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. 

Conservation via Population Genomics Approaches

Population genomics can be briefly described as the use of genome-wide sampling to identify and separate locus-specific effects from genome-wide effects [1].

Although there are different approaches for population genomics, they all share the following basic steps [1]:

 

When answering a conservation-related question using population genomics techniques, the following approaches are available:

Want to know more about these approaches? A thorough description will be available on our next post. Stay tuned!

References:

[1] Luikart, G. et al. (2003) The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet. 4, 981–994.

Conservation Genetics or Genomics?

For all of you who, like me, are new to this field, a brief description of both conservation genetics and genomics would come in handy. According to Ouborg et al. (2010), conservation genetics is characterized by assessing relationships between population size and neutral sequence variation. But, what is neutral sequence variation? Well, there is a theory called The Neutral Theory of Molecular Evolution; it will help us understand what neutral variation is.

According to The Neutral Theory of Molecular Evolution, the vast Majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants which do not affect fitness, therefore referred to as neutral. [1]

On the other hand, conservation genomics assesses relationships between population size and both neutral and selectively important variation, both in terms of sequence variation and gene expression variation, and thereby incorporates potential effects of selection. Conservation genomics also incorporates the influence of environmental conditions on sequence variation (via selection) and on gene expression variation. [2] 

[2]

References:

[1] Kimura, M (1983). The neutral theory of molecular evolution. Cambridge (page xi)

[2] Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R, Hedrick PW (2010). Conservation genetics in transition to conservation genomics. Trends Genet 26: 177-187. http://dx.doi.org/10.1016/j.tig.2010.01.001

Population Genetics

Can Molecular Genetics Help Save the Puerto Rican Parrot?

An unknown but large number of species are already extinct, while many others have reduced population sizes that put them at risk [1]. For example, Amazona vittatas’s population size decreased in the 19^th century to less than 20 individuals. A. vittata, the Puerto Rican parrot, is the only surviving native parrot species in the United States [2]. Although recovery programs have been established, this species is still severely endangered. 

The advancement of the genomics techniques has had a huge impact on this matter. In order to develop more effective conservation plans, having a better understanding of the genetic causes of A. vittata’s decline was imperative. For this and many other reasons, A. vittata’s genome was selected to be sequenced and assembled. This is the first genome project to be initiated and supported by a local community fundraising efforts, and represents a model for the future de novo genome projects for conservation genetics of nonhuman species [3]. 

Although further sequencing is needed, researchers aim to discover genetic variants that may be important for specific ecological adaptations which in turn contribute to species survival, therefore providing insights for future conservation efforts [3].

References:

[1] R. Frankham, J.D. Ballou, D.A. Briscoe, Introduction to Conservation Genetics, Cambridge University Press, Cambridge, UK, 2002.

[2] Brinkley, D. The wilderness warrior: Theodore Roosevelt and the crusade for America, xv, 940 p. (HarperCollins, New York, 2009).

[3] Oleksyk, Taras. A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome Project funded by a Local Community Effort. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2011.6552.1> (2011)

To look at the sequence go to the following link.

www.genomes.uprm.edu

Contribution of Molecular Genetics and Genomics to Conservation Biology

The combination of results from studies of ecological, ethological, physiological, biological and genetic species indicators provide a variety of processes that actually affect or create the reduction or loss of these organisms in the ecosystem.

In recent times advances in the study of population genetics, phylogeny and phylogeography led to understand the natural history and future populations for management and conservation of endangered species.