Interval Mapping
(IM) is an extension of single marker analysis and it can do analysis on any genomic location flanked by two markers. IM uses complete marker
linkage
maps for genomic scanning (LR or LOD profile) for
Quantitative Trait Loci
(
QTLs
).
Composite Interval Mapping
(CIM) is an extension of IM analysis that uses a combination of IM with multiple
regression
. CIM can improve the precision of QTL mapping in the situation of multiple QTLs in one
chromosome
.
The
IM and CIM Analysis (Single QTL Model)
process performs both types of mapping. Three SAS data sets are required: an
Input Data Set
of cross information, an
Annotation Data Set
that includes map information, and a
genotype
probability data set that includes probability information about the QTL genotypes.
Three SAS data sets are required. The first, the
input cross file, lists information about the different genetic crosses used in the study. The
qtlbcsample_geno.sas7bdat
data set, used in the following example, is shown below. This is a wide data set with 300 individuals listed in rows and the status of individuals for two
traits
and 36 markers, spanning 3 chromosomes, listed in columns. Markers are formatted as numeric genotypes.
The second required data set is an
Annotation Data Set
that
lists map information for each of the markers.
The
qtlbcsample_anno.sas7bdat
annotation data set
, used in the following example, is shown below. This data set contains 4 columns listing the name and position (in cM) of 36 markers present on three chromosomes.
The third required data set is a
genotype probability data set
that l
ists the probabilities of observing specific QTL genotypes at each one cM interval along the chromosome(s) represented by the markers in the input data set. The
qtlbcsample_geno_gp.sas7bdat
genotype probability data set, shown below, lists probabilities for QTLs for the 300 individuals listed in the input data set (rows 3 through 302). Row 1 specifies the relevant chromosome, row 2 specifies the position (cM), and row 3 indicates markers (1 indicates marker and 0 inter-marker position).
The
qtlsfsample_geno.sas7bdat
,
qtlsfsample_anno.sas7bdat
, and
qtlbcsample_geno_gp.sas7bdat
data sets are located in the
Sample Data\QtlMapping
directory included with JMP Genomics.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
The output generated by this process is summarized in a Tabbed report. Refer to the
QTL IM, CIM and MIM Analysis
output documentation for detailed descriptions and guides to interpreting your results.