Integration of classical linkage maps and molecular maps

Introduction: Genome mapping, a synthesis of concepts from classical genetics using tools from molecular biology and biometrical techniques is a powerful approach for the study of plant biology. Genome mapping is rooted in classical genetic linkage analysis, but recent methodological advances facilitate the mapping of genes responsible for either simple or complex phenotypes. Application of genetic linkage maps in plant genetics and breeding can be greatly facilitated by integrating the available classical and molecular genetic linkage maps. Genetic recombination and gene mapping: The construction of a genetic map involves the linkage analysis of genes segregating among the progenies of a sexual cross. According to the Mendels Law of Independent Assortment, members of different pairs of alleles assort independently of each other when the germ cell is formed. This is only true if the genes are on different chromosomes. If they are on the same chromosome, they are said to be linked. The frequency of recombination of a pair of linked gene is constant and characteristic for that pair of genes. The strength of linkage and recombination observed is a function of the distance on the chromosome between the genes in question.

Source: (Lobo, I. & Shaw, K. (2008) Thomas Hunt Morgan, genetic recombination, and gene mapping. Nature Education 1(1)).

The greater the distance recombination is expected between genes. In other words, the frequency of recombinants (not similar to both the parents) determines the distance between genes. When multiple genes are considered for their recombination frequency, one can group all the genes, which are linked, and the resultant group is called as linkage group. The number of

linkage groups equals the haploid number of chromosomes. The early work on linkage map construction was mainly based on the segregation of easily observable morphological traits among the progenies of a cross. Construction of genetic linkage maps: A linkage map is a representation of the position of genes (or markers) within a linkage group. The map positions are inferred from estimates of recombination frequencies between genes. The earliest linkage maps contained, in most cases, only a few morphological markers, mostly representing genes for which mutant phenotypes were available. Usually only two or three marker genes were segregating simultaneously, so that linkage maps had to be assembled from a number of different experimental populations. The earliest linkage maps contained, in most cases, only a few morphological markers, mostly representing genes for which mutant phenotypes were available. Usually only two or three marker genes were segregating simultaneously, so that linkage maps had to be assembled from a number of different experimental populations. Nevertheless, even before the advent of molecular markers, so called multi-marker lines were constructed for a number of plant species (barley, maize, Arabidopsis). These multi-marker lines carried mutant alleles at a number of loci, so that these loci would segregate simultaneously in the offspring (F 2) when crossed with a wild type. The problem with multi-mutant lines is that these are very often crippled phenotypes, since most mutants have a deleterious effect (e.g. chlorophyll deficiency, dwarfism, malformation of flowers, deterioration of development, etc.) so that such lines are hard to maintain, and, additionally, the phenotype of one mutant can often only be clearly recognized in absence of another mutant. Sequential assembling of an integrated linkage map from various data sets

Maps A, B and C are obtained from different mapping populations. Integration is possible with the anchor loci that are common to two or more data sets. There are several examples of linkage maps resulted from the morphological traits, otherwise called as morphological markers. Morphological markers are easily observable traits with discrete phenotype. Though these markers are highly advantageous, the number is the limitation. Further, these markers are influenced by the environment and the genetic background of the individual. The rapid development of molecular markers facilitates the utilization of these markers for the construction of molecular genetic maps in plants. To make the most of all the molecular and genetic information currently available, there is, however, one condition to be met and that concerns the correlation of the classical map with the molecular map. As both maps have been made independently with a limited number of markers in common and in different genetic backgrounds, they only partially match and provide as yet limited information about the relative positions of classical and molecular markers. Most of the classical map positions have been calculated on the basis of linkage data collected from different and sometimes relatively small sized populations, without the use of mathematical procedures that take into account standard deviations and correct for double crossovers. Thus, the map position and relative order of various markers is questionable and in some cases already shown to be wrong. Only after integrating the classical and molecular maps, can a physical/genetic map be constructed that allows one to choose the proper DNA probes for walking to a target gene. The integration of the classical genetic and molecular maps would make molecular tagging of agronomically important genes previously located on the classical genetic map relatively straightforward. The amount of time and effort devoted to gene mapping will be minimized because only molecular markers which are located in the region of the target genes need to be evaluated. Construction of integrated map is possible by linkage analysis in crosses that involves chromosomes from the parents that has been utilized for molecular as well as classical genetic mapping and it should segregate for both classical and molecular markers. Here F 2 populations were analyzed for morphological and molecular markers. Mostly integrated map has been developed chromosome wise in different crops. Integrated map act as a bridge to understand between classical and molecular linkage maps.

References: Lobo, I. & Shaw, K. (2008) Thomas mapping. Nature Education 1(1). Hunt Morgan, genetic recombination, and gene

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