Genetic Linkage Maps: Strategies, Resources and Achievements - Genetics, Genomics and Breeding of Crop Plants - page 98

since the advent of molecular markers. Many computer packages have been
developed for constructing linkage maps with molecular marker data
collected from various mapping populations. The sunflower genome
mapping community has used the following three mapping computer
programs.
3.4.2.1 MapMaker
MapMaker is the most popular program for linkage map construction for
crop plant species. An earlier version was released in 1987 (Lander et al.
1987) and was upgraded MAPMAKER/EXP v3.0 in 1992 (Lincoln et al.
1992). MAPMAKER/EXP uses an efficient algorithm to perform full
multipoint linkage analysis for dominant, recessive, and co-dominant
markers segregating in experimental mapping populations such as F 2 , BC 1 F 1
and RILs. MAPMAKER includes an interactive command language that
makes it easy to use. MapMaker has been applied to the construction of
most published sunflower linkage maps. Almost all researchers used the
default LOD value of 3.0 or higher for the grouping and three-point
commands and the Kosambi mapping function (default is Haldane) in the
mapping. The weak point of MapMaker is that it lacks an MS-Windows
operating system interface. But who can complain about such a remarkable,
highly utilized program when it has been free?
3.4.2.2 JoinMap
JoinMap was developed to combine (“join”) data derived from several sources
into an integrated map (Stam 1993, 1995; Van Ooijen et al. 2001). The newest
release of this commercial program is JoinMap 4.0, which has an
MS-Windows user interface and much added practical functionality.
JoinMap can generate publication-ready map charts from experimental data
collected from a variety of population types: BC 1 , F 2 , RIL, F 1 -derived and F 2 -
derived doubled haploid (DH), out-crossing full-sib families. JoinMap is
powerful in linkage group determination, and has the ability to automatically
determine linkage phases for markers segregating in the out-breeding full-
sib family. JoinMap also embodies several diagnostic tools, such as testing
segregation distortion, checking similarity of loci, checking similarity of
individuals, and calculating genotype probabilities conditional on map
and flanking genotypes to discover double recombination before and after
the actual map construction. Detailed information on JoinMap can be found
at http://www . kyazma.nl/index.php/mc.JoinMap . JoinMap has been used by
several researchers in constructing their linkage maps (Gedil et al. 2001;
Mimic et al. 2004, 2005; Lai et al. 2005).