Simple Interval Mapping (SIM), Lander, Bostetein, Composite Interval mapping, Epistasis, Environment interactions

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Home >> Plant Biotechnology and Genomics >>Construction of Molecular Maps and Synteny (Collinearity) >>Simple Interval Mapping (SIM)

Simple interval mapping (SIM) that was proposed initially by Lander and Botstein in 1989, and used subsequently in early 1990s suffered with some serious problems. For instance, it allowed identification of one QTL at a time, ignoring the effect of other QTLs in the background of the concerned genome. Furthermore, it was not possible to determine the precise location and number of QTLs; nor was it possible to estimate the non-allelic QTL x QTL interactions (epistasis) and the QTL x environment interactions. In view of these limitations of SIM, modified forms of interval mapping like composite interval mapping (CIM) and multiple interval mapping (MIM) were suggested and are now being increasingly used for QTL analysis. These modified forms take into account the QTLs that are present in the background and allow estimations of epistasis and (QTL) x environment interactions. A number of softwares that are available for QTL interal mapping include MAPMAKER/QTL QTLSTAT, QTL Cartographer, MAPQTL, QGENE, etc.

In the above methods of QTL marker linkage anaylsis, no distinction can be made between a group of tightly linked loci, each with small effect and a single locus of large effect for a QTL. A distinction between these two situations may be important for fundamental as well as for applied studies, since selection strategies may differ in two cases, and also because studies at the molecular level are often conducted at individual gene level. However, the success of genetic improvement based on selection of markers still remains to be widely used and will be effective only in specific cases. Further, it may not be necessary to use this method in cases where direct selection is more convenient and economic.

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