CHARACTERIZATION OF LOCAL PIGS (Sus scrofa) IN GHANA

BY

ADJEI, DENNIS OWUSU

(10397186)

THIS THESIS IS SUBMITTED TO THE UNIVERSITY OF GHANA, LEGON, IN

PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE AWARD OF
MASTER OF PHILOSOPHY DEGREE IN ANIMAL SCIENCE

DEPARTMENT OF ANIMAL SCIENCE

COLLEGE OF AGRICULTURE AND CONSUMER SCIENCES

UNIVERSITY OF GHANA

DECEMBER, 2014
 DECLARATION

I, DENNIS OWUSU ADJEI, author of this thesis entitled “Characterization of local pigs

(Sus Scrofa) in Ghana” do hereby declare that this thesis is the result of my own original

work and that no part of it has been presented for another degree in this university or

elsewhere. All assistance towards the production of this work and all the references

contained herein have been duly credited.

………………………………

DENNIS OWUSU ADJEI

This work has been submitted for examination with our approval as supervisors:

…………………………….

Dr. Richard Osei-Amponsah

(MAJOR SUPERVISOR)

…………………………..

Prof. Benjamin K. Ahunu

(CO- SUPERVISOR)

i
 DEDICATION

I dedicate this work to my late parents; Emmanuel Kofi Agyei, Cecilia Mensah and
sister; Marian Owusu Adjei, who passed away without seeing any of my achievements.
May all your souls rest in perfect peace.

ii
 ABSTRACT

Characterization is essential for the conservation and sustainable utilization of farm

animal genetic resources, especially indigenous breeds that are at risk of extinction due to

their lower production potential compared to the exotic breeds. The objective of this

study was to characterize local pigs and their production systems in Ghana. A total of 163

local Ashanti Black Pigs and their crossbreds sampled from six regions were involved in

the study. Results indicated meat production (33.2%), savings (32.3%), manure (16.1%),

breeding (11.5%) and cultural and social demands (7.87%) as reasons for raising local

pigs. Local pigs were characterized as having a predominantly concave head profile

(85.89%), black coat colour (67.48%), plain coat colour pattern (72.39%) and erect ears

(84.66%). The production system was mainly free range extensive (56%). Prevalent

diseases were diarrhoea (40%), mange/lice infestation (27%), with few anaemic

conditions (6%) due to poor husbandry practices. Prediction of live body weight using

linear body measurements suggest that either body length alone or body length in

combination with heart girth could be used to estimate live weight in local pigs in

instances where weighing scales are not available. Phylogenetic studies based on

mitochondrial DNA of local pigs from the coastal savannah zone indicated an influence

of European and Asian wild boars on the Ghanaian local pig. Admixtures between local

pigs in the sampled areas were found and these confirmed their multiple ancestries

Although, there appeared to be diverse genetic origins of the Ashanti Black Pigs, the

results showed a remarkable closeness to the European Sus haplotypes. The need to

improve husbandry practices and carry out further characterization studies on local pigs

was recommended.

iii
 ACKNOWLEDGEMENTS

I wish to express my profound gratitude to the Almighty God for the numerous

blessings He bestowed on me throughout my study period.

My heartfelt gratitude goes to my major supervisor, Dr. Richard Osei-Amponsah,

for his noble hearted help, financial support, cooperation, and encouragement which have

instilled in me the spirit of confidence to successfully complete this research work.

I am greatly indebted to my co-supervisor, Prof. Benjamin K. Ahunu, for his

dedication, commitment, critique and invaluable suggestions towards the success of this

research.

I thank the Head of Department of Animal Science and all Senior Members for

their suggestions which helped me to improve on the work. I acknowledge support of

senior staff and AEAs of APD/MOFA particularly Mr. Edwin Bekoe, Mr. Francis

Freeman and Mr. Obrien Nyarko as well as Mr. Benjamin Allenlogre, Miss Mary Awini,

and Mr. Stephen Kanten of the University of Development Studies for their help in data

collection.

My sincere gratitude goes to the Alborada Trust and CAPREX (Cambridge Africa

Partnership for Research excellence) awarded to my Supervisor which enabled us to

undertake the data collection molecular characterization aspect of this work.

Appreciation to Prof. Serekye Yaw Annor, of University of Education, Winneba

(UEW-M), Prof. Getrude Aboagye, Mr. Anthony Amison Agbolosu, Mr. Douglas Amoo

Acheampong, Mr. Coleman Fred Newman, Mr. MacCarthy Vuvor and Mrs. Rejoice

Frimpong, all of Department of Animal Science, University of Ghana, for their

inspiration and encouragement throughout my study period.

iv
 Finally, my warm gratitude to Nana Oheneba Opoku and family, my lovely sisters

(Joana Owusu Agyei and Nancy Owusu Adjei), brothers (Clement Owusu Agyei,

Kingsley Owusu Agyei and Frank Adu Gyamfi) as well as good friends especially Mr.

Richard Owusu, Daniel Kwasi Kpeglo, Kwasi Darkwah and finally to staff of St

Monica’s Junior High School, for their tender-loving care extended to me in the course of

pursuing this work.

To all who contributed in diverse ways for making this work successful, I say

may God richly bless you all.

v
 LIST OF ACRONYMS AND ABBREVIATIONS

ABP Ashanti Black Pig

AEA Agriculture Extension Agent

AGTR Animal Genetics Training Resource

AnGR Animal Genetic Resources

APD Animal Production Directorate

ASF African Swine Fever

CACS College of Agriculture and Consumer Sciences

CGRFA Commission on Genetic Resources for Food and Agriculture

DNA Deoxyribonucleic acid

FAO Food and Agriculture Organization

MAFF Ministry of Agriculture, Fisheries and Food

MCL Maximum Composite Likelihood

MoFA Ministry of Food and Agriculture

MtDNA Mitochondrial DNA

NBAGR National Bureau of Animal Genetic Resources

NCBI National Center for Biotechnology Information

NLBS Nungua Livestock Breeding Station

USDA United States Department of Agriculture

VSD Veterinary Service Directorate

vi
 TABLE OF CONTENT

DECLARATION ................................................................................................................. i
DEDICATION .................................................................................................................... ii
ABSTRACT ....................................................................................................................... iii
ACKNOWLEDGEMENTS ............................................................................................... iv
LIST OF ACRONYMS AND ABBREVIATIONS .......................................................... vi
TABLE OF CONTENT .................................................................................................... vii
LIST OF TABLES .............................................................................................................. x
LIST OF FIGURES .......................................................................................................... xii
LIST OF PLATES ........................................................................................................... xiii
LIST OF APPENDICES .................................................................................................. xiv
CHAPTER ONE ................................................................................................................. 1
INTRODUCTION .............................................................................................................. 1
1.1 Background ................................................................................................................... 1
1.2 Problem Statement ........................................................................................................ 6
1.3 Justification ................................................................................................................... 7
1.4 Hypothesis..................................................................................................................... 7
1.5 Objective of the Study .................................................................................................. 7
CHAPTER TWO ................................................................................................................ 8
LITERATURE REVIEW ................................................................................................... 8
2.1 Livestock in the economy ............................................................................................. 8
2.2 Animal Genetic Resources ............................................................................................ 9
2.3 Origin, genetic diversity and importance of pigs (Sus scrofa).................................... 12
2.4 Local Pig Genetic Resource of Ghana ........................................................................ 15
2.5. Pig production systems .............................................................................................. 17
2.6. Characterization of Animal Genetic Resources ......................................................... 21
2.6.1 Phenotypic characterization of AnGR .............................................................. 25
2.6.2. Genetic characterization of AnGR .................................................................. 27
2.7. Importance of Live Weight in Livestock ................................................................... 28
2.8. Measurement of body weight..................................................................................... 29
2.9. Population Genetic Studies ........................................................................................ 31
2.9.1. Genetic diversity and variation ........................................................................ 32

vii
 2.9.3 Genetic distances .............................................................................................. 36
2.10. Phylogenetic analysis ....................................................................................... 37
CHAPTER THREE .......................................................................................................... 41
MATERIALS AND METHODS ...................................................................................... 41
3.1 Location and period of study ...................................................................................... 41
3.3 Sampling size and sampling technique ....................................................................... 44
3.4. Data collection ........................................................................................................... 45
3.5. Statistical analysis for morphological characterization ............................................. 46
3.6. Molecular Characterization........................................................................................ 48
3.6.1. Sample collection ............................................................................................ 48
3.6.2. DNA extraction................................................................................................ 48
3.6.3 DNA amplification and Sequencing ................................................................. 49
3.6.4. Genetic analysis ............................................................................................... 50
CHAPTER FOUR ............................................................................................................. 51
RESULTS ......................................................................................................................... 51
4.1 General information on local pig farmers ................................................................... 51
4.2 Morphological Characterization of Local Pigs in Ghana ........................................... 52
Morphological characterization of local pigs in Ghana involved both qualitative and
quantitative measurements. ....................................................................................... 52
4.2.1. Qualitative variables ........................................................................................ 52
4.2.2. Quantitative variables ...................................................................................... 53
4.3. Characterization of pig production systems ............................................................... 56
4.3.1 Type of farming systems practiced by local pig farmers .................................. 56
4.3.2. Herd size .......................................................................................................... 57
4.3.3. Reasons for raising local pigs .......................................................................... 57
4.3.4. Preference for the local pig breed .................................................................... 59
4.3.5. Challenges being faced by local pig farmers ................................................... 59
4.3.6. Prevalent pig diseases in the study areas ......................................................... 61
4.4. Prediction of live body weights of ABP and its crossbreds based on linear body
measurements. ........................................................................................................... 62
4.5. Molecular characterization of local pigs in selected districts of the coastal Savannah
zone of Ghana ............................................................................................................ 63

viii
CHAPTER FIVE .............................................................................................................. 66
DISCUSSION ................................................................................................................... 66
5.1 General information on local pig farmers ................................................................... 66
5.2 Morphological characterization of local pigs in Ghana .............................................. 66
5.2.1. Number of teats ............................................................................................... 67
5.2.2. Coat colour type and pattern ............................................................................ 67
5.2.3. Head and snout characteristics ........................................................................ 68
5.2.4. Ear type and orientation ................................................................................... 68
5.2.5. Tail type and backline characteristics .............................................................. 68
5.2.6. Body hair type and skin ................................................................................... 68
5.2.7 Effect of age and sex on linear body measurements ........................................ 69
5.3. Characterization of production systems ..................................................................... 69
5.3.1. Type farming systems practiced by local pig farmers ..................................... 69
5.3.2. Herd size .......................................................................................................... 71
5.3.3. Reasons for raising local pigs .......................................................................... 72
5.3.4. Preference for the local pig breed .................................................................... 72
5.3.5. Challenges faced by local pig farmers ............................................................. 74
5.3.6. Prevalent Pig diseases in the study areas ......................................................... 75
5.3.7. Basic temperament .......................................................................................... 75
5.4. Prediction of live weights of ABP and its crossbreds based on linear body
measurements ............................................................................................................ 75
5.5. Molecular characterization of local pigs in the coastal savannah zone of Ghana ..... 77
CHAPTER SIX ................................................................................................................. 78
CONCLUSIONS AND RECOMMENDATION ............................................................. 78
6.1 Conclusions ................................................................................................................. 78
6.2 Recommendations ....................................................................................................... 78
REFERENCES ................................................................................................................. 80
APPENDICES ................................................................................................................ 113

ix
 LIST OF TABLES

Table 1: Least-squares means for morphological variables by breed type and the

corresponding levels of significance………………………………………………26

Table 2: Prediction equations for live weight based on stepwise regression analysis in

NIPs and Crossbreds………………………………………………………………30

Table 3: Location, sex and type of breed sampled for the study……………………...…44

Table 4: Traits of morphological (Quantitative) measurements in pigs…………………45

Table 5: Traits of morphological (Qualitative) variables in pigs ………………………..46

Table 6: Background local pig farmers………………….……………………………….51

Table 7: Number and percentages of local pigs showing the various morphological

characteristics ……………………………………………………………………52

Table 8: Effect of age on linear body measurements (Means ± Standard Error)………..54

Table 9: Summary statistics on the effect of sex on linear body measurements of local

pigs by age groups…………………………………………………………………...55

Table 10: Other vocations of local pig farmers...…………………………………….….57

Table 11: Herd size of sampled pig farms………………….……………………………57

Table 12: Reasons for raising local pigs in Ghana………………………………………58

Table 13: Reasons for raising local pigs...……………………………………………….58

Table 14: Prediction equations for live weight of ABP and their Crossbreds based on

simple linear and multiple linear regression analysis……………………..…………62

x
Table 15: Mean Genetic Distance within Sus Groups (±Standard Errors)........................65

Table 16: Genetic Distance between Sus Groups (lower diagonal)...................................65

xi
 LIST OF FIGURES

Figure 1: Map of Ghana showing selected ecological zones and regions sampled……...43

Figure 2: Farming systems of local pig production in Ghana……...…………………….56

Figure 3: Prevalent diseases in the study areas…………………………………………..61

Figure 4: Phylogenetic tree involving Ghanaian local pig haplotypes, European Sus

haplotypes, Asian Sus haplotypes and African Warthog…………………………….64

xii
 LIST OF PLATES

Plate 1: ABP (boar) at the Babile Pig Breeding Station, Upper West……………….…..15

Plate 2: Typical housing structures used for local pigs…………………………………..60

Plate 3: Weighing scale used and how local pigs were weighed…………………...…..117

Plate 4: Taking weight of pigs at research or Government farms……………………...118

Plate 5: Picture of how tail of local pigs were measured…………….…………………119

Plate 6: A crossbred (ABP x Large White) showing patchy coat colour pattern, semi-lop

ears projecting forward, a concave head type, long and cylindrical snout type……121

Plate 7: ABP with a long and curly body hair type……….…………………………….122

Plate 8: An ABP with a plain coat colour pattern, straight tail and a swaybacked

backline…………………………………………………………………..…………123

Plate 9: ABP and Large White pig being kept in the same pen……………...…………124

xiii
 LIST OF APPENDICES

Appendix 1: Questionnaire used in characterization of local pigs…………………......113

Appendix 2: Morphometric measurements of local pigs in Ghana………….…………117

Appendix 3: Animal and sampling information for molecular characterization……….120

Appendix 4: Phenotypic diversity of sampled pigs ……………………………….…...121

Appendix 5: Images of husbandry practices………………………………….………...124

Appendix 6: Estimates of live weight for local pigs based on their BL and HG……….125

xiv
 CHAPTER ONE

INTRODUCTION

1.1 Background

Domesticated animals, especially livestock and poultry, are important sources of protein

in human diets. Livestock is a major source of livelihood for many communities’

worldwide, particularly resource-poor smallholder farmers (Wanzala et al., 2005).

Globally, the human population is expected to increase from around 6.5 billion to at least

8.2 billion by 2050 (Rosegrant et al., 2009). More than 1 billion of this increase will

occur in Africa. The demand for animal protein in the world will continue to increase due

to the expanding human population, rapid urbanization and rising incomes leading to

increased consumption of animal products (Swanepoel et al., 2010; FAO, 2011).

Livestock contributes about 40 percent to the agricultural gross domestic product (GDP)

globally and constitutes about 30 percent of the agricultural GDP in the developing world

(World Bank, 2009). The purposes of raising livestock go beyond their output functions

and include other significant socio-economic and socio-cultural roles. These include

savings, insurance, cyclical buffering, accumulation and diversification, as well as

various socio-cultural roles related to status and the obligations of their owners

(Anderson, 2003; Halimani et al., 2010). In marginal areas with harsh environments,

livestock provide a means of reducing the risks associated with crop failure and a

diversification strategy for resource poor small scale farmers and their communities

(Freeman et al., 2007; Thornton et al., 2007; Vandamme et al., 2010). Livestock

production in Ghana is important to the country’s agriculture. The sub sector is estimated

1
to contribute about 9% to the nation’s agricultural gross domestic product (GDP) and is a

source of income for several rural farm households especially in the northern part of the

country where livestock are referred to as a “walking bank” and provide financial

reserves, serving as a “risk–cropping strategy”, which is a buffer during crop failures and

in periods of economic stress (ILRI, 2012).

Most of the indigenous breeds have relatively low production potential encouraging

crossbreeding with exotic breeds to improve upon their productivity. On the other hand,

locally adapted breeds have evolved and adapted to various environmental conditions and

therefore represent an important genetic resource. In most cases, breeds that are not very

profitable under current production and market conditions are left out and run the risk of

extinction and once lost, genetic material is irreplaceable (FAO, 2007).

The global diffusion of the foreign breeds is endangering or even risking the extinction of

many well adapted local breeds. A number of reports show that many locally adapted

animal genetic resources (AnGR) are endangered and, unless urgent concerted efforts are

taken to conserve them, may be lost even before they are described and documented

(Rege and Lipner, 1992). It is known that an increasing loss of genetic diversity has over

the years been observed for all agriculturally used species (Frankham, 1994; Hammond,

1994; Ollivier et al., 1994). In 2007, the State of the World’s Animal Genetic Resources

for Food and Agriculture revealed that approximately 10% of farm animal breeds have

become extinct and an additional 15% are endangered. Moreover, the situation as at 2007

was unknown for 34% of the breeds, most of which are raised in developing countries

2
including Ghana (FAO, 2007) whilst no conservation programmes exist for more than

75% of the threatened breeds (Okeyo et al., 2005).

However, livestock diversity provides genetic alternatives and thus contributes in many

ways to human survival and well-being, including contribution to supporting sustainable

agricultural development pathways. Despite the importance of this diversity, one-third of

livestock breeds worldwide are at risk of becoming extinct and the rate of extinction

continues to accelerate (FAO, 2000; Drucker and Anderson, 2004).

FAO (2011) revealed that the diversity of animal genetic resources is continuously

decreasing and that potential of the remaining diversity for increasing food security and

improving livelihoods is not being fully realized. Globally, this realization has led to

efforts to study genetic diversity in livestock species in order to provide a foundation for

conserving them (FAO, 2011).

Pig contributes significantly to the total development of most developing countries

(Rosegrant et al. 2009). The pig has some unique advantages over all other animals,

which make them a good species of animals to multiply extensively to minimize protein

shortages. Among these advantages are their fast growth rate which is only slightly

exceeded by the best, carefully managed broilers, their prolificacy which is unsurpassed

by that of any other animals species except the birds, their very good efficiency of feed

utilization which brings better returns per units of inputs than most other animals and the

quality of their meat which is both tender and more nutritive in terms of the contents of

protein and the B-vitamins than those of other animals (Ogunniyi and Omoteso, 2011).

3
Two main factors shaped the genetic variability of pig populations and other mammals.

The first comprises of large climate changes in the Pleistocene (Hofreiter et al., 2004)

while the second is human intervention during the Holocene (i.e. roughly the last 10,000

years). Interactions between humans and Sus scrofa have contributed markedly to the

current variation in the latter species due to, most notably, domestication (Larson et al.,

2005, 2007; Scandura et al., 2008). The greatest dangers of climate change relates to its

adverse impact on feed availability, disease distribution and pig welfare (Finocchiaro et

al., 2005; FAO, 2008; Hoffmann, 2010).

The risk of losses of livelihoods due to climate change is very high and only species and

individuals that are responsive to change are likely to survive (Gregory, 2010).

Consequently, genetic resources that are capable of readily responding to directional

forces imposed by a broad spectrum of environments must be maintained.

Local pigs are known to be hardy, tolerant to most common diseases and have the ability

to survive under poor management and extremes of environmental conditions (Ahunu et

al., 1995; Darko and Buadu, 1998). For instance, in 1983, Ghana experienced a drought

which brought about food shortage in the whole country. Most of the exotic breeds could

not withstand as a result of starvation but the indigenous pig breed, Ashanti Black Pig

(ABP) survived (Barnes and Fleischer, 1998).

Although the production potential of indigenous breeds is low, they form a valuable

genetic resource base which must be maintained, since they are well adapted to the

different, sometimes harsh, production systems in our developing countries. It is

important to develop and utilize local breeds that are already adapted to their

4
environments, most of which are harsh, with very limited natural and managerial input

(FAO, 2007).

The pig is a highly prolific animal; however, the growth of the pig industry in Ghana has

for some reasons not been able to keep pace with the growth of the human population,

hence low animal protein availability to the ever growing population (Eledi, 2013). This

situation creates room for the importation of both live pigs and processed pork. Besides,

the situation does not only adversely impose heavy strain on the country’s foreign

exchange reserves but also poses a serious threat to our local pig genetic resources.

The most rational and sustainable way to conserve animal genetic resource is to ensure

that locally adapted breeds remain in the final part of the production system (Wollny,

2003). To ensure that smallholder livestock farmers continue to thrive, improvement in

livestock production and production system is vital. Once diversity is lost, it is expensive

and difficult to make changes. Existing AnGR thus represent a massive past investment

which, if managed appropriately, can provide insurance against an unknowable global

future (Rege and Gibson, 2003).

Studying genetic diversity of AnGR is of immense scientific interest for understanding

phenotypic variation (FAO 2007) and for reconstructing the history of livestock

(Ajmone-Marsan et al., 2010; Groeneveld et al., 2010). It is widely accepted that detailed

molecular data on within- and between-breed diversity are essential for effective

management of Animal Genetic Resources (AnGR) (Toro and Caballero, 2005).

5
1.2 Problem Statement

Small-scale producers rely mainly on local breeds adapted to their particular farming

conditions and scarce feed resources whose hardiness makes them ideal for low-input

production systems. Due to population growth and increased living standards, a rapid

growth in consumption of animal products has motivated the livestock industry to adapt

and expand in order to satisfy societal demands (SAADC, 2013).

The exotic breeds are part of AnGR but their husbandry practices (in terms of feeding,

housing and veterinary care) make them difficult for local farmers to raise. Local pigs on

the other hand have low production potential but do not need any intensive husbandry

systems to survive. The low productivity of local breeds (poor growth and low

reproductive performance) have shifted farmers attention to exotic breeds leading to most

cases indiscriminate introduction of exotic genetic resources, before proper

characterization, utilization and conservation of indigenous genetic resources (FAO,

2007).

Characterization is a key activity in the development of a sustainable management plan of

animal genetic resources (AnGR) and is a priority of the Global Plan of Action for AnGR

(FAO, 2007). Characterization contributes to the reliable prediction of genetic

performance of AnGR in a defined environment and provides a basis for distinguishing

between different animal genetic resources and for assessing available diversity (Rege,

1992).

Despite the multiple adaptive traits of local pigs in Ghana, they have not been

comprehensively characterized. There is therefore a need to characterize these local pigs

to provide required data needed for their sustainable use and conservation.

6
1.3 Justification

The proposed study will help fill the significant gaps of knowledge in phenotypic and

genetic diversity of local pig genetic resources in Ghana.

It will help authorities to put in place conservation schemes to ensure sustainable use of

local pigs. Conservation of indigenous breeds will also help in the future health of the

animal industry in Ghana as they could be a resource for novel genes that can permit

sustained genetic improvement of pigs as well as their adaptation to changing breeding

objectives and environments in the future. It will also provide information on local pig

genetic resources which in turn will enable us to understand the extent of differentiation

within population of the species.

1.4 Hypothesis

Characterization of Ghana’s local pigs genetic resources will provide essential

information on their unique attributes needed to develop breeding programs for their

sustainable use.

1.5 Objective of the Study

In this study therefore, we characterized local pig genetic resources of Ghana and their

production systems.

The specific objectives were to;

 characterize local pigs morphologically

 characterize local pig production systems

 use linear body measurements to predict body weights of local pigs

 determine genetic diversity of local pig genetic resources

7
 CHAPTER TWO

LITERATURE REVIEW

2.1 Livestock in the economy

Agriculture is the primary means of meeting the nutritional needs of the world’s

population and in Ghana, it employs about 60% of the working population and

contributes about 40% to Ghana’s gross domestic products (GDP) (World Bank, 2007).

The livestock industry is an important part of agricultural development growing faster

than any other agricultural subsector and is expected to contribute more than 50% of the

global sales of the total agricultural output by 2015 (Cao, 2013). Livestock products

provide 17% of the global kilocalorie consumption and 33% of protein consumption

globally, but there are large differences between rich and poor countries (Rosegrant et al.,

2009). The increase in food demand will increase demand for livestock and its products

in the world (FAO, 2009).

Biodiversity is the product of thousands of years of activity during which humans have

sought to meet their needs in a wide range of climatic and ecological conditions. Well

adapted livestock have been a key element of agricultural production systems (FAO,

2007). The ability to maintain and increase their productivity, and to adapt to changing

circumstances, remains vital to the food security of the world’s population (FAO, 2014).

The same organization also reported that the livestock sector in particular, is undergoing

dramatic changes as large-scale production expands in response to surging demand for

meat, milk and eggs (FAO, 2007). Genetic variability within and among populations and
8
breeds serves as an indicator of population dynamics, inbreeding, and level of admixture

among populations (Li et al., 2007; Wilkinson et al., 2011). Evaluation of these will

provide valuable information necessary to decide on breeding strategies for individual

breed development, and to identify the suitable production systems and conditions for the

respective breeds (Hanotte and Jianlin, 2005).

2.2 Animal Genetic Resources

Animal Genetic Resources (AnGRs) comprise all animal species, breeds and strains (and

their wild relatives) that are of economic, scientific and cultural interest to humankind in

terms of food and agricultural production for the present or in the future (FAO, 2007).

There are some 40 species and 7616 breeds of AnGR that have been domesticated

(Diamond, 2002). Several of the main farm animals (cattle, sheep, goats and pigs) were

domesticated 9,000 to 11,000 years ago and the chicken ~4,500 years ago (Giuffra et al.,

2000; Larson et al., 2007). Whereas humans seem to have expanded enormously from a

small population present roughly 100,000 years ago, most domestic animals have a much

broader genetic basis (Andersson, 2001). Domestic livestock have since then, spread with

human migrations and trading to all inhabited continents. Reshuffling of genes at each

generation, mutation, and cross-breeding or admixture of different gene pools has created

new dimensions for natural and human selection. This has been the root of the many

returns in output achieved in commercial breeds, and of the adaptation of indigenous

livestock to highly diverse and challenging environments (FAO, 2007).

It has been estimated that about 50% of the total livestock genetic variation is between

species and the remaining is accounted for by variation among breeds within species

9
(AGTR, 2011). Globally, domestic AnGR supply some 30% of total human requirements

for food and agriculture (FAO, 2007). They are particularly vital to subsistence and

economic development in developing countries. In rural areas, livestock are important

sources of food and cash for the purchase of consumer goods and procurement of farm

inputs (Rege and Gibson, 2003) and to provide essential food and other products (hides

and skins), draft power and manure for crop production. Food from livestock and poultry

are rich in energy, protein, vitamins and micronutrients, which are particularly important

in the diets of the most vulnerable groups, that is children and pregnant and breast

feeding women particularly in developing countries (Perry et al., 2002; Ndlovu, 2010).

Domestic animals also play an important role as cash reserves in low-income mixed

farming systems. It has been estimated that more than 70% of the world’s rural poor

depend on livestock as a component of their livelihoods (LID, 1999). In Ghana for

instance, livestock keeping serves as insurance against food deficits that occur frequently

in the Upper East Region (ILRI, 2012).

Production of hides, skin, wool and manure, environmental health, storage of wealth, and

socio-cultural functions and traditions are other roles of livestock (Rege and Gibson,

2003). Empirical evidence of the contribution of livestock to sustainable livelihoods of

the world’s rural poor exists, including the potential for improvement of such livelihoods

through investment in livestock development in all developing regions of the world

(Okeyo et al., 2005).

10
A number of species face risk of extinction and important conservation decisions must be

made. Food and Agriculture Organization (FAO) global survey indicates that more than

730 breeds or lines of pigs throughout the world and more than 270 breeds out of that are

in danger of extinction and others are threatened by inefficient use or loss due to cross

breeding (FAO, 2007). The 2010 report on the global survey on breed diversity also

classified 631 breeds as extinct, and 1,710 breeds (21%) as being at risk (CGRFA, 2010).

For a population to survive environmental modification it must have sufficient genetic

diversity to adapt to new conditions; less genetically diverse populations are thus at a

greater risk. Animals genetically adapted to these conditions are expected to be more

productive at lower costs, support food, agriculture and cultural diversity, and be

effective in achieving local food security objectives (Ruane and Sonnino, 2006). Local

communities depend on these adapted genetic resources in many countries and their

disappearance or drastic modification may therefore have serious negative impacts on

human population (FAO, 2006).

The combination of environmental change and dwindling genetic diversity means that

many species must survive greater stress with reduced genetic resources. Exotic livestock

breeds have been introduced into developing countries for pure breeding and crossing

with indigenous breeds to increase productivity and food production (Okeyo et al., 2005).

Farmers have shifted their attention to exotic breeds because of higher income gained

than the indigenous breed when they are sold. These exotic breeds are considered to be

more productive, but the problem is that these animals are mainly suited to the conditions

11
of the countries they were developed and as such have difficulty in adapting to the

environment of Africa (Wollny, 2003). Thus a significant threat to domestic animal

diversity in the developing world is the continuous importation of high performing

animals from developed countries for crossbreeding and replacement of local breeds

(Chimonyo et al., 2005; 2010). Local pigs for instance are often crossed with imported

boars to take advantage of heterosis (Madzimure, 2011).

2.3 Origin, genetic diversity and importance of pigs (Sus scrofa)

The genus Sus includes ten species: Sus ahoenobarbus, S. barbatus, S. bucculentus, S.

cebifrons, S. celebensis, S. oliveri, S. philippensis, S. salvanius, S. scrofa, and S.

verrucosus (Grubb, 2005; Chen et al., 2007). Sus scrofa shows the largest geographic

distribution (Oliver and Leus, 2008). It is estimated that around 3.0 - 3.5 million years

ago Sus scrofa emerged in South East Asia and dispersed into India and East Asia

moving westwards until reaching Europe (Larson et al., 2005, 2010; Ramirez et al., 2009;

Groenen, 2012).

These historical events have had an enormous impact on the genetic diversity of pig

breeds, leaving a footprint that can be recognized nowadays. A series of genetic studies

have also demonstrated that the consequence of this process have been a higher genetic

diversity of Sus scrofa in Asia and Europe (Larson et al., 2005; Wu et al., 2007; Ramirez

et al., 2009; Luetkemeier et al., 2010).

Domestic pigs can be found worldwide because of their extraordinary importance in the

production of red meat, lard and cured products (Amills et al., 2010; Timoneda et al.,

2014). The profitability of a pig industry depends on the ability of the sow to produce

12
large litters and wean most of them under ideal environmental conditions and

management techniques (Okai et al., 1982). The survivability of the weaned litters

depends on several factors including good nutrition, good health care, and good

sanitation. These also ensure that they reach mature body weight within a short period

after weaning (Sarpong, 2009). They have the potential to be highly prolific as they

produce large litters after a relatively short gestation period, and have a short generation

interval. Pork is one of the most widely eaten meats in the world. According to the

USDA’s Foreign Agricultural Service, over 100 million metric tons of pork was

consumed worldwide from 2009 up to date (USDA-FAS, 2014). In 2011, pork was

reported to be the most popular meat consumed in the world, totalling 37% of all meat

eaten and about 109 million tons of pork produced worldwide (McDermott, 2012). Pig

production makes a significant contribution to household economies and food security.

Apart from pork production, pigs are also kept primarily for supplying pigskin for soft

leather, bristles for brushes, lard (fat) for cooking, hormones for medicinal purposes and

manure for soils and fish ponds (Youdeowei et al., 1986).

Among all the livestock, pigs are the ones that hold the immediate to short term solution

to animal protein deficiency (Annor-Frempong and Segbor, 1994) since they are able to

efficiently convert feed into edible meat. Thus, they would convert a variety of crop

waste, kitchen waste and agro-industrial by-products into high quality meat (Barnes,

1994). Pigs have fast growth rate, which is only slightly exceeded by the best, carefully

managed broilers and reach sexual maturity within 5-7 months (Ogunniyi and Omoteso,

2011). Payne (1990) revealed that on account of the pig’s high fecundity and growth rate,

13
pig production can yield a relatively rapid rate of return on the capital employed. The

ability of pigs to mature and multiply faster than cattle and sheep confers an advantage in

terms of opportunity for meat production. The inherent prolificacy and early sexual

maturity of the sow means that pigs’ numbers can be expanded very rapidly. This always

has been an economically attractive feature of keeping pigs and is one of the reasons why

the pig, with the fowl, have for many years been the peasant or small-holder’s traditional

livestock (Taverner and Dunkin, 1996).

Pigs are particularly appropriate in densely populated areas and as a consequence, they

are not subject to the same problems which confront cattle, sheep and goat production in

many regions where communal land tenure is common. Pigs’ requirement for feed and

other digestible nutrients are much less when compared to other farm animals. In addition

to that they give a relatively rapid return on investment as even on low planes of nutrition

and are ready for slaughter even at the age of twelve months (Sarpong, 2009).

Moreover, the size of pigs compared to cattle makes slaughter and marketing more

flexible and easier process. In terms of dressing percentage, pigs are superior to most of

the livestock species; Beef Cattle (57 – 64%), Sheep and Goat (49 – 52%) and 68 – 72%

for pig (Schweihofer, 2011). Furthermore, Holness et al. (2005) indicated that pigs do not

contribute to erosion and land degradation when they are kept in pens. They also produce

relatively rich manure which becomes a very important resource to the crop farmer when

the price of inorganic fertilizer is prohibitive. These diverse roles entail that there is need

14
for conservation of livestock diversity to support sustainable agricultural development

(Drucker and Anderson, 2004).

2.4 Local Pig Genetic Resource of Ghana

The local Ashanti Dwarf Pig (APD) also known as the Ashanti Black Pig (ABP) is

adapted and mostly raised in subsistence farming systems in Ghana. These local pigs are

generally black with a small short body (Plate 1).

Plate 1. A well-bred ABP boar at the Babile Pig Breeding Station, Upper West (MoFA,

2013).

15
In general, local pigs are smaller than the imported genotypes (Nengomasha, 1997;

Madzimure, 2011) and have less demand for feed because of their small body size when

compared to imported pigs (Ndindana et al., 2002). These pigs can utilize fibrous and

tannin-rich diets more efficiently than imported genotypes (Kanengoni et al., 2002;

Mushandu et al., 2005).

The ABP has a relatively long and narrow head with a prolonged snout (Barnes and

Fleischer, 1998). They are considerably less susceptible to heat stress and more resistant

to most local diseases and parasites. According to Ahunu et al. (1995), the ABP is hardy,

tolerant to most common diseases and stresses and survive under poor management and

extremes of environmental conditions. Holness et al. (2005) and ILCA, (1992) also

described indigenous pigs as better-adapted to 'harsher' environments and poor

management systems. Under extensive management conditions, the ABP breed attains a

mature body weight of 60kg with low litter sizes at birth (5-7 piglets) and high pre-

weaning mortality (Devendra and Fuller, 1979).

Local pigs such as the ABP are superior in traits of economic importance such as heat

tolerance, tasty carcasses, excellent foraging ability (Madzimure, 2011) and good

mothering ability which are particularly useful in free ranging pigs where there is need to

defend piglets from predators (Chimonyo et al., 2008). They also have a great propensity

to put on fat tissues (Serres, 1992). The dressing percentage of the ABP (70.2%) was

found to be favourable than that of the Large White (69.4%) in a study conducted by

Manyo-Plange and Barnes (1996). The efficiency with which feed is converted into pig

16
meat is governed by the genetic quality of the stock, their environment, stage of growth,

feeding method and level of feeding (MAFF, 1977).

Generally, indigenous pigs have relatively low cost of production and their growth rate is

faster (Osaro, 1995). Aside the advantages of the ABP over most of the other pig breeds

in Ghana, it has poor growth and low reproductive performance. Productivity of these

indigenous pigs is generally low, with low litter size and low growth rates (less than

120g/day) largely due to poor management, parasites and diseases (Holness et al., 2005).

Most farmers have therefore shifted their attention to the exotic breeds even with

consideration of ABP’s dominance, adaptation and survival under harsh local

environmental conditions. A number of locally adapted exotic breeds that can be found in

Ghana include; Large White/ Yorkshire, Landrace, Hampen (Landrace × Hampshire) and

Duroc (MoFA, 2003). In the 1980’s, ABP was dominant but due to their low

productivity, most producers preferred the exotic breeds (Livingstone and Fowler, 1984).

Baffour-Awuah et al. (2005) revealed that, the ABP may function well in cross breeding

programmes with the exotic breeds like Large White and Landrace by exploiting the

complementarities of the hardiness of the local breed and the fast growth and better

reproductive performance of the exotic breeds.

2.5. Pig production systems

Description of the predominant production systems and the environment in which an

AnGR is predominantly found as well as population trends, information on its genetic

distinctiveness and its evolutionary relationship with other genetic resources in the

species are all important in the characterization of the production systems (AGTR, 2011).

17
Livestock systems are categorized according to agro-ecological circumstances and the

demand for livestock commodities. These systems are largely shaped by biophysical and

socio-cultural factors (Steinfeld et al., 2006).

Pig production systems in Ghana include free-range scavenging or extensive (traditional),

intensive (commercial) and semi-intensive production systems. Free range is a form of

husbandry where pigs are not confined indoors during the day and either penned or un-

penned at night but are allowed to roam freely in the community (Mashatise et al., 2005).

Free-range scavenging (extensive) pig production system is a system that provides a

household emergency fall-back fund, whilst also supplying it with a little meat from time

to time, with little investment of time or money (Van't Klooster and Wingelaar, 2011). In

this system, pigs feed on kitchen wastes, brewery and cereal by-products, grass, plant

roots and fruits (Lekule and Kyvsgaard, 2003).

Under this system of pig production, controlled breeding is not practiced because males

always move around with females. Animals reared under this system are in general more

active and present a daily pattern of behaviour whereas confined pigs are more sedentary

and have a more stable behavioural pattern along the day (Velazco et al., 2013). Pigs

produced under extensive conditions present different meat characteristics mainly due to

exercise (Daza et al., 2009) or to pasture intake (Moisa et al., 2007) and these may affect

meat colour (Echenique et al., 2009) and fat deposition (Gentry et al., 2002). Free range

pig production is one of the risk factors for outbreak and spread of diseases (Lekule and

Kyvsgaard, 2003). Furthermore, improper feeding produces fatty carcasses or cysts in

18
muscles as a result of tape worm infestation rendering the whole animal unwholesome

(Sarpong, 2009).

In the intensive (commercial) system of production, animals are housed and more

attention is paid to their health and feeding. In Ghana, the intensive system of production

is mostly carried out in the peri-urban areas. This system aims at producing meat for the

market efficiently and profitably, usually with larger numbers of pigs. It requires

significant inputs of time and money, with careful calculation of the costs and the

resulting benefits (Van't Klooster and Wingelaar, 2011). The exotic breeds, Large White

and Landrace and their crosses are mostly used, especially, in the southern sector of the

country (Barnes, 1994). The animals are housed permanently in especially designed

structures all year round and are fed (Ahunu et al., 1995). Pigs raised on-station do much

better because of better management (Sarpong, 2009).

Semi-intensive system is a production system where pigs are confined in a limited space.

Some amount of fodder (agricultural waste and kitchen refuse) and water are provided by

the producers at certain times of the day. This system of pig keeping opens up

possibilities for improved feed and disease control, which in turn can result in faster

growing and healthier pigs in larger litters (Dick and Geert, 2004). As the animals are

confined, it prevents the destruction of crops and pigs from being stolen. Over 95% of

farmers in the rain forest zone engage in keeping small ruminants under the semi-

intensive system (Van't Klooster and Wingelaar, 2011).

19
In Ghana, the pig industry is confronted by a number of challenges such as housing,

feeding, marketing and diseases such as African Swine Fever (ASF) disease (Barnes,

1994). The intensive system in particular has a number of obstacles to overcome

including finances, health problems, feed, housing among others. Factors of major

importance for commercial meat production are the market age and weight at which an

animal produces a carcass of desired conformation (Payne, 1990). Age, sex, health and

conformation of the animal selected for fattening, system and level of feeding,

management and handling practices are some of the most important on-farm and pre-

slaughter determinants of meat quality for processing (Teye et al., 1996). The efficient

feed conversion and ability to utilize a wide range of feed materials by pigs are valuable

attributes; the pig’s outstanding feature is its phenomenal rate of meat production,

especially when expressed in terms of output per breeding female. It is resultant of three

factors which includes the ability of the sow to produce large numbers of progeny at

frequent intervals, early sexual maturity and (with appropriate nutrition and housing) a

rapid growth rate. In combination, these traits translate into much higher annual meat

output per breeding female than those of sheep, beef cattle and broiler chicken (Taverner

and Dunkin, 1996).

With the increase in worldwide demand for meat, fast-growing species with efficient feed

conversion rates, such as pigs are likely to account for a major share of the growth of the

livestock subsector (FAO, 2014). In Ghana, the production of all major livestock types,

used for human consumption increased from 1995 to 2006 except pigs. This was due to a

major outbreak of African Swine Fever (ASF) in 1995 and 2006 that led to massive

20
losses in pigs as most of the pigs were destroyed and many producers lost their parent

stock. However, the pig population started increasing in 2006 (VSD, 2007) following re-

stocking of affected farms through the assistance of FAO (Sarpong, 2009). The Babile

Pig breeding Station of the Animal Production Directorate (APD) has been established

and is mandated to carry out breed improvement of the local pig through breed selection

and breeding and to supply the superior breed to farmers for multiplication. The station

collaborates with research institutions and the universities in upgrading the reproductive

performance of the ABP and has built capacity over the years in rearing and management

pigs (MOFA, 2013). The Nungua Livestock Breeding Station (NLBS) keeps grandparent

stocks of exotic breeds from which parent stocks are produced and sold to farmers to

upgrade their stock (MOFA, 2013).

2.6. Characterization of Animal Genetic Resources

Characterization of Farm Animal Genetic Resources (FAnGR) is a precondition for

designing conservation-based utilization programs and is primarily concerned with the

classification and description of populations into management units or breeds (Gizaw,

2008). Characterization should include the population size of the animal genetic resource,

its physical description, predominant production systems, indications of performance

levels, among others as well as genetic parameters of the performance traits and

information on genetic distinctiveness of the animal genetic resource and its evolutionary

relationship with other genetic resources in the species (Weigend and Romanov, 2002;

Gizaw et al., 2011; Addis, 2012).

21
The Global Plan of Action (GPA) on AnGR is being implemented by countries to ensure

sustainable utilization of their AnGR and it contains four strategic priority areas, which

provide a basis for enhancing sustainable use, development and conservation of AnGR

throughout the world. The first of the strategic priority area is characterization, inventory

and monitoring of trends and associated risks of AnGR (FAO, 2007). The goal of this

strategic priority is to facilitate decision-making. Apart from the evaluation of phenotypes

and production systems, involvement of collection and molecular analysis of biological

samples in characterization is basically to explore genetic diversity within and between

animal populations, and to determine genetic relationships among such populations

(FAO, 2007).

Conservation of indigenous animal resources has been proposed as a method for slowing

down the loss in diversity in livestock breeds through extinction (FAO, 2007).

Conservation of pig genetic resources entails the identification, monitoring,

characterization and utilization of pigs for best short term use and to ensure their

management for longer term availability (FAO, 1993). The need for conservation is

greater when the size of the population is getting smaller as is the case with ABP in

Ghana. The risk status of losing a genotype can be described as critical, endangered or

extinct (FAO, 2007) and the situation of the ABP can be described as close to critical.

However, to ensure proper conservation and utilization of indigenous breeds, it is

necessary to evaluate genetic variations within and among breeds. Breeds are linked to

their origin with regards to tradition and history or geographical region. They may also

share a large proportion of their genome with another breeds but each possesses

22
distinctive combination of genes. These may include distinctive traits particularly for

adaptation to specific environment (Alderson, 2010).

High rates of loss of genetic variation within breeds lead to reduced chances of survival

due to decreased fitness through inbreeding depression. Hlophe (2011) indicated that

these breeds become subject to faster changes in gene frequencies, greater rate of loss of

genes and genetic constitutions (haplotypes). With more variation, it is more likely that

individuals in a population will possess variations of alleles that are suited for the

environment and those are more likely to survive to produce offspring bearing that allele.

The population will continue for more generations because of the success of these

individuals (Agrafioti, 2011). Conservation and development of local breeds is very

important since many of them utilize lower quality feed, are more resilient to climatic

stress and to local parasites and diseases, and represent a unique source of genes for

improving health and performance traits of industrial breeds. Animals genetically adapted

to their harsh environment with very little natural and managerial input are expected to be

more productive at lower costs, support food, agriculture and cultural diversity, and be

effective in achieving local food security objectives. Local communities depend on these

adapted genetic resources in many countries (FAO, 2006).

In Africa, since the observable traits and genetic characteristics of breeds often have not

been defined and validated, it is difficult to consider certain breed as a priority for the

purpose of conserving as much diversity as possible across breeds. This situation occurs

more in developing countries where there is limited infrastructure to conserve the whole

23
range of breeds. Information on genetic diversity is useful in optimizing both

conservation and utilization strategies for farm animal genetic resources (Drucker et al.,

2006). A greater number of the existing classification of livestock breeds in most of the

developing countries is based on historical, anthropological and morphological evidence

(Zulu, 2008). However, these are most often not enough for the purpose of conservation

(Mwacharo et al., 2006). Genetic erosion within livestock species, including their wild

ancestors, is of particular concern because of its implications for the sustainability of

locally adapted agricultural practices and the consequent impact on food supply and

security. If care is not taken, the rapid loss of the AnGR will make it more difficult or

even impossible to breed for production in new environmental conditions, for resistance

to new diseases or for novel consumer needs (Globaldiv, 2004).

Conservation of genetically unique breeds/populations is critical to prevent loss of

genetic diversity within each domestic species. Maintaining variation is important for

future animal breeding strategies, to match animals to a variety of husbandry systems and

for adaptations to environmental changes (Toro et al., 2009). Kunene et al. (2009)

reported that in order to ensure proper conservation and utilization of indigenous breeds,

it is necessary to evaluate genetic variations that exist within and among breeds. There is

therefore the need to do diversity studies (phenotypic and molecular characterization) of

the local pig genetic resources to inform authorities as to how to develop breeding

strategies to minimize the threats of dilution and extinction.

24
2.6.1 Phenotypic characterization of AnGR

Phenotypic characterization of AnGR refers to the identification of distinct breed

populations and description of their external and production characteristics within a given

production environment (FAO, 2012). This includes data collection on qualitative and

quantitative traits. Phenotypic characterization of livestock breeds as well as their

adaptive traits is important in identifying breed attributes for immediate use (Zulu, 2008).

The driving force of characterization is to avail information for appropriate use to support

human livelihood by improving productivity and adaptability of their livestock

(Cunningham, 1992). According to National Bureau of AnGR (NBAGR), phenotypic

characterization includes the process of identifying distinct breed populations and

describing their characteristics and those of their production systems. It is used to identify

and document diversity within and between distinct breeds based on their observable

attributes. A breed is used in phenotypic characterization to identify distinct AnGR

population as a unit of reference and measurement (NBAGR, 2013).

Phenotypic characterization involves collecting a number of different kinds of data: the

breeds’ geographical distribution; the breeds’ phenotypic characteristics (morphology),

information on the breeds’ origin and development; any known functional and genetic

relationships with other breeds within or outside the country; biophysical and

management environment(s) in which the breeds are maintained; responses of the breeds

to environmental stressors among others (FAO, 2007). Oseni et al. (2006) revealed that

morphometric measurements have been useful in characterization and establishment of

25
breed standards in the production of livestock breeds in rural communities. Table 1 is an

example of morphological description of Local pigs and their crossbreds in Nigeria.

Table 1: Least-squares means for morphological variables by breed type and the

corresponding levels of significance

Variables (cm) Crossbreds Local pigs

Live weight 20.5a 16.4 b

Body Length 50.3 a 36.6 b

Height at withers 40.7 a 26.1 b

Heart Girth 45.6 a 38.0 b

Snout Length 9.9 a 13.5 b

Tail Length 12.5 a 12.0 b

Ear Length 10.3 a 12.95 b

Teat Numbers (TN) 14.0 a 11.5 b

Crossbreds (crossbreed pigs): Local pigs (Nigerian Indigenous Pigs (NIPs)): Means with the same

superscript are not significantly different (P < 0.05). TN = measured by counting, LW =

measured in kg and other variables measured in cm.

Assessment of the population characteristics also includes estimates of population sizes,

flock/herd structure, and assessment of the level of indiscriminate or irrational

crossbreeding which are all indicators of threat to the survival of the adapted indigenous

genetic resources (Gizaw et al., 2011).

26
2.6.2. Genetic characterization of AnGR

Genetic characterization refers to the distillation of all knowledge, which contributes to

the reliable predictions of genetic performance of an AnGR in a defined environment and

provides a basis for distinguishing between different animal genetic resources and for

assessing available diversity (Rege and Gibson, 2003). This is the first step in considering

the sustainable management or conservation of a particular population (FAO, 2000). It is

important to know how unique or how different one breed is from other populations.

Genetic variation within livestock species is partly attributed to differences between

breeds and partly to differences among individuals within breeds. Selection in both

between and within breeds has the potential to contribute to development (FAO, 2007).

Genetic variation is the basis of animal breeding and selection. To preserve the maximum

amount of genetic diversity, it is important to characterize different breeds to know how

unique or different a breed is from other native populations. Genetic characterization is a

further step to answer questions on taxonomy, evolution, domestication processes,

management of genetic resources and setting conservation plans for effective utilization

(NBAGR, 2013). Genetic improvement is an important element of sustainable use of

AnGR as it allows livestock keepers to adapt their animals to changing conditions.

Sustainable breeding and on-farm conservation programmes for local pig genetic

resources can help farmers to adapt to future environmental shocks. For example, local

pig genetic resources are useful in the development of appropriate genotypes as the

27
environment; animal production trends, market and human needs change (Philipsson and

Okeyo, 2006).

2.7. Importance of Live Weight in Livestock

Weighing of animals remains one of the most important tasks to perform in livestock

production. Generally, about 60% of the total production costs are accounted for by feed

preference and as such, maintaining the optimum growth rate and food conversion

efficiency would help to minimize the high cost of production. Live weight serves as an

important tool in the determination of growth rate and feed conversion efficiency

(Gunawan and Jakaria, 2011), which are highly significant parameters in the control of

production costs to maintain profits on commercial pig operations. Growth rate and feed

conversion efficiency are influenced by several factors including genetic potential,

environmental conditions, diet formulation and ingredients, among others. It is only when

the pig producer measures the live weights regularly and accurately in order to be able to

assess the effect that any changes in husbandry, feed quality, or environment have on the

animals (Schofield et al., 1999; Sarti et al., 2003; Wang et al., 2006).

Live weight also serves as an indicator of animal health and growth such that it provides

valuable information regarding the nutritional and environmental conditions on the farm.

Costs are also reduced in the treatment of diseases as overestimation of weights and

underestimation of weight could be potentially dangerous due to the development of drug

resistance (Sungirai et al., 2014). Moreover, live weight helps to determine the time when

the animals attain market weight. Some factors such as space allowance affect the output

28
of the herd; live weight again helps in the understanding of those factors (Brandl and

Jorgensen, 1996).

In the cattle industry, information on live weight can be used to help producers in

achieving goals for age at first calving and to determine the value of culled animals and

the efficiency of rearing replacement heifers (Dingwell et al., 2006). Moreover, such

information can be used in the development of nutritional management programmes for

replacement heifers (Donovan and Braun, 1987), the evaluation of feed efficiency, the

determination of pharmaceutical doses of drugs, and in the appraisal of the overall health

status of the animals (Enevoldsen and Kristensen, 1997).

2.8. Measurement of body weight

There are basically two main approaches which could be used to estimate the weight of

pigs. These are the direct and indirect approaches (Zaragoza, 2009). The direct method

involves physically moving the pigs to a weighing location and placing them on a

weighing scale. On the other hand, the indirect method involves visual estimation of

weight. This involves the use of linear body measurements and image analysis. Based on

the indirect methods, the use of linear body measurements is the most common tool that

is used to predict body weight in farm animals. Weight predictions using linear body

measurements have been used in different species of animals (Enevoldsen and

Kristensen, 1997; Thiruvenkadan, 2005). Groesbeck et al. (2010) reported a strong

correlation between weight and girth measurements in calves. Chest girth has been

suggested as a better indicator of weight for Brahman cattle (Vargas et al., 2000).

Afolayan et al. (2006) reported heart girth as the best predictor of live weight in Yankasa

sheep. In South Africa, heart girth has also been proposed as good predictor of body

29
weight in KwaZulu-Natal goats (De Villiers et al., 2009). Similar studies in goats have

been carried out in Botswana (Nsoso et al., 2003), Nigeria (Hassan and Ciroma, 2007),

Pakistan (Khan et al., 2006). Based on multiple body measurements in pigs, body length

and heart girth have been reported as the best estimator of the live weight in Philippines

(Murillo and Valdez, 2004). Machebe and Ezekwe (2010) concluded that heart girth,

body length and flank-to-flank as being the best estimators of live body weights in pigs

reared in the tropics of Nigeria. Mutua et al. (2011) also revealed that body length and

heart girth were the best estimators for live body weight of pigs in rural Western Kenya.

Table 2 is an example of prediction equations for live weight of local pigs and their

crossbreds in Nigeria (Adeola et al., 2013).

Table 2: Prediction equations for live weight based on stepwise regression analysis in
NIPs and Crossbreds.

Genotype Simple regression equation (R2)

Local pigs (NIPs) -5.03 + 0.58 HG 0.89
Crossbreds -5.95 + 0.51 BL 0.83

Multiple regression equation

Local pigs (NIPs) -11.47 + 0.32 RH + 0.34 BL 0.90
Crossbreds -25.71 + 0.43 HG + 2.21 TL 0.93
NIPs: Nigerian Indigenous Pigs, HG: Heart girth, BL: Body Length, TL: Tail Length, RH: Rump
Height.

Heart Girth (HG) fits best in simple regression equation NIP with an R2 value of 0.89

while that of Crossbreds had R2 value of 0.83 with BL. For multiple regression equation,

HG in combination with BL had the highest R2 value of 0.90 for NIPs while HG and TL

had an R2 value of 0.93 for Crossbreds (Table 2).

Although morphometric measurements have been useful for estimating and predicting the

live weight in Livestock (Adeola et al., 2013), most farmers in developing countries

30
estimate live weight based on visual appraisal because of unavailability of weighing

scales. These farmers walk through their pens and select the biggest animals on the basis

of visual description to estimate weights of their pigs. Differences exist between

individuals in their ability to predict the live weight of pigs from visual appraisal, which

in turn increases the variation in the weight of the pigs that are sent to market (Schofield

et al., 1999). Although, this can be reduced by using weighing scales, there are other

challenges such as the time involved, the increased labour needed, the stress on the pigs,

the people involved, and the lack of availability of weighing scales on the unit (White et

al., 2004; Wang et al., 2008; Beretti et al., 2009; Machebe and Ezekwe, 2010). If farmers

underestimate the weight of their pigs, they may settle for a price below market value and

subsequently lose money. Unfortunately prediction of the pig live weight using based on

body measurements has not been well studied in Ghana.

2.9. Population Genetic Studies

Population genetics is the study of the distributions and changes of allele and genotypic

frequencies in a population. The population is subjected to the four main evolutionary

processes; natural selection, genetic drift, mutation and gene flow (Wade, 2008).

Evolution occurs when there are changes in the frequencies of alleles within a population

(Hall and Hallgrímsson, 2008). Population genetics also takes into account the factors of

recombination, population subdivision, and population structure (Dorak, 2014).

Population structure is the presence of genetic similarities and differences within and

between groups of individuals (Shringarpure, 2012). Genetic population structure has

shed light on the evolutionary history and migrations of modern populations (Conrad et

al., 2006; Rosenberg et al., 2002). It also provides guidelines for more accurate

31
association studies (Roeder et al., 1998) and is useful for many other population genetics

problems (Hammer et al., 1998; Templeton, 2002). Studies on genetic diversity,

phylogeny, and the preservation of diminished indigenous breeds all over the world have

been very important steps for the development of AnGR (Charoensook et al., 2011).

2.9.1. Genetic diversity and variation

Genetic diversity is the variety of alleles and genotypes present in a population and this is

reflected in morphological, physiological and behavioural differences between

individuals and populations (Frankham et al., 2002). Domesticated species often have

low levels of genetic diversity due to artificial selection, mutations, genetic drift, local

adaptation, or preferential breeding of animals for traits that humans find preferable.

While this can have positive short-term results, low genetic diversity among domesticated

species pose risks (Doehring, 2014). For instance, several differences in appearance,

physiology and agricultural traits are recorded in domesticated animals (FAO, 2012).

These are also emphasized by the emergence of breeds, more or less isolated populations

that are subject to systematic selection especially in the temperate zones where the

demands of food supply led to a rationalization of agriculture (Philipsson et al., 2011).

Genetic diversity is very important for the survival, the evolution and the adaptation of

both wild and domestic species to changing conditions. Genetic diversity is distinguished

from genetic variability, which describes the tendency of genetic characteristics to vary

and permits flexibility and survival of a population in the face of changing environmental

circumstances (Scitable, 2014).

32
Generally, genetic variation is accepted as the raw material of evolution, without which

populations cannot evolve in response to changing environments (Zulu, 2008). It is

necessary for selection, adaptation, disease resistance and production traits. Maintaining

genetic variation within breeds reduces chances of inbreeding depression and ensures

survival of the breed (Hlophe, 2011). Although much less talked about, genetic erosion in

farm AnGR is much more serious than in crops because the gene pool is much smaller

(6000–7000 breeds/strains of some 40 species) and only very few wild relatives remain

(Rege and Gibson, 2003).

The investigation of genetic variation is very important for future monitoring of gene

flow in populations, conservation of species, determination of the level of inbreeding and

crossbreeding within and between breeds (Hetzel and Drinkwater, 1992; Kunene et al.,

2007). Genetic characterization through the use of molecular markers associated with

powerful statistical approaches has provided avenues for decision making choices for the

conservation and rational management of AnGRs (Hanotte and Jianlin, 2005).

2.9.2. Important parameters in genetic diversity analysis

There are a number of indices used to measure genetic diversity and these include Hardy-

Weinberg equilibrium Test (HWE), average heterozygosity (He), effective population

size (Ne), polymorphism and F- Statistics.

A population is said to be in Hardy-Weinberg equilibrium (HWE) when gene and

genotype frequencies remain constant from generation to generation (AGTR, 2011).

There are factors which can cause changes in these frequencies and these include

33
selection, sexual reproduction, random mating, migration and mutation resulting in non-

random union of gametes. Deviation from HWE indicates that one or some of the

mentioned factors make disequilibrium from the test (Dorak, 2014). The data required to

perform HWE tests are gene and genotype frequencies and the size of sample population

at each locus.

Heterozygosity is a measure of genetic variation within a population. It is one of the most

widely used measures to describe genetic variation at a single locus or a number of loci.

Heterozygosity is believed to be a good predicator of chances for long-term survival of a

population because it reflects the number of genetic options available within a population

(Zhou et al., 2005). A low level of heterozygosity may be due to isolation with the

subsequent loss of unexploited genetic potential. High heterozygosity values for a breed

may be due to long-term natural selection for adaptation, to historic mixing of strains of

different populations or to the mixed nature of the breeds. A high level of average

heterozygosity at a locus could be expected to correlate with high levels of genetic

variation at loci with critical importance for adaptive response to environmental changes

(Kotzé and Muller, 1994). Average heterozygosity at each locus and for each breed can

be estimated from allele frequencies at each locus. The observed heterozygosity is the

percentage of loci heterozygous per individual or the number of individuals heterozygous

per locus. Individual breed average heterozygosity is estimated by summing

heterozygosities at each locus and averaging these values over all loci. The expected

heterozygosity is calculated from individual allele frequencies (Nei, 1987).

34
The effective population size, Ne, is the inverse of the expected homozygosity used to

measure the amount of genetic variation in a population. Ne determines both the amount

of genetic drift and the rate of inbreeding (Falconer and Mackay 1996) and can be

estimated from demographic data such as the number of parents and the variance in their

progeny number (Caballero, 1994).

Genetic polymorphism is the occurrence in the same population of two or more alleles at

one locus, each with appreciable frequency, where the minimum frequency is typically

taken as 1% (Hedrick, 2011). A polymorphic gene is usually defined as one for which the

most common alleles have a frequency of less than 0.95. Average number of alleles per

locus also provides complementary information to the polymorphism. Genetic

polymorphism promotes diversity within a population. It often persists over many

generations because no single form has an overall advantage or disadvantage over the

others regarding natural selection.

Wright's fixation indices (F-statistics) are the parameters most widely used to describe

population structure. F stands for fixation index, defined as the correlations between

uniting gametes (Wright 1969, 1978). F-statistics is a measure of the difference between

the mean heterozygosity among the subdivision in a population and potential frequency

of heterozygote if all members of the population mixed freely and none assertively

(Nagylaki, 2014). Wright developed three fixation indices to evaluate population

subdivision: FIT (total population), FIS (inter individual) and FST (subpopulations).

35
 _
FIT This is the inbreeding coefficient of an individual relative to the whole set of

population. It is rarely used and can range from -1 to +1 indicating maximal inbreeding

and outbreeding respectively (Dorak, 2014).

FIS – This is the inbreeding coefficient of an individual relative to the sub-population it

belongs to. The parameter can range from -1 to +1 indicating minimal inbreeding and

outbreeding respectively. A positive FIS value indicates inbreeding that observed

heterozygosity is lower than the expected heterozygosity.

_
FST This is the mean inbreeding coefficient of sub-population relative to the entire

population. It is considered to be the most informative statistic for examining the overall

level of genetic divergence among subpopulations. This parameter is a function of how

heterozygosity is partitioned within and among populations, based on differences in allele

frequencies (Wright 1969, 1978).

2.9.3 Genetic distances

Genetic distances are metrics which have been developed to summarize allele frequency

differences among populations (Mogesse, 2007). The calculation of a genetic distance

between two populations gives a relative estimate of the time that has passed since the

populations have existed as single cohesive units. Genetic distance based on DNA

sequences, is a more reliable measure of genetic variation between breeds since it is not

influenced by the environment. Genetic distance could also be measured by the method

Nei (1978).

36
2.10. Phylogenetic analysis

Phylogenetic trees often are constructed to accompany distance measurements (Zulu,

2008). During the eighties, development of molecular biology techniques for the study of

genetics, led to improvement in genetic characterization and has been the method of

describing and classifying livestock breeds using measures of genetic distances between

populations (Cavalli-Sforza and Edwards, 1967; Nei, 1972; Nei et al., 1983). The

molecular DNA markers that have been used for breed characterization include amplified

fragment length polymorphisms (AFLPs), restriction fragment length polymorphisms

(RFLPs), microsatellites or simple sequence repeats, randomly amplified polymorphic

DNA (RAPD) and mitochondrial DNA (mtDNA).

Mitochondrial DNA (mtDNA) polymorphisms have proven valuable in the phylogenetic

and genetic diversity studies of both plants and animals (Zulu, 2008). It is a circular DNA

molecule found outside of the cell nucleus. It can easily be isolated and evolves 5 to 10

times more rapidly than nuclear DNA, especially the D-loop (Displacement loop) region.

The D-loop occurs in the main non-coding area of the mitochondrial DNA molecule, a

segment called the control region or D-loop region (Huang et al., 1999; Avise, 2000; Fish

et al., 2004; Gongora et al., 2004). The polymorphisms in the hyper-variable region of

the D-loop of mtDNA have contributed greatly to the understanding of livestock

domestication, the identification of wild progenitors of domestic species and the

establishment of geographic patterns of genetic diversity (Bruford et al., 2003). D-loop

region is the most variable part of mtDNA (Ishida et al., 1994) due to a higher

37
substitution rate than in the rest of the mtDNA genome (Cann et al., 1984). Larson et al.,

(2005) have studied the domestication process of European and Asian wild boar and

domestic pigs based on mitochondrial D-loop sequence analyses in a wide range of pig

breeds.

The MtDNA is maternally inherited in most species (exceptions with paternal leakage

detection in mice, Gyllesten et al., 1991; bi parental inheritance in marine mussels,

Zouros et al., 1992), which means mtDNA haplotypes should be shared by all individuals

within a maternal family line. The maternal inheritance pattern of mtDNA provides

definite information on evolutionary relationships in phylogenetic analysis (Garrime,

2007). MtDNA is not highly conserved and because of its rapid mutation rate, it is useful

for studying the evolutionary relationships phylogeny of organisms. Biologists can

determine and then compare mtDNA sequences among different species and use the

comparisons to build an evolutionary tree for the species examined (RFR, 2014). Careful

assessment of mtDNA relationships can provide insights to the multiple origins of

introduced pigs and the genetic diversity of disparate populations (McCann et al., 2014).

MtDNA has many advantages over molecular marker for phylogenetic analysis (Moore,

1995). It is highly polymorphic compared to nuclear DNA. It is also a haploid, non-

recombining and its evolutionary rate of base substitution is much faster than that of

nuclear genome (Brown et al., 1982), probably due to lack of replication repair

mechanism (Clayton, 1982).

38
Molecular data have shed light on pig domestication by tracing mtDNA and mtDNA

studies have shown that European and Chinese pigs were domesticated independently

from European and Asian subspecies of wild boar (Giuffra et al., 2000). The study also

suggested the occurrence of introgression of Asian domestic pigs into some European

breeds during the 18th and 19th centuries. Identification of variations in mtDNA sequence

analysis is straightforward but depends on the recognition of nuclear mtDNA insertions

(Hassanin et al., 2010; Calvignac et al., 2011) especially when diverse species specific

primers are used (Den Tex et al., 2010). Most studies, however, focus on the highly

polymorphic displacement loop (D-loop) but whole genome sequences have been

reported to add significant information (Achilli et al., 2008). Classical approaches to the

detection of genetic differences in farm animals have been based on the use of blood

proteins, protein in blood plasma and serum and blood groups (Hines, 1999). Nowadays,

DNA polymorphisms have become more popular in genetic characterization of most farm

animals (Adebambo et al., 1999; Arranz et al., 1996; Nijman et al., 2003). DNA

fingerprints (Ponsuksili et al., 1998) and mitochondrial DNA (mtDNA) sequences have

been utilized to determine genetic diversity in chicken (Niu et al., 2002; Liu et al., 2004).

Throughout Eurasia, mitochondrial DNA (mtDNA) has been used successfully for

phylogeographic studies of wild boar and domestic breeds (Larson et al., 2005; Scandura

et al., 2008; Luetkemeier et al., 2010).

The combined analysis of mitochondrial, autosomal and Y-chromosome markers in a

sample of pigs and wild boars with a worldwide distribution has revealed two clearly

distinct genetic patterns in Africa (Ramirez et al., 2009). West African pigs do not

39
display Far Eastern alleles suggesting that they descended from the admixture of

indigenous populations and exotic breeds with an European ancestry. East African pigs

harbour Far Eastern alleles at significant frequencies evidencing that they have a mixed

European/Chinese origin (Ramirez et al., 2009).

40
 CHAPTER THREE

MATERIALS AND METHODS

3.1 Location and period of study

The study was carried out in six out of ten regions in Ghana namely Ashanti, Central,

Eastern, Greater Accra, Northern and Upper West (Figure 1). Ghana lies at the shore of

the Gulf of Guinea in West Africa and occupies a total area of about 24 million ha. It lies

between latitudes 40˚ and 120˚ N and longitude 40˚ E and 20˚ W. It is bounded by the

Atlantic Ocean in the south, La Côte d’Ivoire in the west, Burkina Faso in the north and

Togo to the east. The country is divided into ten administrative regions and six ecological

zones, dominated by semi-deciduous forest and Guinea savannah (Gumma et al., 2011).

The Guinea savannah is the largest zone and lies in the north of the country. The Guinea

savannah zone has one distinct rainy season beginning in late April or early May, peaking

in August-September and abruptly declining in October-November. The rainy season is

followed by a long dry period (Oppong-Anane, 2001). Annual rainfall in this zone ranges

from 800 - 1200mm/yr and that of annual temperature is 27.5 °C. The vegetation of

Guinea savannah is of wooded grassland, consisting of a ground cover of grasses of

varying heights (Minia, 2008; Boateng et al., 2014).

The Forest zone includes two primary forest types: moist semi-deciduous forest and dry

semi-deciduous forest. The northern boundary of the zone follows the Kwahu Plateau,

and the southern edge blends into the moist evergreen forest type. The Forest zone has a

more clearly defined dry season than the evergreen forest types. In the Forest zone, mean

annual rainfall ranges from 800 - 2800mm/yr and that of temperature is 26.4 °C (Minia,

2008; Boakye, 2010).

41
The Coastal savannah zone is a narrow belt paralleling the coast with annual rainfall

ranging from 600 - 1200mm/yr. There are two distinct rainy seasons in the zone that is

from May-June (major rains) and August-September (minor rains). The major vegetation

types are classified as southern marginal forest from about Accra Westward, southern

outlier forest in the Accra plains and savannah in the Ho plains (Menczer and Quaye,

2006; Boateng et al., 2014). The study was carried out from October, 2013 to May, 2014.

42
Figure 1: Map of Ghana showing regions sampled for study

43
3.2 Study population

The study targeted only the ABPs which are the local breed in Ghana and their

crossbreds. Table 3 below gives a detailed description of study population.

Table 3: Location, sex and type of breed sampled for the study

Region Sample Sex Type Of Breed

Size Male Female ABP Crossbreds
Ashanti 20 7 13 6 14
Central 23 9 14 8 15
Eastern 28 12 16 12 16
Accra 50 18 32 44 6
Northern 15 6 9 11 4
Upper West 27 11 16 25 2

Total 163 63 100 106 57

3.3 Sampling size and sampling technique

Purposive sampling (Kumar, 2005) was used to collect data on 163 local pigs sampled

from six regions in the study (Table 3). These regions were selected from three out of the

six ecological zones of the country. Two from each of the three zones as shown in the

map. Farmers and communities where local pigs are raised were identified with the

assistance of District Directors of the Ministry of Food and Agriculture (MoFA) and

Agricultural Extension Agents (AEAs). Sampling was done in such a way that different

districts within the regions were covered, animals from the same family were excluded

and a balance of their sexes. Apart from the Babile pig breeding station and some few

farms, most of the farmers often did not have birth records. Each animal was gently

restrained while taking the measurements. Measurements of morphological features of

the pigs were taken and questionnaires administered to farmers. The data was recorded

according to the procedure described by FAO (2007) (Appendix 1). Body weights were

44
recorded with the aid of weighing scale whiles the linear body measurements in

centimetre were recorded using a standard measuring tape (Appendix 2). In most cases,

age was estimated by either the year or the month in which the animal was born. Most

farmers did not keep records but were able to estimate the ages of their pigs especially the

month or year they were born. Pigs were assigned to one of five in age-groups: 0 - 8, 9 –

12 and over 12 months.

3.4. Data collection

The data was collected based on these qualitative and quantitative variables (Table 4&5).

Table 4: Traits of morphological (Quantitative) measurements in pigs

Trait Description

Body length (BL) The horizontal distance from the point of

shoulder to the pin bone.

Height at withers (HW) The (vertical) height from the bottom of the
front foot to the highest point of the
shoulder between the withers.
Tail length (TL) From the base to the tip of the tail

Snout length (SL) The distance between the frontal nasal

suture and upper part of the snout;
Heart girth (HG) The circumference of the body immediately
behind the shoulder blades in a vertical
plane, perpendicular to the long axis of the
body.
Ear length (EL) The distance between the tip of the ear and
the base
Head length (HL) The distance between the snout and
occipital tip of the animal
Body weight (BW) The fasted live body weight in kilograms.

Source: FAO, 2007.

45
Table 5: Traits of morphological (Qualitative) variables in pigs

Trait Description

Hair Curly, straight, short, long, dense or sparse

Snout Long and thin, short and cylindrical or long

and cylindrical.

Coat colour type White, black, dark red, black and white, fawn
or other.

Coat colour pattern Plain, patchy, spotted or other.

Head profile Concave (dished) or straight

Ear type Droopy (pendulous), semi-lop (e.g. Pietrain),

lop or prick (erect).

Ear orientation Project forwards, backwards or upwards.

Skin Smooth or wrinkled

Tail type Straight or curly (kinked).

Backline Straight, swaybacked (i.e. markedly convex

ventrally) or other.

Source: FAO, 2007.

3.5. Statistical analysis for morphological characterization

Data was analysed using the GenStat (13th edition) statistical package. In the analyses,

age and sex was included as fixed variables while body length, heart girth, and height at

withers, tail length, head length, teat numbers, fore limb, hind limb, facial length and ear

length were used as continuous variables. The significance of means of all variables was

46
separated via protected Least Significant Difference (LSD) (GenStat, 13th edition,

statistical package). Means and standard error for body weight and linear body

measurements were calculated. Prediction equations that related to body weight and

linear body measurements were chosen based on values of the adjusted R2 and RSD,

reporting the equation with the highest R2 and the lowest RSD values. Data was subjected

to analysis using a simple linear and multiple linear regression models of GenStat (13th

edition).

The following model was used:

Yij = a + biХi + Eij,

Where, Y = BW = body weight, the dependent variable

a = constant

bi = Regression coefficient of the ίth independent variable

Хi = The value of the ίth independent variable

Such that: Х1 = Body length (BL)

Х2 = Heart girth (HG)

Х3 = Height at withers (HW)

Eij = Random error term

The R2 (the square of the multiple correlation coefficient between Х’s and Y) was a

measure of the proportion of the variance of Y explained by variation in Х’s.

47
3.6. Molecular Characterization

3.6.1. Sample collection

Using purposive sampling, a total of 35 ear tissue samples (21 females and 14 males) of

local pigs obtained from selected districts in Central and Greater Accra region were

collected. Different districts within the regions were covered and animals from the same

family were excluded. Due to financial constraints, the molecular studies focused only on

one of the six ecological zones in Ghana. Using an ear notcher, the tissue samples were

collected in a test tube containing RNAlater and transported to Biotechnology Centre of

the College of Agriculture and Consumer Sciences (CACS), University of Ghana for

genomic DNA extraction. In addition, questionnaire was administered to the farmers

before samples were taken as prescribed by FAO (2007) to help describe the husbandry

system (Appendix 3).

3.6.2. DNA extraction

Total genomic DNA was extracted from the peripheral pig ear tissue samples using the

Qiagen DNA blood and tissue kit and following the manufacturer’s protocol (Gilardi,

2013). Briefly, the ear tissues were cut up to 25 mg into small pieces to enable more

efficient lysis and placed in a 1.5 ml microcentrifuge tube. 180 µl Buffer ATL was then

added. Addition of 20 µl proteinase K was done and mixed thoroughly by vortexing.

Samples were then incubated at 56˚C until the tissues were completely lysed. After 3 hrs

of incubation, samples were vortexed for 15 seconds and 200 µl Buffer AL added.

Samples were mixed thoroughly and 200 µl ethanol added and mixed again by vortexing

to yield a homogeneous solution. The mixture was then pipetted into DNeasy Mini spin

column placed in a 2 ml collection tube and centrifuged at 8000 rpm for 1 minute. Flow-

48
through and collection tubes were then discarded. The DNeasy Mini spin columns were

then placed in a clean 1.5 ml microcentrifuge tube and 200 µl Buffer AW1 pipetted

directly onto the DNeasy membrane. Samples were again incubated at room temperature

for 1 minute and then centrifuged at 8000 rpm to elute. Elution was done with 100 μl.

The extracted DNA were then stored at -20˚C until further analysis. The DNA was

subsequently transported to the Laboratory of Mammalian Genetics Group of the

department of Pathology, University of Cambridge, for further analysis.

3.6.3 DNA amplification and Sequencing

The D-loop region (approximately 680bps) of the mitochondria DNA (mtDNA) was

amplified using the following primer pairs:

 Forward primer 5-CTCCGCCATCAGCACCCAAAG-3’

 Reverse primer 5’-ATGAGCTAATAATTACCTGC-3’ (Larson et al., 2005).

PCR’s were set up using 20ml volumes containing 2.0ml 10s buffer, 4.0ml cube solution

buffer, 1.6ml dNTPs, 2.0ml forward primer, 2.0 ml reverse primer, 0.1 taq polymerase,

6.3ml purified water and 2.0 ml DNA. PCR products were purified after agarose gel

electrophoresis using ExoSAP-IT (USB Cooperation, USA) following the manufacturers

recommendation. Amplicons were sequenced using Big Dye Version 3.1 (Applied

Biosystems, Foster city, CA, USA) and run on an AB_I3100 capillary sequencer at the

sequencing facility in the Department of Genetics, University of Cambridge. A 620bp

fragment of the D-Loop region of the mtDNA was amplified using touchdown PCR.

Traces were edited using chromax version 2.2 (technelysium Pty limited). The sequences

were viewed using the multAlin program (http:// prodes.toulouse.inra.fr/multalin/

49
multalin.html) and within the ClustalW2 program (http://www.ebi.ac.uk/Tools/msa/

clustalw2/).

3.6.4. Genetic analysis

The Muscle module implemented in MEGA version 5 software was used to generate

multiple alignments of all sequences (Tamura et al., 2011). The frequency of each local

haplotype was compared to those of Asian and European wild boar haplotypes (3 and 7

respectively) to infer the possible origin of Ghanaian pigs. The evolutionary history was

inferred by using the Maximum Likelihood method based on the Tamura-Nei model

(Tamura and Nei, 1993). The bootsrap consensus tree inferred from 500 replicates

(Felsenstein, 1985) is taken to represent the evolutionary history of the taxa analyzed.

Branches corresponding to partitions reproduced in less than 50 percent bootstrap

replicates were collapsed. The percentage of replicate trees in which the associated taxa

clustered together in the bootstrap test (500 replicates) was shown next to the branches

(Felsenstein, 1985). The initial tree of the heuristic search were obtained automatically

neighbor joining and Biomj algorithms to a matrix of pair wise distances estimated using

the Maximum Composite Likelihood (MCL) approach and the selecting the topology

with superior log likelihood value. Evolutionary analyses were conducted in MEGA 5

(Tamura et al., 2011). The corresponding mtDNA sequence of the African warthog

(Phacochoerus aethiopicus); (GenBank accession number - AB046876) was used as an

out-group.

50
 CHAPTER FOUR

RESULTS
4.1 General information on local pig farmers

The background of local pig farmers sampled for the study is shown in Table 6. The

numbers of male owners of the local pigs for this study were twice more than their female

counterparts. Among these farmers, few were literates and have completed at least junior

high school whiles majority have not been to school before. Most of these farmers were

Christians with few being traditionalists and non-religious. No Muslim was engaged in

local pig production from the sampling.

Table 6: Background of sampled local pigs

Category Frequency Percentage (%)

Sex of farm owners
Males 57 72.15
Females 22 27.85
Educational status
Literate 19 24.05
Illiterate 60 75.95
Religion

Christians 65 82.28

Muslims 0 0.00

Other* 14 17.72

*Others include traditionalists and non-religious bodies.

51
4.2 Morphological Characterization of Local Pigs in Ghana
Morphological characterization of local pigs in Ghana involved both qualitative and

quantitative measurements.

4.2.1. Qualitative variables

In general, sow teats ranged between 4 and 8 pairs. Local pigs with 4 pairs constituted

(2.45%), 5 pairs (41.10%), 6 pairs (30.67%), 7 pairs (23.93%) and 8 pairs (1.84%). The

results of the other morphological features are presented in Table 7.

Table 7: Number and percentages of local pigs showing the various morphological
characteristics

Category Trait Total (%)

Ear type Semi-lop 25 15.34
Erect 138 84.66
Ear orientation Forward 46 28.22
Backward 85 52.15
Upwards 32 19.63
Smooth 153 93.87
Skin Wrinkled 10 6.13
Tail type Straight 92 56.44
Curly 63 38.65
Docked 8 4.91
Head profile Concave 140 85.89
Straight 23 14.11
Coat colour type Black (B) 110 67.48
White & B 38 23.31
Brown & B 15 9.20
Coat colour Plain 118 72.39
pattern Patchy 26 15.95
Spotted 19 11.66
Snout Short & cylindrical 102 62.58
Long & cylindrical 61 37.42
Body hair type Short & straight 71 43.56
Long & dense 46 28.22
Long & curly 35 21.47
Sparse 11 6.75
Backline Straight 25 15.34
Swaybacked 138 84.66

52
As indicated in Table 7, ears of local pigs in Ghana were droopy, semi-lop with majority

having erect ears with forward, backward or upward orientation. These local pigs also

possessed mainly smooth skin with a few showing wrinkled skin. Curled as well as

straight tails could be noticed among the local pigs with majority presenting straight tail

type. Head profile of most of the local pigs was concave (Appendix 4) and the rest had a

shape classified as straight. Coat colour pattern among the local pigs were white, black,

brown and their mixtures whiles black was predominant. The patterns of these coat

colours were plain (Appendix 4), patchy or spotted. A large number of the local pigs had

short and cylindrical snout whiles the rest were long and cylindrical. Hair types of local

pigs were short, long, straight, curly (Appendix 4), dense or sparse. Predominantly, local

pigs presented short and straight hair types with swaybacked backline.

4.2.2. Quantitative variables

The Table 8 and 9 show the effect of age and sex on linear body measurements. The ages

of the animals were grouped into three categories (0 – 8, 9 – 12 and over 12 months). The

results indicated an increasing order of measurements (Means ± Standard Errors) of the

local pigs with respect to their age groups in all the variables. On the other hand, female

local pigs had higher linear body measurements than their male counterparts with respect

to their age groups in almost all the quantitative variables involved. However, age of the

local pigs had a significant effect (P < 0.05) on their linear body measurements whiles

sex had no significant influence (P > 0.05) on them.

53
Table 8: Effect of age on linear body measurements (Means ± Standard Errors)

Age (months)

Body measurement 0-8 9 - 12 Over 12

Body Length 53.6 ± 1.19a 68.1 ± 2.26b 83.8 ± 4.1c

Height at Withers 36.9 ± 0.77 a 48.6 ± 1.38 b 53.1 ± 2.14 c

Heart Girth 49.1 ± 0.96 a 62.6 ± 2.04 b 72.1 ± 3.5 c

Snout Length 18.4 ± 0.43 a 25.1 ± 0.97 b 27.7 ± 1.37 c

Hind Limb 23.7 ± 0.48 a 29.9 ± 0.75 b 34.3 ± 1.34 c

Fore Leg 19.7 ± 0.52 a 26.4 ± 0.70 b 30.3 ± 1.24 c

Head Length 13.7 ± 0.28 a 18.2 ± 0.49 b 20.7 ± 0.94 c

Tail Length 12.5 ± 0.50 a 17.5 ± 1.02 b 20.5 ± 1.09 c

Facial Length 15.7 ± 0.37 a 20.8 ± 0.60 b 23.7 ± 1.06 c

Ear Length 5.7 ± 0.23 a 8.4 ± 0.55 b 10.0 ± 0.56 c

Teat numbers 11.5 ± 0.19 a 11.5 ± 0.30 b 11.8 ± 0.28 c

* Means within same row with different superscripts are significantly different (P <0.05).
* All measurements are in centimetres (cm) except teat numbers that were counted

54
Table 9: Summary statistics on the effect of sex on linear body measurements within age groups (means ± Standard Error)
BM Age (months)
0–8 9 – 12 Over 12

M (n= 41) F (n=45) M(n=8) F(n=26) M(n=14) F(n=29)

Body Length 51.4± 1.51* 55.6 ± 1.76* 66.9 ± 2.14* 71.8 ± 6.83* 80.9 ± 3.89* 89.7 ± 9.73*

Height at Withers 35.7 ± 0.97* 38.1 ± 1.17* 48.1 ± 1.37* 50.2 ± 3.95* 52.6 ± 2.44* 54.1 ± 4.33*

Heart Girth 47.1 ± 1.26* 50.9 ± 1.40* 61.5 ± 4.2* 66.4 ± 4.21* 70.2 ± 3.72* 75.9 ± 7.80*

Hind Leg 23.8 ± 0.66* 23.8 ± 0.66* 29.8 ± 0.72* 30.6 ± 2.28* 34.4 ± 1.62* 34.0 ± 2.60*

Fore Limb 19.4 ± 0.66* 20.1 ± 0.79* 25.9 ± 0.57* 27.9 ± 2.37* 30.1 ± 1.38* 11.4 ± 1.19*

Ear Length 5.1 ± 0.29* 6.3 ± 0.32* 7.9 ± 0.49* 9.9 ± 1.65* 9.4 ± 0.61* 21.1 ± 2.37*

Tail Length 11.7 ± 0.78* 13.2 ± 0.64* 17.6 ± 1.15* 17.2 ± 2.29* 20.2 ± 1.13* 21.1 ± 2.37*

Head Length 13.8 ± 0.42* 13.7 ± 0.38* 18.3 ± 0.51* 18.0 ± 1.32* 20.3 ± 1.08* 21.6 ± 1.88*

Snout Length 18.4 ± 0.64* 18.5 ± 0.54* 25.0 ± 0.90* 25.3 ± 3.05* 26.3 ± 1.22* 30.6 ± 3.29*

Facial Length 15.5 ± 0.50* 15.8 ± 0.56* 21.0 ± 0.59* 20.1 ± 1.73* 23.2 ± 1.25* 24.6 ± 2.02*

Teat numbers 11.8 ± 0.25* 11.8 ± 0.25* 11.5 ± 0.34* 12.0 ± 0.66* 11.6 ± 0.32* 12.3 ± 0.55*
*Means in the same row within the same age group are not significantly different (P > 0.05).
* n = the number of males (M) and females (F) sampled within each age group

55
4.3. Characterization of pig production systems

4.3.1 Type of farming systems practiced by local pig farmers

Extensive/scavenging system of producing local pigs was the predominant system of

rearing local pigs (56%) followed by the semi-intensive system (25%). Figure 2 shows

the percentage of various production systems practiced by local pig farmers in the

sampled areas.

60

50
Percentage of farmers

40

30

20

10

0
Extensive Intensive Semi-intensive
Figure 2: Farming systems practiced by local pig farmers sampled

All the seventy-nine farmers interviewed had at least one other vocation in addition to the

pig production. Majority of the farmers who keep local pigs were involved in crop

cultivation and fishing (Table 10). Most of these farmers fed their local pigs with

household wastes such as peels of yams, potatoes, cocoyam, boiled cassava, brans and

cereal grains like maize.

56
Table 10: Other vocations of local pig farmers

Occupation Responses Percentage of farmers

(%)
Crop cultivation 50 30.7

Fishing 38 23.1

Government 30 18.4

Labour 25 15.3

Private 20 12.4

4.3.2. Herd size

The size of local pig herd varied between farmers in Ghana with predominant numbers

falling within the small herd size as shown in the Table 11 below.

Table 11: Herd size of sampled pig farms

Herd size Number Percentage

of farmers
1 – 10 49 62.03

11 – 20 22 27.85

Above 20 8 10.13

4.3.3. Reasons for raising local pigs

Most farmers rear pigs for meat and cash or as savings (Table 12). Other minor reasons

for keeping pigs were for manure, breeding and cultural or social demands.

57
Table 12: Reasons for raising local pigs in Ghana

Reason Responses Percentage of farmers

(%)
Meat/consumption 72 33.2

Saving/cash from sales 70 32.3

Manure 35 16.1

Breeding 25 11.5

Cultural and social reasons 15 6.9

As indicated in Table 13, category (B) reasons for keeping local pigs were diverse, while

the predominant reasons were easy management, low disease incidences and cost

effectiveness.

Table 13: Reasons for raising local pigs

Reason Responses Percentage (%)

Easy management (A) 18 22.78

Cost effective (B) 10 12.66

Adaptability (C) 6 7.60

Low disease occurrence + A + B + C 32 40.51

A+B 13 16.46

58
4.3.4. Preference for the local pig breed

Although most local pigs sampled showed aggressive temperament (70.73%), farmers

reported that the ABP is well adapted to their environment and can eat vegetation that is

much more fibrous than the exotic breeds. They are resistant to many of the prevalent

diseases and have good mothering ability. Other reasons included their small body sizes,

production of tasty pork than imported ones and their excellent foraging ability.

4.3.5. Challenges being faced by local pig farmers

Farmers reported feeding (41%), housing (35%) labour (14%) and diseases (10%) as the

major limiting factors affecting their pig production (Plate 2). Few farmers also reported

some common diseases affecting their local pigs. Access to veterinary care was difficult.

Lack of capital and support from the Government, no planned breeding program and the

poor husbandry practices (record keeping and sanitation among others) were other

concerns of these local pig farmers.

59
Plate 2: Typical housing structures used for local pigs

60
4.3.6. Prevalent pig diseases in the study areas

Most of the local pig keepers complained of a number of diseases that affected their

animals (Figure 3). Those that kept the ABP’s indicated diarrhea being a common disease

condition in the pigs, followed by mange/lice infestation, worms, pneumonia and

aneamia in that order.

6%
17% 40%
10% Diarrhea
Mange/Lice infestation
27% Cough/Pneumonia
Worm
Aneamia

Figure 3: Prevalent pig diseases in the study areas

61
4.4. Prediction of live body weights of ABP and its crossbreds based on linear body

measurements.

Using various linear body measurements to predict live body weights, the following

results were obtained as shown in the Table 14.

Table 14: Prediction equations for live weight of ABP and their Crossbreds based on

simple linear and multiple linear regression analysis

Model Equation R2 (%)

Simple linear regression LW = - 12.26 + 0.56 BL* 88.90

LW = - 8.44 + 0.54 HG* 79.60

LW = - 12.33 + 0.68 HW 81.30

Multiple linear regression LW = - 12.90 + 0.41 BL + 0.18 HG 90.5

LW = - 12.59 + 0.51 BL + 0.07 HW 88.4

LW = - 13.92 + 0.39 HW + 0.28 HG 89.0

LW = - 13.53+ 0.30 BL + 0.19 HG + 0.13 HW 90.3

*LW = live weight, BL = body length, HW = height at withers, HG = heart girth.

62
4.5. Molecular characterization of local pigs in selected districts of the coastal

Savannah zone of Ghana

The phylogenetic tree below (Figure 4) depicted three major clades: the first, containing

the local pigs from the two coastal regions in Ghana. The second clade contained

European Sus haplotypes and Ghanaian local pigs. The last clade contained Asian Sus

haplotypes and Ghanaian local pigs. Some of the Ghanaian haplotypes form distinct

clusters within the European clade as supported by the high bootstrap values. At the same

time, there was another distinct cluster containing Ghanaian haplotypes branching

together with Asian haplotype with a very high nodal value. The Ghanaian haplotypes

clustering differently with both European and Asian haplotypes indicates that they have

different ancestries.

63
 Clade
1

Clade
2

Clade
3

Figure 4: Phylogenetic tree involving Ghanaian local pigs, European Sus haplotypes (EH), Asian
Sus haplotypes (AH). Figures on the internodes are bootstrap probabilities based on 500
replications. GARF (Greater Accra Region female pig), GARM (Greater Accra Region male pig),
CRF (Central Region female pig), CRM (Central Region male pig), AFW (African Warthog).

64
The results of the average genetic distance within the Sus haplotypes indicated a slightly

higher variation within the Central Region haplotypes than all the other haplotypes.

However, those that were from Greater Accra Region were very much alike (Table 15).

Table 15: Mean Genetic Distance within Sus Groups (± Standard Errors)

Sus Haplotype Average Genetic Distance

1. Asian 0.009 ± 0.003

2. Central Region 0.015 ± 0.003

3. European 0.006 ± 0.002

4. Greater Accra Region 0.003 ± 0.001

With respect to the average genetic distance between the Sus groups, the variations

between the AWH and all the other Sus haplotypes were much higher. Between Asian

haplotypes and the others, there was also a slightly higher variation. In the case of

European haplotypes, the results indicated a smaller variation between them and that of

the CR and GR Sus haplotypes.

Table 16: Genetic Distance between Sus Groups (lower diagonal)

AWH Asian CR European GR

AWH* 0.013 0.013 0.013 0.014
Asian 0.091 0.005 0.006 0.007
CR* 0.094 0.026 0.002 0.003
European 0.090 0.028 0.011 0.003
GR* 0.094 0.030 0.011 0.008
*Standard Errors on upper diagonal
*AWH = African Warthog, CR = Central Region, GR = Greater Accra

65
 CHAPTER FIVE

DISCUSSION

5.1 General information on local pig farmers

Local pigs in the study areas were mostly owned by men but generally managed by

women indicating their role in animal rearing compared to the men who manage the crop

farms. This agrees with FAO report that women play a critical role in subsistence

agricultural production including livestock keeping and food processing (FAO, 1995).

Pigs are generally considered as small stock and therefore managed by women like other

small stock that includes poultry and goats (FAO, 2005). The results of this study also

revealed that majority of the local pig farmers were illiterates and this influenced their

poor husbandry practices. Among those farmers who were not illiterates, most of them

could hardly read and write. Similarly, Aina (2007) reported that majority of African

farmers are illiterates and most of them cannot read or write in any language. Religious

background also influences the choice of livestock. Most of the local pig farmers were

Christians because Muslims were not found to be involved in pig farming due to the

religious taboos with respect to pork consumption.

5.2 Morphological characterization of local pigs in Ghana

The study sampled more female pigs than males. This was expected as male pigs in the

areas under study had a higher culling rate than female pigs. The low mean live weight

and body measurements recorded in these samples show that the ABP are generally

smaller than the exotic or imported breeds and their crosses. The differences could be

influenced by environmental conditions such as climate, nutrition and management.

66
Lekule and Kyvsgaard (2003) reported that smaller size of local pigs may impact a

greater ability to survive under harsh conditions than larger size, as an evolutionary

adaptation to conditions of low-input production. A research conducted also revealed that

local genotypes have less demand for feed because of their small body size (Ndindana et

al., 2002) and can utilize fibrous and tannin-rich diets more efficiently than imported

genotypes (Kanengoni et al., 2002; Mushandu et al., 2005).

5.2.1. Number of teats

Variation in number of teats among pigs is also a widely used criterion in morphological

diversity studies. The number of teats in the local pigs ranged between 4 and 8 pairs with

5 pairs being the most common. Teat number is an important fertility trait reflecting the

mothering ability of sows. Improved local pigs were those that had high number of paired

teats. The higher the number of teats, the better the mothering ability of the pig.

5.2.2. Coat colour type and pattern

Coat colours obtained included black, white, brown and black, and white and black.

There was varied colouration patterns amongst the local pig populations sampled with

predominantly plain followed by patchy and spotted of various colours. Similar coat

pattern and colour were reported for indigenous pig types in other countries (Holness,

1991; Nengomasha, 1997; Mhlanga et al., 1999; Ncube et al., 2003; Chiduwa, 2006) who

reported that local pigs have many coat colour variations with black and brown being

most common while white is infrequent. The white and black colour type could be

attributed to the influence of crossbreeding with the Large White.

67
5.2.3. Head and snout characteristics

Head profile of local pigs was mostly concave with a few being straight. Majority of the

local pigs presented short and cylindrical snouts as compared to long and cylindrical. The

finding is contrary to that of an earlier study on ABP by Barnes and Fleischer (1998) who

found the snout of ABP to be long and cylindrical. The difference could be attributed to

the indiscriminate crossbreeding with the exotic breeds as a result of free ranging system

of producing pigs.

5.2.4. Ear type and orientation

Majority of the local pigs had erect ears projecting backwards. Sahaayaruban et al.

(1983) also reported that the Sri Lankan local pigs have short, erect ears pointed

backwards. Likewise, majority of prick-shaped (erect) ears in local pigs have been

reported in Zimbabwe (Mashatise et al., 2005; Chiduwa, 2006; Subalini et al., 2010)

5.2.5. Tail type and backline characteristics

Local pigs presented curled and straight tails with their backline either swaybacked or

straight. Majority of the local pigs possessed swaybacked backline and straight tail. A

large number (72%) of village pigs have also been reported to possess straight tails in Sri

Lanka (Subalini et al., 2010).

5.2.6. Body hair type and skin

Local pigs showed different hair types with the short and straight type being the most

common. Local pigs mostly had smooth skin with few having wrinkled skin type. The

wrinkled skin of local pigs could be attributed to old age of the animals and continuous

parasitic infestations which result in itching of their body.

68
5.2.7 Effect of age and sex on linear body measurements

Results of the survey indicated that age of local pigs had a significant influence (P <

0.05) on their body measurements. They increase in size and weight as they grow.

Additionally, female local pigs sampled had slightly higher linear body measurements

than their male counterparts but were not statistically different (P > 0.05). The difference

in linear body measurements could be as a result of their age differences since most of the

female local pigs sampled were older than the male local pigs.

5.3. Characterization of production systems

5.3.1. Type farming systems practiced by local pig farmers

Production system determines the type of pigs that can be raised by farmers under those

prevailing conditions (Lekule and Kyvsgaard, 2003; Mashatise et al., 2005). The most

common pig husbandry practices used in local pig production systems in Ghana include

extensive/scavenging/free range, semi-intensive and intensive systems of production.

Free range and semi-intensive systems of producing local pigs were common due

possibly to the fact that, majority of the farmers who kept local pigs were involved in

crop cultivation or fishing. Farmers who were into intensive farming system mostly

reared crosses and few exotics.

Most often, available resources of the area is the deciding factor in selecting the

component of mixed farming system. In most of the communities, because pigs can be

destructive to crops, local pigs are typically kept indoors or in an enclosure during the

rainy season and are fed harvested plant matter. They are allowed to roam freely during

the dry season. Often they are fed on the by-products or brewers waste and in some

places, cassava is specially grown for them. Extensive/free range production system

69
allows pig (sows) farmers who do not have boars to be mated and reproduce. However,

these pigs rely on low inputs and as a result, they have slow growth rates and low feed

conversion efficiency (Chimonyo et al., 2005). Productivity is also compromised by the

seasonal fluctuations in feed supply.

Pigs produced in extensive/free range production system have the advantage to forage on

a variety of feedstuffs (Chimonyo et al., 2005). Commonly used feeds include fish meal,

cassava peels, maize husks, kitchen waste, vegetables, water melons, fruits, grasses and

brewers waste. Housing for these local pigs were however very poor except on few

commercial farms. A greater number of farmers kept both ABP, and Large White in the

same pen as shown in Appendix 5. However, free range system of producing pigs permits

outbreak and spread of diseases as the animals scavenge. Similar case was reported in

South Africa on the outbreak of Classical swine fever (CSF) in 2005. The South African

government recommended that farmers must enclose their pigs in specially built pens to

minimize the risk of such outbreaks (Madzimure, 2011).

Mating was uncontrolled as a result of the free ranging system of production.

Indiscriminate crossbreeding occurs as a result within the local pigs and with other exotic

pig breeds. Under these circumstances, cross breeding does not benefit farmers since it

needs to be directional to become beneficial. Similarly, Subalini et al. (2010) reported

that crossbreds may not be the best choice under the scavenging system compared to pure

indigenous, because of their adaptability to be raised under scavenging system.

Under semi-intensive system, local pigs performed better than those pigs raised under

extensive system, because apart from scavenging freely during the day, they were

70
supplemented with feed. This finding is in agreement with a research conducted by

Ironkwe and Amefule (2008) who reported that local pigs raised under semi-intensive

system of farming tend to have better nutrition and body conditions than pigs under the

extensive system. Unlike the extensive system of producing local pigs, productivity is

generally high in the intensive system but because it demands high investment (for

nutrition and management); farmers find it difficult to increase their production. Few

farmers and Government farms practiced intensive system of rearing local pigs due to

expensive nature of keeping pigs as compared to semi-intensive and extensive systems.

There is one pig breeding station in Upper West region of Ghana that is mandated to

improve upon the ABP performances.

5.3.2. Herd size

Most of the local pig farmers tend to keep all categories of pigs including boars, sows,

young boars, gilts and piglets. Farmers that reared between 1 and 10 local pigs were in

the majority. This may be due to difficulties in feeding relatively larger number of

animals. Indeed, small herd sizes (3-9) of indigenous pigs have been reported in other

countries (Chiduwa et al., 2008; Subalini et al., 2010). Although extensive/free range

system was common, few farmers kept more than 20 local pigs. High cost of feed was the

major reason influencing the small herd in pig production. This contributed to boars

being culled or sold early to minimize cost/pressure of feeding. Subalini et al. (2010) also

concluded that several factors influence village pig herds and these include; level of

investment, level of income generated by pig farming, pig keeping experience and size of

the household.

71
5.3.3. Reasons for raising local pigs

Pigs reared for meat and savings/cash from sales revealed by almost all the farmers

indicated that pig production was a source of protective income to the farmers. Huynh

(2005) reported that pigs are usually sold when there is an urgent need for cash, such as

paying for school fees, medical expenses, travelling, cultural celebrations and debts.

Raising local pigs for manure production was also eminent. This shows the

interdependence of crop and animal production in smallholder farming areas. Thorne and

Tanner (2002) reported that the manure can be used to generate biogas and the residue

can be used as fertilizer for crop production. Selling to raise income followed by

consumption as the major functions of pig production have been reported elsewhere

(Mashatise et al., 2005; Ajala et al., 2007). However, in Tanzania, Vietnam and Southern

Botswana native pig farming is very attractive as they served as the family bank as well

as a source of valuable fertilizer for paddy and vegetable plots (Ranald, 2000).

Reasons for keeping local pigs were diverse as reported by the farmers. However, these

observations are slightly different from a research by Subalini et al. (2010) who reported

easy management, low disease incidences and cost effectiveness as predominant reasons

of keeping local pigs in Sri Lanka. Likewise, Sovann and San (2002) reported that in

Cambodia, local pig keeping is not very attractive due to high cost of feeding.

5.3.4. Preference for the local pig breed

Results of the survey indicated that the local pig (ABP) is well adapted in the country and

can eat vegetation that is much more fibrous than the exotic breeds. Darfour-Oduro et al.

72
(2009) reported that the ABP is well adapted to tropical temperatures because of its

resistance to sunstroke (sudden prostration due to exposure to the sun or excessive heat).

Local pigs are also resistant to many of the prevalent diseases and have good mothering

ability. Selection for disease or parasites resistance is important since farmers cannot

afford to purchase commercial drugs. Local pigs have been reported to survive drought

incidence in Ghana (Barnes and Fleischer, 1998) and outbreaks of ASF in Malawi and

Mozambique (Haresnape and Wilkinson, 1989). Roessler et al. (2008) also reported that

local pigs’ ability to survive natural calamities, such as droughts could be more important

than high productivity for communal farmers in South Africa. Apart from these things,

small body sizes of local pigs, their production of lean meat with very low fat make them

popular with farmers. The findings of this study is in agreement with a research

conducted by Lemke and Zárate (2008) who concluded that meat from pigs raised under

free ranging rearing system has a better taste than imported ones because it is lean.

Similarly, a number of researches have revealed that local pigs have multiple adaptive

traits to harsh environments (Holness, 1991; Chimonyo et al., 2005; Marufu et al., 2008).

These traits include small body sizes, heat tolerance, and production of tasty pork, good

mothering ability of sows and excellent foraging ability (Madzimure, 2011).

Foraging ability for instance is an advantage to smallholder pig farmers because they

usually do not have sufficient money to buy feed and pay for labour to feed the pigs.

Thus foraging ability of local pigs implies that there is reduced production cost for the

rural farmers. Foraging ability can be measured by the free ranging pigs’ ability to

reproduce and maintain good body condition without any feed supplementation.

73
5.3.5. Challenges faced by local pig farmers

Apart from feed, housing and labour that farmers complained as major limiting factors to

increasing pig herd size, lack of capacity to manage large number of pigs, low

productivity, old age of pigs and the outbreak of diseases could be other factors

responsible for the low herd numbers. Little or lack of Government support to these

farmers is a factor of this poor husbandry practices. Farmers indicated that a constant

flock size essentially depends on a large number of reproductively active females that

must be kept for long periods of time. This is in agreement with the findings by Adeola et

al. (2013) and Holness (1991) who stated that smallholder pig producers have a higher

number of females due to high boar culling rates.

No planned breeding program was established and this led to the uncontrolled mating

among the pigs. Farmers constant complain about common diseases (Figure 3) affecting

their pigs were as a result of lack of veterinary services. As such, farmers used herbs to

treat diseases that affected their pigs as an example, pawpaw leaves were used for

treatment of internal parasites.

The free ranging system also limits the number of pigs that can exist in the community.

Farmers indicated that local pigs are destructive in nature and are mostly killed by crop

farmers whose farm produce are destroyed by these pigs. The finding of this work is also

in line with research conducted in different countries by Mashatise et al. (2005) and

Lemke et al. (2007).

74
5.3.6. Prevalent Pig diseases in the study areas

Low disease incidences were reported even though the majority of local pigs were reared

under harsh conditions. This may be due to the disease resistibility of local pigs to a

certain extent. Farmers reported diarrhoea being a common disease that attacked the local

pigs. Majority of farmers who kept both ABP and crossbreds reported that the exotic

(Large white) and their crossbreds are easily attacked by diseases than the ABP’s. Mange

and lice infestation caused considerable losses because of the extreme itching and

continuous scratching of the affected area, especially when prevalence is high during the

dry season. In several cases, the entire body surface becomes affected. There is loss of

appetite and body weight gain is severely depressed. Farmers noted that the incidence of

diarrhoea was more common with young pigs (piglets) and was observed to be probably

responsible for their mortalities.

5.3.7. Basic temperament

The aggressiveness of local pigs signifies their mothering ability in terms of protection of

their piglets against predators.

5.4. Prediction of live weights of ABP and its crossbreds based on linear body

measurements

Knowing the weight of livestock at a given time helps in the determination of feed

requirement (Gunawan and Jakaria, 2011), determination of animal health status, growth

rates, space allowances, drug dosages and time when animals are to be sent to the market

(Brandl and Jorgensen, 1996).

75
Based on the results (R2 value) of the simple linear and multiple regression analyses of

body weight on linear body measurements, the high and significant correlation coefficient

between body weight with body length and heart girth suggest that either of these

variables or their combination would provide a good estimator for live body weight in

Ghanaian local pig ecotypes (both sexes), especially in areas where weighing scale is not

available. This ability could adequately reward farmers rather than the middlemen that

tend to gain more profit in livestock production business. However, a guide is provided in

Appendix 6 for prediction of body weight based on BL and combination with HG.

Compared to Nigerian indigenous pig (NIP), which is known to have originated from the

same ancestor as the ABP, equations involving HG and TL (TL = tail length) (R2 =90.3)

have been established for predicting the live weight of male NIP while HG and IW (inter

orbital width) (R2 =90.6) for females. For their crossbreed pigs (CBP), BL and RH (rump

height) (R2 =80.4) were useful for predicting live weight in both sexes (Adeola et al.,

2013). Machebe and Ezekwe (2010) reported heart girth, body length and flank-to-flank

being linear body measurements to estimate live body weights in growing-finishing gilts

raised in Nigeria. A research conducted by Mutua et al. (2011) indicated that body length

and heart girth were the best estimators for live body weight for young, market-age and

breeding age pigs in rural Western Kenya. The two linear body measurements explained

88% to 91% of the total variation in weight. Walugembe et al. (2014) also reported that

body length, heart girth, height and body width were strongly predictive (R2 = 90.2) of

live weight in Ugandan village pigs. However, using many measurements (multiple

regressions) on one animal to determine its body weight may confuse the illiterate farmer.

76
As such, farmers have to use measurements which are simple and not complex.

Therefore, BL alone should be used to predict the live weight of local pigs.

5.5. Molecular characterization of local pigs in the coastal savannah zone of Ghana

We found a largely European influence on the local pig population from the coastal

savannah zone of Ghana. This could be due to trade between the then Gold Coast and

many European countries. Our results confirm an earlier study by Blench (1999) who

revealed that African native pigs were extensively admixed with exotic breeds as a result

of the Portuguese exploratory journeys, beginning in the 15th century and colonization of

the continent by several European countries in the 19–20th centuries. Similarly, Ramirez

et al. (2009) reported the existence of a clear genetic dichotomy between East and West

African local pigs. Their result was that local pig haplotypes from West Africa (Nigeria

and Benin) clustered together with European haplotypes with a mean frequency of 50%

and to a lower extent, Near Eastern Sus scrofa populations. More significantly, pigs from

West Africa did not display any of the haplotypes that are characteristic of Asian (Far

Eastern) populations. On the other hand, pigs from East Africa confirmed the presence of

Asian alleles. This might be as a result direct introgression with Far Eastern breeds, or

they might have been introduced through either a European intermediary, given that

British breeds were strongly admixed with Chinese pigs in the 18–19th centuries (Porter

1993; Ramirez et al., 2009). However, result of this study indicates an introgression of

both European and Asian haplotypes into the local swine genetic resources of Ghana. In

terms of origin, estimates of genetic distance between groups have revealed that the

Ghanaian haplotypes seem to be more closely related to European than the Asian pigs.

77
 CHAPTER SIX

CONCLUSIONS AND RECOMMENDATION

6.1 Conclusions

 Government has given little attention to local pig production.

 Illiteracy rate among farmers is high as seen in their lack of appreciation for good

husbandry practices. Housing, feeding, health care for local pigs is poor to non-

existent.

 Morphologically, local pigs were characterized as having a predominantly

concave head profile, black coat colour, plain coat colour pattern and erect ears.

 In times of selection, drug administration and determination of market weight and

prices, farmers can easily estimate the body weight of their local pigs based on

their linear body measurements.

 Phylogenetic studies based on mitochondrial DNA of local pigs sampled from the

coastal savannah zone indicated an influence of European and Asian wild boars

on Ghanaian local pigs. Admixtures between local pigs in the sampled areas were

found and these confirmed their multiple ancestries. Although, there appeared to

be diverse genetic origins of the ABP, molecular characterization showed their

remarkable closeness to European Sus haplotypes.

6.2 Recommendations

 Local pig production system in Ghana needs support from government and other

stakeholders to avoid undesirable breeding practices.

78
 When appropriately utilized in breeding programmes, local pigs can contribute to

increased productivity. Research institutions and universities should therefore

take lead in appropriate crossbreeding programmes and sell the improved

crossbreds to farmers.

 Breeding farms like APD/MOFA’s pig breeding station at Babile needs to be

sustained to ensure a pure gene pool of the ABP.

 Improvement in husbandry practices (housing, record keeping, sanitation and

feeding) should be encouraged to protect pigs from direct rainfall, sun, minimize

heat stress and help control parasitic infections. Development agencies should be

approached to fund proper housing structures for pig projects and assist farmers

through training and provision of improved breeding stock. Education and

training of farmers especially women will help them appreciate the importance of

good husbandry practices.

 To minimize the inconveniences in restraining of the animals, BL alone could be

reliable to predict the body weight of local pigs and a ruler can be prepared based

on the BL.

 Local pigs display multiple sources of origin and there is a need to do further

genetic characterization on their origin, coat colours and unique economic traits

such as disease resistance and carcass quality. This will help use their favourable

and unique genetic attributes to develop crossbreds to improve the productivity of

the pig industry.

79
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 APPENDICES

Appendix 1: Questionnaire used in characterization of local pigs and their

production systems in Ghana.

UNIVERSITY OF GHANA NO: ………

COLLEGE OF AGRICULTURE AND CONSUMER SCIENCES

DEPARTMENT OF ANIMAL SCIENCE

CHARACTERIZATION OF LOCAL PIGS AND THEIR PRODUCTION SYSTEMS

IN GHANA

- QUESTIONNAIRES FOR DATA COLLECTION

A. PHENOTYPIC CHARACTERIZATION

1. GENERAL INFORMATION

Farm ID _____________________ Animal ID _____________________

Village / town: ____________________ Sex of animal: female male

District: _____________________ Year of birth of the animal :____(YYYY)

Region of the farm: ______________ GPRS: _________________________

Farmer’s occupation: _______________ Religion: _________________________

Educational Status:

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 2. MORPHOLOGICAL DATA

Quantitative variables

 Body weight (kg)…………………………………………………………….

 Body length (cm)……………………………………………………………

 Head length (cm)……………………………………………………………

 Tail length (cm)………………………………………………………………

 Ear length (cm) ……………(measure length or code it as large, medium or small)

 Chest girth (cm)……………………………………………………………..

 Height at withers (cm)……………………………………………………

 Teat numbers: ………………(numbers of normal and rudimentary teats counted

on the sow or gilt)

Discrete or qualitative variables

 Hair: = Short & straight; = Long & dense; = Long & curly; = sparse

 Snout: = long and thin; = short and cylindrical; = other (specify)…………

 Coat colour pattern: = plain; = patchy; = spotted; = other (specify)

 Coat colour type: = black; = black and white ; = black and brown; =other

 Head profile: = concave (dished); = straight; = convex

 Ear type: = droopy (pendulous); = semi-lop (e.g. Pietrain); = prick (erect)

 Ear orientation: = project forwards; = backwards; = upwards

 Skin: = smooth; = wrinkled

 Tail type: = straight; = curly (kinked); = docked

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 Backline: = straight; = swaybacked (i.e. markedly convex ventrally); =

other(specify)

3. PRODUCTION SYSTEMS CHARACTERIZATION

 Source of parent stock: = market; = family/inherited; = own herd; = within

country; = within village; = within district

 Type of holding/system of production: = Extensive/scavenging/free range;

= Intensive system; = Semi–intensive system

 Type of feed given to animals; ………………………………………………….

……………………………………………………………………………………

 Herd composition; ………………………………………………………………..

 Mating practice: = uncontrolled = controlled

 Reasons for raising local pigs

Category (A) reasons

= meat/consumption; = savings/cash from sales; = Manure production;

= breeding; = cultural & social purposes

Category (B) reasons

= Easy management; = Cost effective; = Adaptability; = Easy management

+ Low disease occurance + Adaptability + Cost effective; = Easy management

+ Cost effective.

 For how long have you kept the breed? ……………………………………………

 Basic temperament: = placid and friendly; = aggressive (wild)

 Why do you prefer the local breed? .................................................................

…………………………………………………………………………………..

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 ………………………………………………………………………………………

………………………………………………………………………………………

 Challenges being faced……………………………………………………………..

………………………………………………………………………………………

………………………………………………………………………………………

………………………………………………………………………………………

 Reason(s) for culling ……………………………………………………………….

………………………………………………………………………………………

………………………………………………………………………………………

 Prevalent diseases in the area……………………………………………………….

………………………………………………………………………………………

………………………………………………………………………………………

………………………………………………………………………………………

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 Appendix 2

Morphometric measurements of local pigs in Ghana

Plate 3: Figure of type of weighing scale used and how local pigs were weighed

117
Plate 4: Figure of how weight of pigs was taken at research or Government farms

118
Plate 5: Figure of how tail of local pigs were measured

119
 Appendix 3

Animal and sampling information for Molecular Characterization of Local pigs in the

Coastal Savannah zone of Ghana.

Date of collection: _______________________________________ (DD.MM.YYYY)

Breed's full name: _______________________________________________________

Local names: _______________________________________________________

Breed of Boar: _____________________ Breed of Sow: _____________________

Boar ID: _____________________ Sow ID: _____________________

Size of herd: ___________________________________

Type of biological material: blood tissue hair other (specify)

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 Appendix 4

Phenotypic diversity of sampled pigs

Plate 6: A crossbred (ABP x Large White) showing patchy coat colour pattern, semi-lop
ears projecting forward, a concave head type, long and cylindrical snout type.

121
Plate 7: ABP with a long and curly body hair type

122
Plate 8: An ABP with a plain coat colour pattern, straight tail and a swaybacked backline

123
 Appendix 5

Image of husbandry practices

Plate 9: ABP and Large White pig being kept in the same pen.

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 Appendix 6

The table below is an estimate of body weights based on BL alone and combination of

BL and HG which had higher R2 values.

Prediction equations: LW* = - 12.26 + 0.56 BL and LW = -12.90 + 0.41 BL + 0.18 HG*

A table of live weight estimates for local pigs based on BL and combination with HG.

Body measurements Estimated weights Actual weights

BL HG Based on BL Based on BL & HG

52 53 16.8 17.9 14
55 51 18.5 18.8 18.5
58 54 20.2 20.6 20
60 57 21.3 21.9 20.5

59.5 63 21.0 22.8 22.5

56 54 19.1 19.8 20.5

54.5 50 18.2 18.4 20

66 64 24.7 25.7 24.5

68 62 25.9 26.1 26.5

70 60 26.9 26.6 26

*BL = body length, HG = Heart Girth, LW = Live weight

125