The proposed PhD project will be linked to the activities of the Centre for Tropical Livestock Genetics and Health (CTLGH). SRUC is a founding partner of CTLGH together with the University of Edinburgh and the International Livestock Research Institute (ILRI).
Poultry production holds an important position in the agricultural sector in sub-Saharan Africa and is a key protein source. The majority of production is in smallholder village farms where birds are raised in scavenging conditions.
The objectives of the proposed project are to (i) characterise survival, health, growth and meat production in a sub-Saharan African chicken population raised in village conditions and (ii) identify genomic regions, markers and genes involved in the molecular control of these traits.
The student will have access to phenotypic and genotypic data on 2,500 chickens raised in said conditions in Ethiopia. Phenotypes available on each bird include: (i) Live bodyweight (weekly) and growth rate (ii) survival during the growth period and cause of death, when applicable, (iii) specific disease episodes and treatments recorded during the growth period, (iv) carcass weight at slaughter and (v) breast meat weight at slaughter. Genome-wide genotypes will also be available for all birds. Furthermore, whole-genome sequence data will be available on 24 birds with extreme aggregate phenotypes and genotypes (combination of the studied traits). Within the project, the above data will be collated by the student and quality controlled. Phenotypic data will be analysed to assess impact of environmental effects on the studied traits. Phenotypic variances and correlations between bird traits will be calculated. Subsequently, genomic association and prediction analyses will take place using bird genotypes and phenotypes. Genomic heritability estimates will be derived for each trait. These analyses will reveal genetic markers and genomic regions associated with bird survival, health, growth and meat production. Birds will then be split into groups of high and low values for each studied trait, and genotypes will be further analysed to detect selection signatures and compare between groups. Finally, the student will analyse the whole-genome sequencing data mentioned above using systems biology approaches to highlight relevant gene pathways and networks controlling the studied traits.
In addition to advanced statistical methodology, Machine Learning approaches based on deep-learning will be considered in the analyses, using existing infrastructure at SRUC.
Key outcomes: (1) Phenotypic and genomic characterisation of survival, health, growth and meat production in chickens raised under scavenging conditions in Ethiopia. (2) Tools (genetic markers, genomic regions) for selection to improve the studied traits of these chickens. (3) Candidate genes and mutations affecting the studied traits of the chickens. These outcomes will inform genetic improvement programmes aiming to enhance chicken productivity in sub-Saharan Africa.
The PhD student will have the opportunity for training in advanced statistics, genomic association and sequence data analyses, Machine Learning, and systems biology approaches. The student will interact with collaborators at SRUC, the University of Edinburgh and ILRI in Ethiopia.
Applicants should download the required forms from http://www.eastscotbiodtp.ac.uk/how-apply-0
and send the following documents to [email protected]
a. EASTBIO Application Form
b. EASTBIO DTP Equality Form
d. Academic transcripts (a minimum of an upper second class or first class honours degree or equivalent is required for PhD study
e. Two references should be provided by the deadline using the EASTBIO reference form (http://www.eastscotbiodtp.ac.uk/how-apply-0
). Please advise your referees to return the reference form to [email protected]
f. If you are nominated by the supervisor(s) of the EASTBIO PhD project you wish to apply for, they will provide a Supervisor Support Statement.