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Genomics of African indigenous cattle


Project Description

Queen Mary University of London is announcing an exciting opportunity for an allocated four-year PhD position in the Evolution and Development group in the School of Biological and Chemical Sciences. The successful candidate will start their project in September 2019 and will participate in training and cohort activities of the London NERC DTP.

The London NERC Doctoral Training Partnership brings together eight of the world’s leading research centres in environmental science. Our partnership provides innovative doctoral training in a multidisciplinary research environment and fosters links between centres of research excellence, spanning NERC’s environmental science remit.

About the Project


CASE Partner: Silverstreet Capital

Sub-Saharan Africa is home to a rich but poorly understood diversity of indigenous cattle breeds. Many of the region’s ~150 indigenous breeds show unusual resistance to extremes of climate and disease, and these phenotypic traits are likely to become increasingly important in the face of climate change and mixing of stocks. Despite this, the genes and gene complexes that confer these traits are not known, and this is especially worrying given that many of these local cattle breeds are endangered, facing threats from uncontrolled crossbreeding, as well as from replacement by exotic yet ill-adapted European breeds.

There is a now an urgent need to identify and characterise the genomic diversity of African cattle, to better manage and retain genetic diversity and avoid the permanent loss of desirable traits. This information is not only of research interest: our nonacademic partner SilverStreet Capital has committed substantial funds so that our results can be quickly used to develop a genetic screening programme across the region, with potentially far-reaching impacts. SilverStreet capital focuses on investing in agriculture to improve livelihoods of rural African communities, and is exceptionally well-placed to achieve this goal. The goal of this PhD studentship project will be threefold:

Generate genomic data for representative indigenous cattle breeds. The student will have access to samples from multiple breeds from each of the four broad groups present, termed: Bos indicus (zebu), Bos taurus, sanga (B. taurus/B. indicus hybrids) and zenga (sanga/zebu backcross). With consumables funds contributed by our partner, the student will be able to generate genome–wide data for more than 200 samples. These will include those resident in Silverland Ranching farms, invested in by SilverStreet Capital, as well as those represented by >100 samples collected by collaborators Daniel Bradley (Trinity College, Dublin), and Olivier Hannote (University of Nottingham) [1], and Albano Beja-Pereira (University of Porto) [2]. We will also include trypanosome-tolerant breeds from tsetse fly infested areas. All data will be analysed using existing pipeline developed by supervisor Frantz (see publications list).

Identify genes associated with particular adaptive traits so that these can be used for screening. Recent advances in genomic-assisted breeding (genomic selection) in European breeds have demonstrated that it is now possible to use genomic tools to improve production in specific populations, while limiting inbreeding. Currently these genomic tools are only available for European populations, reflecting the relative lack of genomic research on indigenous African cattle despite their genetic diversity, and the potential socioeconomic importance of their traits. The student will perform analyses to quantify genetic diversity available in African cattle populations, and identify key genetic markers for disease, fertility and drought resistance in the genome of specific populations. Newly discovered markers will then be used to develop a screening panel (Affymetrix SNP array; see impact below). This genomic tool is necessary to pave the way for future genomic selection of cattle breeds in Africa.

Perform genomic analyses to reconstruct the population histories of indigenous cattle breeds. Genetically-varied African cattle breeds have evolved from a complex history of artificial and natural selection. The student will use genomic methods to reconstruct these processes. These analyses will be able to address key questions concerning African cattle, such as the origin and number of introductions of zebu cattle.

For further information please contact the relevant supervisor. Candidates are strongly advised to make contact with the potential supervisor to prior to applying.

How to Apply

Applicants should include a supporting statement, CV, transcripts and certificates, details of two referees, and indicate the relevant supervisor and project title in the application form. Shortlisted candidates will be invited to interview in March 2019.

Please click here to apply: https://mysis.qmul.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app&code1=RFQM-C1ZF-09&code2=0010

Funding Notes

This is a competition funded project. Further details of the studentship and projects offered can be found here: View Website

Please note: NERC funding is subject to candidates meeting RCUK eligibility criteria and we encourage eligible students from the EU to apply. For details of eligibility please click here: View Website

References

[1] Hanotte et al (2002) African pastoralism: genetic imprints of origins and migrations. Science, 296, 336-339.
[2] Beja-Pereira et al (2006) The origin of European cattle: Evidence from modern and ancient DNA. PNAS 103, 8113-8118.

How good is research at Queen Mary University of London in Biological Sciences?

FTE Category A staff submitted: 23.39

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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