joint and single trait likelihood ratios G x E interactions Still a work in progress: not yet

integrated into Preplot

Visualization SchematicVisualization Schematic

Rqtl.out Rmap.out c#t#.?

Zmapqtl.out LRmapqtl.out

Eqtl Preplot GNUPLOT(pictures)

VisualizationVisualization

Use Zmapqtl.out, LRmapqtl.out and Rmap.out

Summarize QTL positions and effects with Eqtl

Display graphs with Preplot and GNUPLOT

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LR Statistic

Position in Morgans

Results of mletest.plt for Trait 1 and Chromosome 1

'c1t1.s''c1t1.lr''c1t1.z3''c1t1.z6'

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0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6

LR Statistic

Position in Morgans

Results of mletest.plt for Trait 1 and Chromosome 2

'c2t1.s''c2t1.lr''c2t1.z3''c2t1.z6'

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0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6

LR Statistic

Position in Morgans

Results of mletest.plt for Trait 1 and Chromosome 3

'c3t1.s''c3t1.lr''c3t1.z3''c3t1.z6'

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0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6

LR Statistic

Position in Morgans

Results of mletest.plt for Trait 1 and Chromosome 4

'c4t1.s''c4t1.lr''c4t1.z3''c4t1.z6'

Computing EnvironmentComputing Environment

Programs written in C language UNIX, MS-Windows and Macintosh

versions are available Command line and menu driven

interfaces Same look and feel over all platforms

AvailabilityAvailability

Free. Source code with UNIX version, binaries for Windows and Macintosh

Anonymous ftp: in /pub/qtlcart on statgen.ncsu.edu

See also: http://statgen.ncsu.edu/ Manual in pdf and html