The idea of using markers to map in such families is to trace inheritance of existing human pedigrees as if one had set up crosses in the laboratory. After a decade of first discovery of molecular markers, the very first genome map in plants was reported in maize and tomato (Helentjaris et al., 1986) using RFLP marker in a F2 population. The familial linkage methods were very popular for qualitatively inherited molecular markers and traits of interest in humans, animals and plants. Later on the focus was turned to more complex traits – quantitatively inherited traits with high environmental influence. Such complex traits are affected by both environment and genes. Study designs for mapping: Experimental Population vs Natural Population  Natural populations include collection of individuals from a natural habitat connected with or without having pedigree. Pedigree data, if available are unmanipulated i.e. not crossed in experimenter’s interest. Pedigree can not be manipulated in human and some of animals and leaves no options of using natural populations including families whatever available in nature (for review: mapping in natural populations by Slate, 2005). QTL analysis in such population is challenging because the number of alleles segregating at the QTL is unknown, the marker phases may be unknown or only partially known, the marker and QTL allele frequencies must be estimated from the data, inbreeding loops may exist in the pedigree, and markers may be noninformative or ungenotyped. Although it is possible to simplify the analysis of complex pedigree data by fragmenting the pedigree into smaller component families, methods that fully account for complex relationships between individuals are expected to provide greater power to detect QTL (Almasy and Blangero 1998). General natural pedigree are analyzed using a mixed effects model in which components of variance (e.g. additive genetic variance, maternal effects, environmental variance) can be estimated from a pedigreed population of individuals of any structure (Slate, 2005. Variance components are usually estimated by restricted maximum-likelihood (REML). Natural population can be further classified into mapping populations consisting of related individuals (family pedigrees) or unrelated populations. Experimental crosses  The traditional experimental crosses are based on single experimental cross, such as the backcross, F2 or full-sib family, initiated with two different lines. The principle behind genetic mapping that uses an experimental cross is the occurrence of recombination events between genetic loci (measured by the recombination fraction) when gametes are formed and transmitted from parents to offspring. By estimating the recombination fraction between markers and QTLs, the genomic location of the QTL of traits can be determined.