Association mapping

[1][2] Association mapping is based on the idea that traits that have entered a population only recently will still be linked to the surrounding genetic sequence of the original evolutionary ancestor, or in other words, will more often be found within a given haplotype, than outside of it.

It is most often performed by scanning the entire genome for significant associations between a panel of single nucleotide polymorphisms (SNPs) (which, in many cases are spotted onto glass slides to create "SNP chips") and a particular phenotype.

In response to this concern, Falk and Rubenstein (1987) suggested a method for assessing relative risk that uses family based controls, obviating this source of potential error.

(B) Association mapping in population where members are assumed to be related In the real world it is very hard to find independent (unrelated) individuals.

Still there is one other limitation in population based QTL mapping; when the frequency of the favorable allele should be relatively high to be detected.

The advantages of population based association mapping, utilizing a sample of individuals from the germplasm collections or a natural population, over traditional QTL-mapping in biparental crosses, primarily are due to availability of broader genetic variations with wider background for marker and trait correlations.

Association mapping offers the opportunity to investigate diverse genetic material and potentially identify multiple alleles and mechanisms of underlying traits.

These indirect associations are not randomly distributed throughout the genome and are less common than false positives arising from population structure.

Also called the Q+K model, it was developed to further reduce the false positive rate by controlling for both population structure and cryptic familial relatedness.