Candidate Gene, Genome Scanning and Association Mapping Approaches

As we mentioned on our last post, there are different approaches for answering conservation-related questions, using population genomics techniques. Today, we are going to describe three of them.

A candidate gene is a gene known to have a biological and or functional impact on a specific trait or disease. Usually, the candidate gene approach is used in case-control studies in which mutations on a certain gene (or genes) are analyzed. For example, to identify genetic risk factors for complex disorders such as alcoholism, this approach tests the effects of genetic variants of a potentially contributing gene in an association study [1].

The genome scan approach identifies marker loci that are linked to selectively-relevant target loci through ‘genetic hitch-hiking’ [2].

v  Marker loci: DNA sequence with a known location on a chromosome that can be used to identify individuals or species

v  Genetic hitch hiking: process by which an allele may increase in frequency by virtue of being linked to a gene that is positively selected [3]

ü  Positive selection: increases the prevalence of adaptive traits

Method of mapping quantitative trait loci that involves searching for genotype-phenotype correlations in unrelated individuals [4].

v  Quantitative trait: a trait that has measurable phenotypic variation and/or environmental influences. Two classic examples of quantitative traits are height and weight. The loci that modulate these traits are therefore called QTLs [5].   

References:                        

[1] "The candidate gene approach". Alcohol Res Health 24 (3): 164–8. 2000. PMID 11199286.

[2] Smith, J.M., Haigh, J., 1974. Hitch-hiking effect of a favorable gene. Genet. Res. 23, 23–35.

[3] Barton, N H (2000-11-29). "Genetic hitchhiking". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 355 (1403): 1553–1562.

[4] Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, et al. (2009) Association mapping: critical considerations shift from genotyping to experimental dsign. Plant Cell 21: 2194-2202.

[5] Abiola O, Angel JM, Avner P, et al. (2003) The nature and identification of quantitative trait loci: a community’s view. Nat Rev Genet. Nov;4(11):911-916.