ABSTRACT
A total of 272 individuals from 12 indigenous Nigerian cattle breeds – Sokoto Gudali (21), Red Bororo (22), Adamawa Gudali (25), Kuri (2), Wadara (3), Bunaji (23), Friesian × Bunaji (24), N‘Dama (23), Azawak (2), Keteku (13), Yakanaji (12) and Muturu (12) with five indigenous Ugandan cattle breeds – Karamonjong (16), Sereres (13), Sahiwal Zebu crosses (13), Nganda (23) and Ankole (25) were genotyped for 777,962 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, admixture levels, and relationships. Among the Nigerian cattle populations, the observed heterozygosity varied from 0.582 in Friesian × Bunaji to 0.773 in Muturu with a mean of 0.676 and varied from 0.648 in Karamonjong to 0.622 in Nganda with a mean of 0.637 across all Ugandan cattle populations. The expected heterozygosity in the Nigerian cattle breeds ranged from 0.642 in Muturu to 0.638 in Red Bororo with a mean of 0.641 and ranged from 0.635 in Karamonjong to 0.632 in Serele/Teso Zebu with a mean of 0.633 across all Ugandan cattle populations. The gene flow (N(nm)) value combining all 12 Nigerian breeds, amounted to 0.979 and that of Ugandan cattle breeds amounted to 0.953. In turn, when gene flow was examined within breed and country, gene migration in the Nigerian cattle population ranged from 0.981 in Muturu to 0.975 in Red Bororo with the greatest gene migration of 0.955 observed in Karamonjong and the lowest was observed in the Serere (0.950) in the Uganda cattle population. The inbreeding coefficient estimate (FIS) in Nigerian cattle revealed that within population variation accounted for approximately 10.5% of the total genetic variation and 1.6% of the total genetic variation in Ugandan cattle. In the Nigerian cattle populations, only 3056 (0.46%) of 4235 SNPs markers significantly deviated from HWE (p < 0.05, p < 0.01), as where in Ugandan cattle
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populations, 98 (0.02%) of the markers appeared to be in disequilibrium. The first and second principal components explained approximately 15.54 % and 3.66% of the total variation in Nigerian and Ugandan cattle populations respectively and supported the clustering of the populations according to their historical origins and geographical locations. A considerable source of variation among cattle was exhibited at low cross-validation (K = 2, 3, and 4) clustering the populations into African Taurine, European Taurine, African Zebu and detecting the Zebu introgression in African Taurine breeds. Genetic distance, principal component analysis, and population structure analyses, admixture analyses and phylogenic tree, clearly differentiated the cattle population according to their historical origins, and confirmed that Nigerian cattle populations were genetically distinct from the Ugandan cattle populations. This study indicated the necessity for a balance between improving livestock productivity and the conservation of cattle breeds at risk of extinction in Nigeria and the Nganda in Uganda. Hitherto, these populations have represented a unique genetic resource and unexploited opportunity that warrants initiatives for their sustainable conservation and utilization.
TABLE OF CONTENTS
Cover page…………………………………………………………………………….
Title page…………………………………………………………………………….. Declaration…………………………………………………………………………….
Certification……………………………………………………………………………….
Dedication………………………………………………………………………………
Acknowledgement…………………………………………………………………….
Abstract…………………………………………………………………………………..
Table of contents.……………………………………………………………………….
List of tables…………………………………………………………………………..
List of figures…………………………………………………………………………..
List of plates…………………………………………………………..……………….
CHAPTER ONE: Introduction………………………………………………………………..
Problem statement………………………………………………………….
Justification of the study……………………………………………………
Research questions…………………………………………………………
Aim and objectives of the study………………………………………….
CHAPTER TWO:
Literature review…………………………………………………………..
Classification of cattle………………………………………………………
The origin of the domesticated cattle….………………………………….
African cattle genetic resources……………………………………………
Cattle sub-species and breeds in Nigeria…………………………………..
Cattle sub-species and breeds in Uganda………………………………….
Conservation of domestic animal diversity………………………………
Meaning and importance of domestic animal diversity…………………….
Loss of genetic diversity in domestic animals………………………………
Loss of diversity within population…………………………………………
Loss of diversity among populations………………………………………..
Approach to conservation of animal genetic diversity………………………
Genetic markers……………………………………………………………
Microsatellites……………………………………………………………….
Single Nucleotide Polymorphisms (SNPs)………………………………….
Genetic distances in population genetics………………………………….
Genetic distances between individuals using the proportion of shared alleles…………………………………………………………………………
Genetic distances between subpopulations………………………………….
Methodologies in population structure analysis………………………….
Distance based methods……………………………………………………..
Model based methods (STRUCTURE/ADMIXTURE)……………………..
CHAPTER THREE:
Materials and methods……………………………………………………
Location of the study……………………………………………………..
Nigeria……………………………………………………………………….
Uganda………………………………………………………………………
Tissue sampling……………………………………………………………..
Deoxyribonucleic Acid (DNA) extraction………………….……………
Single Nucleotide Polymorphisms (SNP) genotypes.……………………
Data Analyse……………………………………………………….………
Determination of the genetic diversity in the indigenous cattle populations from Nigeria and Uganda…………………………………………………….
Determination of the population structure and admixture levels in the indigenous cattle populations from Nigeria and Uganda…………………….
Determination of the relationship within and between the indigenous cattle populations from Nigeria and Uganda……………………………………….
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CHAPTER FOUR:
Results………………………………………………………………………
Genetic diversity in the indigenous cattle populations from Nigeria and Uganda………………………………………………………………………
Population structure and admixture levels in the indigenous cattle populations from Nigeria and Uganda…………….………………………
Exploratory factor analysis of the indigenous cattle populations from Nigeria and Uganda……………………………….……………………..…..
Population structure of the indigenous cattle populations from Nigeria…….
Population structure of the indigenous cattle populations from Uganda……
Population structure of the indigenous cattle populations from Nigeria and Uganda………………………………………………….……………………
Estimation of genetic admixture proportion in the indigenous cattle populations from Nigeria and Uganda……………………………….………
Admixture levels in the indigenous cattle populations from Nigeria……….
Admixture levels in the indigenous cattle populations from Uganda……….
Admixture levels in the indigenous cattle populations from Nigeria and Uganda……….……………………………………………………………………..
Phylogenetic relationship among the indigenous cattle populations within and between Nigeria and Uganda…………………………………
Phylogenetic relationship among the indigenous cattle populations within Nigeria……………………………………………………………………………………………….
Phylogenatic relationship among the indigenous cattle populations within Uganda………………………………………………………………………………………………
Phylogenetic relationship among the indigenous cattle populations within and between Nigeria and Uganda………………………………………………………….
CHAPTER FIVE:
Discussion………………………………………………………….…………
Genetic diversity in the indigenous cattle populations from Nigeria and Uganda………………………………………………………………………
Population structure and admixture levels in the indigenous cattle populations from Nigeria and Uganda……………………………………
Phylogenetic relationship among the indigenous cattle populations within and between Nigeria and Uganda………………………..………..
CHAPTER SIX:
Summary, conclusion and recommendations…………………………….
Summary……………………………………………………………………
Conclusion………………………………………………………………….
Recommendations…………………………………………………………..
References……………………………………………………………………
CHAPTER ONE
INTRODUCTION
Domesticated animals, especially cattle, are an important source of protein in African countries including Nigeria and Uganda. Increasing this protein resource requires the conservation of diversity among indigenous cattle breeds. In order to cope with an unpredictable future, genetic reserves that are capable of readily responding to directional forces imposed by a broad spectrum of environments must be maintained (Hannotte and Jianlin, 2005).
Maintaining genetic diversity is an insurance against future adverse conditions. In Africa, diversity among environments and nutritional standards as well as challenges from multiple infectious agents require diverse breeds and populations. The breeds therefore act as storehouses of genetic variation, which form the basis for selection and may be drawn upon in times of biological stress such as famine, drought or epidemics. The wide range of breeds and species that have evolved in various environments represent unique sets of genetic diversity (Hanotte and Jianlin, 2005).
It has been estimated that since domestication, over 6,379 documented breed populations from 30 species of livestock have been developed globally in the last 12 thousand years (FAO, 2000). It is generally accepted that the highest amount of genetic diversity in these populations of livestock is found in the developing world, where record- keeping is poor and the risk of extinction is high and is increasing. Recently, loss of genetic diversity within indigenous livestock breeds has been a major concern. The number of mammalian breeds at risk of extinction has increased from 8 to 19% since 1995 (FAO, 2000). The situation with bird breeds is even more serious with the total percentage of breeds at risk of being lost
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increasing from 20% in 1995 to 34% in 1999″ (FAO, 2000). More particularly, it is estimated that 22% of known livestock breeds have become extinct in the last 100 years and another 27% are at varying degrees of risk (Rege and Tawah, 1999). The losses, as well as the risk to existing cattle breeds, have been partially blamed on indiscriminate crossbreeding between exotic breeds and indigenous animals (Rege and Tawah, 1999).
Globally, this realization has led to efforts to study genetic diversity in livestock species in order to provide a foundation for conserving these potentially-useful germplasms. In addition to loss of diversity, a large proportion of domestic animal breeds in the world is believed to be in danger of extinction (Cardellino, 2004). According to Hanotte and Jianlin (2005), though it may be too late for many livestock and poultry breeds in Europe, optimism in the developing world about slowing down the loss of both diversity and indigenous animals is high. Conservation of indigenous animal resources has been proposed as a method for slowing down the loss in diversity in livestock breeds through extinction.
Apart from preventing extinction, conservation of indigenous cattle breeds is also important for the future health of the animal industry globally as they could be a resource for novel genes that can permit sustained genetic improvement as well as enable adaptation to changing breeding objectives and environments (Notter, 1999). In order to ensure proper conservation and utilization of indigenous cattle breeds, it is necessary to evaluate genetic variations that exist within and among breeds. A large proportion of indigenous livestock populations in the developing world have yet to be characterised or evaluated at phenotypic and genetic levels (Hanotte and Jianlin, 2005).
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In the case of African cattle, genetic classification of cattle breeds is still needed. Most existing classifications of cattle breeds in Africa including Nigeria and Uganda are based on historical, anthropological and morphological evidence, which are most often not enough for the purpose of conservation (Tawah and Rege, 1996; Rege and Tawah, 1999; Rege, 1999; Mwacharo et al., 2006). Relative genetic diversity can be determined using phenotypic characteristics and/or molecular markers. Phenotypic characteristics of cattle breeds as well as their adaptive characteristics are important in identifying breed attributes for immediate use by farming communities. In one of the few studies reported, Mwacharo et al. (2006) phenotypically characterised two breeds of Zebu in Kenya. The authors identified 12 morphometric measurements to differentiate the Masaai Zebu from the Kamba Zebu in Kenya. The apparent wide within-breed and between-breed variations in linear body dimensions that were observed in the study were indicative of the large genetic diversity inherent in the small East African Zebu cattle (Mwacharo et al., 2006).
The advent of molecular techniques has led to an increase in studies that focus on the genetic characterisation of domestic breeds using genetic markers (Giovambattista et al., 2001). As a tool used in evaluating genetic variation, markers can provide useful information at different levels and purposes such as structure of animal populations, levels of gene flow, phylogenetic relationships, patterns of historical biogeography, and parentage (Feral, 2006). In addition, genetic assessment is also of interest for the design of genetic improvement programmes including appropriate choice of breeds for crossbreeding (Mwacharo et al., 2006).
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1.1 Problem Statement
The indigenous cattle populations of Western and Eastern Africa are vital to the subsistence and economic development of these regions, providing essential food products, sustaining the employment and income of millions of West and East Africans living in the rural areas, and providing manure as well as draught power used in ploughing and transport. In comparison to their exotic counterparts, these cattle are better adapted to survive and reproduce under the region’s harsh environments. Many of the cattle breeds are named after the community, which keeps the population, or according to geographical localities they inhabit, and the true genetic relationship among the major populations is not yet well known or documented. They are currently at risk of extinction due to indiscriminate crossbreeding and replacement with exotic breeds, uncontrolled introgression and interbreeding, absence of breed development programmes and political instability, and immediate steps must be taken to conserve them (Rege and Gibson, 2003; Hanotte et al., 2010).
The erosion of locally-adapted genetic resources will significantly limit the option and capacity to cope with changes to production environments and breeding goals. Understanding of farm animal genetic diversity is therefore required to contribute to meeting current production needs in various environments, to allow sustained genetic improvement, and to facilitate rapid adaptation to changing environments and breeding objectives (Notter, 1999; Köhler-Rollefson et al., 2009; Hanotte et al., 2010).
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1.2 Justification of the study
Despite their importance, these cattle have not been well-defined, classified or studied adequately in the past. Their current classification based on historical and anthropological evidence, and phenotypic data is inaccurate, making implementation of rational conservation and utilisation strategies difficult. The high levels of Zebu genes reported in some African Taurine breeds by Hanotte et al. (2002) is particularly alarming and the African Taurines stand to lose their identity should this trend continue. It is therefore necessary to assess the levels of African Zebu genes, African Taurine and the European Taurine genes in African cattle breeds, particularly the Taurines to enable their effective management.
Previous studies focused on genetic diversity and structures of Nigerian cattle populations (Adebambo et al., 1998) and Ugandan cattle populations (Okomo, 2002; Kugonza et al., 2011) have used low density microsatellite, mitochondrial, or Y-chromosome markers. However, in recent years, analyses of single nucleotide polymorphism (SNP) markers are becoming the standard approach for diversity analysis and genome-wide studies. They represent one of the more interesting approaches for genotypization because they are abundant in the genome, genetically stable, and amenable to high throughput automated analysis (Vignal et al., 2002).
The usefulness of SNPs in analyses of population diversity and structure has been demonstrated in several studies (McKay et al., 2008; Lin et al., 2010). The identification of genomic SNPs will provide an opportunity to apply genome based association studies in the future (Matukumalli et al., 2009; The Bovine HapMap Consortium, 2009). Despite a large number of SNPs identified in the bovine genome sequencing project, few have been
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validated in tropical cattle populations. Breed characterisation requires basic knowledge of genetic variations that can be effectively measured within and between populations.
1.3 Research questions
Africa is rich in cattle genetic resources being the repository for a number of native breeds adapted or selected for production in tropical, sub-tropical, or marginal production environments. This gives rise to the following research questions for this study:
1. To what extent are the native cattle breeds from Nigeria and Uganda genetically diversified?
2. What is the genetic population structure and admixture levels of the native cattle breeds from Nigeria and Uganda?
3. What is the genetic relationship between the indigenous cattle populations from Nigeria and Uganda?
1.4. Aim and objectives of the study
The broad objective of this study is to apply genomic tools to aid the characterisation of the structure of bovine genomes of selected Nigerian and Ugandan native breeds of cattle and then analyze this data to better understand the relationships among African breeds and also between native and popular European breeds. To be able to distinguish between breeds for conservation and utilization purposes, the determination of the genetic variability, population structure and phylogenetic relationships using genomic tools led to the formulation of the following specific objectives for this study.
1. To quantify the extent of genetic diversity within the indigenous cattle breeds in Nigeria and Uganda based on 777,962 SNP marker genotypes.
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2. To determine the population structure and admixture levels of the indigenous cattle breeds in Nigeria and Uganda.
3. To determine the phylogenetic relationships among the indigenous cattle breeds within Nigeria and Uganda.
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