Why use linkage maps?
On the basis of recombination frequencies between loci, we may compare genetic distances between loci, and draw them on a linear map according to their estimated genetic distances. Such a drawing we call a linkage map. The most important use for linkage maps is to identify DNA regions that contain markers and genes that are associated with traits of interest. Linkage maps are also referred to as 'genetic maps'. Linkage maps result from statistical calculations of pairwise recombination frequencies between markers and/or genes and ordering and integrating them according to linkage groups, estimating their relative positions and distances. Linkage maps are useful in genetic research and in breeding, because:
- breeding is more efficient if the position of genes of interest is known; also for traits determined by a single gene. For example, when two genes of interest are located on the same chromosome, selection for one gene influences selection for the other gene. If the favorable alleles are linked in coupling phase, the breeder is lucky; if they are linked in repulsion, the breeder should look for recombinants to find both alleles together.
- if such recombinants are needed, given the distance between the genes (or between a gene and a marker), the required population size can be calculated in order to have a certain probability of one or more of the desired recombinants to be found.
- quantitative traits (e.g. yield) usually are controlled by a large number of genes, each possibly with a small effect: a genetic map may help to reveal the genome regions where such genes are
- also for qualitative traits it is sometimes more efficient to select on a closely linked marker allele, or combination of marker alleles, than on the phenotype itself. A genetic map may help to choose the best marker or combination of markers (closely linked, possibly flanking the allele of interest) for selection for a desired allele in breeding
- quantitative traits are often highly dependent on the environment which modifies the phenotype considerably: a genetic map may be useful to bring together genes that contribute to favorable trait values without the disturbing influence of the environment
- genetic maps can be the starting point for a procedure in which a gene of interest is cloned: map-based cloning
- genetic maps can be used for comparative studies among related species, or in evolutionary studies (physical maps might be even more useful)
- genetic maps are used in combination with gene expression studies, metabolomics and proteomics studies to find functional genes and regulatory genes and study gene regulation and genetic and metabolic pathways and networks
Genes that contribute to quantitative traits are often found on different chromosomes. Knowing the number of genes that are associated with variation in the phenotypic trait tells us about the genetic architecture of a trat. It may tell us, for example, that plant length is controlled by many genes with small effects, or by a few genes with relatively large effects. The details of such quantitative trait locus analysis (QTL analysis) will be treated later.
Uses of linkage maps
Once the association between a gene and a marker is shown, markers can be used in breeding programs to select for desirable traits. We will see how this works in the following pages.
Alternatively, once a region of DNA is identified as contributing to a phenotype, the entire region can be sequenced. The DNA sequence of any gene in this region can then be compared to a database of DNA for genes whose function is already known, possibly also from genomic data of other plant species (e.g. the plant model species Arabidopsis thaliana)
The linkage map will show the distribution of markers over linkage groups, ideally corresponding to different physical chromosomes, and approximate positions of markers relative to one another on these linkage groups, and possibly also of markers relative to a linked gene in a genome region. The same linkage map or linkage maps developed on a mapping population developed from different parents, may contain additional markers that are also in that same region. Such additional markers may be used to screen material that segregates for the gene of interest to find markers that are even more closely linked to the gene. The closest linked markers may be used in marker-assisted selection for the trait conferred by the gene.
Summary
→ Linkage maps result from combining all the statistical calculations on recombination frequencies between all marker pairs and converting these into genetic map distances expressed in centiMorgan units
→ Linkage maps indicate which markers are linked and show their relative positions and genetic distances
→ Linkage maps are very useful in genetic research
→ Linkage maps are very useful in breeding for selecting markers that are linked to important genes that confer or contribute to traits of interest. In some cases, such markers may also be used to select in segregating populations for which no linkage map has been constructed.
→ A linkage map can be used to show the approximate position of a qualitative trait gene relative to linked markers, and may suggest which markers in the gene region may be developed as selection markers if these are even more closely linked to the gene of interest.
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