Our research uses a combination of QTL and eQTL mapping using a chicken model to map the genetic basis of behavior, weight, bone density, color and other domestication traits.
The term QTL is a combination of Quantitative Trait, that is a continuous trait like height, weight, or behavior, and Loci, meaning location. QTL mapping as a technique enables geneticists to find the regions in the genome which control for specific traits. For example: there are lots of genes which affect height, meaning there are lots of QTLs that affect height.
Because the domestic phenotype is so far removed from the original wild state, studying domestic by wild crosses gives us a great deal of variation to work with. For example a modern broiler chicken is six or seven times heavier than the original Red Jungle fowl chicken. This large variation in continuous traits make it easier to map individual QTLs and their effects. The figure opposite shows the different traits that we have analysed and the genes that appear to be responsible.
In the late 1980's and early 1990's several powerful hurricanes struck Hawaii, destroying thousands of chicken coops. The domesticated chickens that escaped started becoming feral and interbreeding with the locally present Red Junglefowls. This has led to a fantastic opportunity to study large-scale feralisation, the process by which previously domestic animals become feral, and most specifically the genomic changes associated with feralisation.
In collaboration with Dr. Eben Gering from Michigan State University, I now study the process of feralisation amongst Hawaii's escaped chickens. We study which regions of the chicken genome responds to feralisation and what genes change i frequency, in order to start mapping the corresponding traits and creating a model for the ‘reverse of domestication’.
Group members: Rie Henriksen, Maria Luisa Martin Cerezo, Robin Abbey-Lee
illustration taken from Callaway et al. 2016 Nature from a News Feature highlighting our work (copyright Nature Publishing).
Genetic Basis for Brain-to-Body Ratio
The predominant view on brain-to-body ratio has for a long time been that there is an allometric relationship between brain and body size, i.e. that you need a certain brain size to maintain a certain body size. However, my group's research has shown that in chickens it is possible to independently select genes for brain size and body size. For example, domestic animals have often been thought of as somewhat less smart, and when one looks at their brain-to-body ratio they have a lower ratio than their wild progenitor.
By looking at the underlying genetic architecture for brain mass and body mass, however, my group has discovered that domestic chickens actually have larger, not smaller, brains than their wild counterparts. Thus brain size and body size can be decoupled, and it is possible to select for a larger birds without selecting for a larger brain. This can have large repercussions in terms of evolutionary biology, as relative brain size (that is brain size over body size) is often used to compare different species.
If it is possible to select for increased body size without selecting for increased brain size, this method may be flawed. Further to this, by looking at individual substructures of the brain, it is possible to pinpoint the regions that are most associated with domestication selection – in the case of the chicken, the cerebellum seems to be particularly enlarged in the domestic bird.
Group members: Rie Henriksen
The genetic basis of quantitative colour variation
Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic x wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.
Group member: Jesper Fogelholm
The Genetics of Anxiety Behavior
It has been postulated that the first thing to change in domestic animals is their fear of humans as domestic animals cannot be too afraid of humans without impairing our ability to breed them. This has enabled my group to use a domestic by wild cross to discover which genes affect anxiety behavior.
My group has found that some of the genes that are central for anxiety selection in chicken intercrosses are also present in a mouse cross, and were affecting the same behavior in the mice as in the chickens. When comparing these particular genes with gene sets in humans with bi-polar disorder and schizophrenia, we also found evidence that the same genes may be related to anxiety disorders in humans. We have even found evidence to support this in the fruit fly where, by down-regulating some of the genes found in chickens, we were able to affect the same type of open field behavior in transgenic flies.
This gives the idea that the genes found in the domestic by wild paradigm can be transferred to practical applications in other fields. For example, we found genetic links to schizophrenia and has used the chicken as a model for osteoporosis.
The genetic basis of cave adaptation in Asellus aquaticus
A new project that is just starting in the group aims to identify the genetic basis that underlies adaptation to a cave environment in a small water-borne crustacean, Asellus aquaticus. We are using a cave population and a nearby stream population that is closely related yet does not display the pigment or other adaptations (eye loss, body shape) seen in the cave individuals.
Group members: Vid Bakovic