Landscape genomic approach to investigate genetic adaptation in South African indigenous goat populations by Khanyisile Mdladla Submitted in fulfilment of the academic requirements of Doctor of Philosophy in Genetics School of Life Sciences College of Agriculture, Engineering and Science University of KwaZulu-Natal Pietermaritzburg South Africa December 2016 PREFACE The research contained in this thesis was completed by the candidate while based in the Biotechnology Platform, Agricultural Research Council and the Discipline of Genetics, School of Life Sciences of the College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa. The research was financially supported by University of KwaZulu-Natal, National Research Foundation-Department of Science and Technology (NRF-DST) and the Agricultural Research Council. The contents of this work have not been submitted in any form to another university and, except where the work of others is acknowledged in the text, the results reported are due to investigations by the candidate. _________________________ Signed: Edgar Farai Dzomba Date: _________________________ Signed: Farai Catherine Muchadeyi Date: i DECLARATION 1: PLAGIARISM Note that two declaration sections are required if there are papers emanating from the dissertation/thesis. The first (obligatory) declaration concerns plagiarism and the second declaration specifies your role in the published papers. I, Khanyisile Mdladla declare that: (i) the research reported in this dissertation, except where otherwise indicated or acknowledged, is my original work; (ii) this dissertation has not been submitted in full or in part for any degree or examination to any other university; (iii) this dissertation does not contain other persons’ data, pictures, graphs or other information, unless specifically acknowledged as being sourced from other persons; (iv) this dissertation does not contain other persons’ writing, unless specifically acknowledged as being sourced from other researchers. Where other written sources have been quoted, then: a) their words have been re-written but the general information attributed to them has been referenced; b) where their exact words have been used, their writing has been placed inside quotation marks, and referenced; (v) where I have used material for which publications followed, I have indicated in detail my role in the work; (vi) this dissertation is primarily a collection of material, prepared by myself, published as journal articles or presented as a poster and oral presentations at conferences. In some cases, additional material has been included; (vii) this dissertation does not contain text, graphics or tables copied and pasted from the Internet, unless specifically acknowledged, and the source being detailed in the dissertation and in the References sections. ______________________________________ Signed: Khanyisile Mdladla Date: ii DECLARATION 2: PUBLICATIONS My role in each paper and presentation is indicated. The * indicates corresponding author. Chapter 2 1. Mdladla, K., Dzomba, E.F., and *Muchadeyi, F.C. 2016. The potential of landscape genomics approaches in the characterization of indigenous goat genetic resources: A South African Perspective. Submitted to Small Rumuinant Research. Chapter 3 2. Mdladla, K., Dzomba, E.F. and *Muchadeyi, F.C. 2017. Characterization of the village goat production systems in the rural communities of the Eastern Cape, KwaZulu-Natal, Limpopo and North West Provinces of South Africa. Tropical Animal Health and Production. DOI 10.1007/s11250-017-1223-x. Chapter 4 3. Mdladla, K., Dzomba, E.F. and *Muchadeyi, F.C. 2016. Seroprevalence of Ehrlichia ruminantium antibodies and its associated risk factors in indigenous goats of South Africa. Preventive Veterinary Medicine 125, 99-105. Chapter 5 4. Mdladla, K., Dzomba, E.F., and *Muchadeyi, F.C. 2014. Linkage disequlibrium and population structure of South African indigenous goat populations using genome wide SNP data. A poster presented during the 47th South African Animal Science (SASAS), held on the 6-8th July 2014 in Pretoria, South Africa. Presented by Mdladla K. 5. Mdladla, K., Dzomba, E.F., Huson, H.J., and *Muchadeyi, F.C. 2014. The 47th South African Animal Science (SASAS), held on the 6 to 8th July 2014 in Pretoria, South Africa. Work was presented at the student session held on the 6th July 2014. Presented by Mdladla K. 6. Mdladla, K., Dzomba, E.F., Huson, H.J., and *Muchadeyi, F.C. 2014. Linkage disequlibrium and population structure of South African indigenous goat populations using genome wide SNP data. iii A poster presented during the 34th International Society for Animal Genetics Conference, held on 27th July 2014 to 1st of August 2014 in Xian, China. Presented by Mdladla K. 7. Mdladla, K., Dzomba, E.F., Huson, H.J., and *Muchadeyi, F.C. 2014. Linkage disequlibrium and population structure of South African indigenous goat populations using genome wide SNP data. The 34th International Society for Animal Genetics Conference, held on 27th July 2014 to 1st of August 2014 in Xian, China. Work was presented at the Livestock Genomics for Developing Countries Workshop, held on 29th of July 2014. Presented by Mdladla K. 8. Mdladla, K., Dzomba, E.F., Huson, H.J., and *Muchadeyi, F.C. 2014. Linkage disequlibrium and population structure of South African indigenous goat populations using genome wide SNP data. The 34th International Society for Animal Genetics Conference, held on 27th July 2014 to 1st of August 2014 in Xian, China. Work was presented at the ISAG-FAO Workhop on Animal Genetic Diversity, held on 29th of July 2014. Presented by *Muchadeyi F.C. 9. Mdladla, K., Dzomba, E.F., Huson, H.J., and *Muchadeyi, F.C. 2015. Population structure and Breed relations of South African indigenous goat ecotypes using genome-wide SNP data. The 23rd International Plant and Animal Genome research, held on 10th to 14th January 2015 the in San Diego, CA. Work was presented at the International Goat Genome Consortium Workshop held on 12th of January 2015. Presented by Mdladla K. 10. Mdladla, K., Dzomba, E.F., Huson, H.J., and *Muchadeyi, F.C. 2015. Population structure and Breed relations of South African indigenous goat ecotypes using genome-wide SNP data. A poster presented at the 23rd International Plant and Animal Genome research, held on 10th to 14th January 2015 the in San Diego, CA. Presented by Mdladla K. 11. Mdladla, K., Dzomba, E.F., Huson, H.J. and *Muchadeyi, F.C. 2016. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data. Animal Genetics 47, 471-482. Chapter 6 12. Mdladla, K., Dzomba, E.F., and *Muchadeyi, F.C. 2016. Landscape genomics approach in understanding adaptation of indigenous goats to their environment. The 35th International Society for Animal Genetics Conference, held on 23rd July 2016 to 27th of July 2016 in Utah, Salt Lake City, USA. Work was presented at the Applied Sheep and Goat Genetics Workhop, held on 26th of July 2016. Presented by Mdladla K. iv 13. Mdladla, K., Dzomba, E.F., and *Muchadeyi, F.C. 2016. Landscape genomics approach in understanding adaptation of indigenous goats to their environment. A poster presented during 35th International Society for Animal Genetics Conference, held on 23rd July 2016 to 27th of July 2016 in Utah, Salt Lake City, USA. Presented by Mdladla K. 14. Mdladla, K., Dzomba, E.F., and *Muchadeyi, F.C. 2016. A landscape genomics approach to explain the genetic diversity in South African indigenous goats. A poster presented during 4th South African Genetics Society (SAGS) and South African Society for Bioinformatics (SASBi) Joint Congress, held on 20th September 2016 to 23rd of September 2016 in Durban, KwaZulu- Natal. Presented by Mdladla K. _______________________ Signed: Khanyisile Mdladla Date: v EXTENDED ABSTRACT Traditional indigenous goat breeds have evolved the crucial ability to adapt and survive in challenging environments and ecological conditions associated with their geographical origins. The environments are heterogeneous and production conditions fluctuate with seasons. Although indications of local adaptation have been reported in most indigenous goats and other livestock species, there are many unknowns regarding the genetic mechanisms that determine the response of indigenous goats to their production and climatic environments. There is potential for these goats to be used for sustainable improvement of productivity in the tropics through combining ecologically adaptive and economically important production traits. Identifying regions that are potentially adaptive in indigenous goats will allow us to explore the adaptive potential for specific environments. This is particularly relevant now when goats and other livestock species are faced with immense production, climatic and other natural selection pressures. South Africa for example is endemic to heartwater and a number of goat populations are frequently exposed and need to adapt. There has been major developments in appropriate genomics technologies such as next-generation sequencing (NGS) and genome wide single nucleotide polymorphism (SNP) BeadChips, and bioinformatics analytical methods, which will facilitate comprehensive characterization of these genetic resources. The study targeted the major goat producing provinces and analysed the diversity in production systems, and the morphological variations of the indigenous goats that they keep, prevalence of heartwater and how