THE BOVINESNP50 GENOTYPING ARRAY IN FOUR SOUTH AFRICAN CATTLE POPULATIONS

Get Complete Project Material File(s) Now! »

Chapter 2 Literature review

Introduction

Farm animal genetic resources include all species, breeds and strains of animals, particularly those of economic, scientific and cultural interest to mankind used for agriculture either at present or potentially in the future (FAO, 2005; Alderson, 2010). A breed is a homogenous group of domestic livestock with definable and identifiable external characteristics that allow it to be separated by visual assessment from other similarly distinct groups within the same species (FAO, 2005). Breeds may share a large fraction of their genome with other breeds, but each holds distinctive combination of genes that may confer unique traits particularly for adaptation to specific environments (Scherf, 2000; FAO, 2010). Breeds are also linked to their origin with regard to tradition and history or a geographical region (Alderson, 2010). Indigenous and local developed breeds possess adaptive traits that are usually associated with tolerance to various diseases, extreme temperatures and humidity, changes in the availability of feed, adaptation to low capacity management and ability to survive, produce and reproduce for extended period of time (Scherf, 2000). These specific breeds hold potential in times of biological stress such as famine, drought or disease epidemics due to years of adaption to the pressures of the specific local environments. This review was aimed at unveiling the characterisitics of South African indigenous and locally developed cattle breeds (Afrikaner, Nguni, Drakensberger and Bonsmara), their genetic potential and to discuss opportunities for application of genomics tools.

Historical overview of South African indigenous and locally developed breeds Afrikaner breed

The Afrikaner cattle is one of the oldest indigenous cattle breeds in South Africa. This breed was brought to South Africa by the Khoi-Khoi people who migrated along the western side of Southern Africa to areas of the Western Cape Province in 1652 (Scholtz, 2010). This Southward migration through some of the harshest country of the subcontinent led to the evolution of a hardy, heat, parasite and drought tolerant breed. The first selection of this breed was carried out by the transporters who carried goods around the country in ox wagons before the advent of railways; and selected for cattle of uniformity in build and color (Scholtz, 2010). At the end of the 18th century, the Afrikaner was well-defined as a cattle breed and was greatly appreciated by the settlers for the power, speed, stamina, and hardness and also for their meat and milk (Bergh et al., 2010) The Afrikaner (Figure 2.1), which belongs to the Sanga type of cattle, was the first indigenous South African breed to form a breed society in 1912 (Bergh et al., 2010).
The modern Afrikaner is medium-framed, yellow to red coloured with lateral horns with a typical twist or sometimes dehorned. This breed has the characteristics of heat, parasite and tick tolerance, disease resistance (e.g. redwater, heartwater and gallsickness), good walking and grazing ability, easy calving and exceptional mothering ability, ideal mothering line for cross breeding and development of hardy composite among others. The Afrikaner has mature weight of 820 – 1090 kg and 550 – 730 kg, average birth weight of 34 kg and 32 kg and average weaning weight of 210 kg and 195 kg for males and females respectively. Their age at first calving is between 36 to 41 months and they have an average inter-calving period of 445 days. This breed has an average carcass weight and dressing percentage of 181.7 kg and 54 % respectively (Bergh et al., 2010). It is known for good meat quality being tender, tasty and succulent. In crossbreeding programs the Afrikaner has been shown to improve the quality of the meat of the breed with which it is crossed, especially with regard to tenderness (Strydom, 2008). The Afrikaner breeders have over the past two decade focused on economically important traits in the modern beef production environment, namely fertility, all aspects of functional efficiency and the implementation of performance recording information in the breeding programs (Bergh et al., 2010).

Nguni breed

The Nguni cattle breed was brought to South Africa by the Khoi-Khoi people who migrated southwards from the central lake of Africa between 600 and 700 AD. These people have their lives centered around these cattle i.e. their ceremonies, their wealth and dowry, their links with other tribes, their food, clothes and welfare (Scholtz et al., 2011). The Nguni cattle are still found wherever the descendants of the original groups of the Nguni tribe settled, namely in Swaziland, Zululand and Mozambique. This breed is classified as a Sanga type (with low cervico-thoracic humps, in front legs, instead of the high thoracic humps of pure Zebu) that is native to Africa. The protein analyses indicated that they have characteristics of both Bos Taurus and Bos Indicus cattle (Meyer, 1984). The Nguni cattle are small to medium sized with bulls weighing between 500 kg and 600 kg, and cows weighing between 300 kg and 500 kg. They are characterized by their multi-coloured skin, which can present many different patterns (white, brown, golden yellow, black, dappled, or spotty), but their noses are always black-tipped and they present a variety of horn shapes. Different ecotypes of Nguni cattle were developed in the different agro-ecological regions and these are still maintained within the breed (Scholtz et al., 2011). Bothma (1993) recorded that they are about fourteen ecotypes of Nguni, however, Nortier et al. (2002) reported that the genetic differentiation determined with the aid of microsatellite markers, did not reflect differences between various ecotypes in Namibia.
Data from the South African national performance scheme shows that Nguni cattle have an average birth and weaning weight of 25 kg and 155 kg respectively (Bergh et al., 2010). Their average age at first calving is 31 months and their average inter calving period is 404 days (Muchenje et al., 2007). Scholtz et al. (1990) reported that Nguni cows are the lightest and they weaned light calves, however their growth rate and feed conversion ratio compare well with other breeds. Nguni are also the most fertile beef breed in South Africa and this might be the result of natural selection to which these animals were subjected to under the management system of Nguni people (Scholtz, et al., 2011). Strydom (2008) reported that the Nguni showed no difference in terms of meat tenderness compared to Bonsmara, Afrikaner and Brown Swiss. In addition Gertenbach et al. (2011) reported that the Nguni steers provided a satisfactory carcass in terms of classification and in their subsequent trial concluded that the carcasses of both yearling and two year old Nguni were comparable to the carcasses of Sussex steers in terms of grading and dressing percentages. The Nguni cattle has the ability to produce and reproduce under harsh environment conditions (Scholtz et al., 1991). Research has revealed that the Nguni has the most resistant to ticks in South Africa and has shown to be tolerant to tick borne diseases (Muchenje et al., 2008; Marufu et al., 2011), which are considered to be the most important problem for livestock farmers in most parts of Africa. In the study by Spickett et al. (1989), Nguni’s productivity as measured by the weaning weight of their calves was shown to be least affected by tick infestation due to its natural resistance to ticks. The Nguni is also an excellent dam line for crossbreeding, with little calving difficulties. It has an increased ability to recycle nitrogen back to the rumen, which improves microbial growth and organic matter digestion, reducing the requirement on low quality pastures and therefore need little or no supplementation during winter (Scholtz et al., 2011).
The Nguni breed was regarded as inferior in the past due to the lack of performance recording during the colonization. This perception was the results of African man living in a symbiotic relationship with his animals and also due to the fact that the Nguni had variety of colours amongst animals of the breed, which was in contrast to the general tendency in the stud breeding industry that emphasize uniformity (Scholtz & Ramsay, 2011). Thus, the breeding industry was unable to identify the much emphasized antiquated breed standard (Bonsma, 1980) and regarded these animals as an indiscriminate mixture of breeds (Scholtz, 1988). As a result little attention was paid to the improvement of this indigenous breed (Scholtz & Ramsay, 2011). Only in 1959 was the potential of the Nguni recognized following the introduction of the beef cattle recording scheme and the publication of results on the Nguni in the early 1980’s. Thus in 1983 the Nguni was recognized as a developing breed under the livestock Improvement Act (1977) of South Africa and in 1986 a breed society was established for this breed (Scholtz et al., 2011). Nguni cattle have survived over several decades in the dry, hot and harsh environment which was usually affected by tick and parasite and thus they were forced by natural selection to retain those characteristics that ensure theirs survival. Today Nguni cattle are very popular as a beef breed and also for their skin, with its Society being the second largest seed stock beef breed in South Africa (Scholtz & Ramsey, 2011).

Drakensberger breed

The Drakensberger cattle was bred and developed in South Africa. Its origin can be related back to the indigenous cattle of the Khoi-Khoi and other indigenous groups of the Cape and the adjacent areas (Dreyer, 1982). In 1837 several “Voortrekker” families left Cape Province to travel north with herds of similar black oxen, by then referred as the “Vaderland” cattle. Most of these trekkers settled along the Drakensberg Mountain range, among them were the Uys family who began farming in Volksrust area in the Mpumalanga province. This family played a significant role in the development of the Drakensberger, with strong selection within a closed herd. They bred exceptional animals in the district of Wakkerstroom and Utrecht, where they chose to settle. Their breeding program resulted in a definitive breed type, which was later known as “Uys-cattle” (Scholtz, 2010). Thirteen years later, the Department of Agriculture recommended that the “Uys-cattle” be acknowledge as a breed in terms of the Stock Improvement Act of 1934. Since the “Uys-cattle” were more prevalent in the pastures of the Drakensberg Mountains, it was recommended that the name of the “Uys-cattle” be changed to Drakensberger (Scholtz, 2010). The breeding society for this breed was recognized in 1969 and in 1980 the Society made performance recording compulsory (Dreyer, 1982). Today this breed has spread throughout the country, from Humansdorp in the south, throughout the eastern Free State, KwaZulu-Natal and eastern Mpumalanga to Messina in the Northern Province.
The Drakensberger breed date back to history, where there were no dipping fluid or proven medicine, thus it was able to withstand harsh conditions, flies, mosquitoes, ticks and parasite-borne diseases. Therefore, this breed has an edge over other breeds regarding adaptability, hardiness and tick and disease resistance (Scholtz, 2010). The Drakensberger cattle are black in color with a smooth coat, long and deep bodied medium to large framed cattle. Mature bulls weigh from 820 kg to 1100 kg and cows from 550 kg to 720 kg, calves weigh approximately 35 kg at birth. Cows remain in production for up to 20 years. The Drakensberger cows have good milk production; 240 kg weaning weight is common in stud. Cows have up to 90 % fertility and low incidence of abortion (Bergh et al., 2010). In a study by Strydom (2002), Drakensberger were shown to have the juiciest and most tasty meat with the best cut ability compared to British and Europe breeds.Drakensberger have also been shown to be resistance to heat, this could be attributed to a loose skin as well as short and shiny blue-black hair color which reflect sunlight (Scholtz, 2010). Over the last decade the emphasis for beef cattle breeding moved to meat production and thus animals with a distinctive long and well balanced, well-muscled beef carcass were developed. The modern Drakensberger is the product of such development brought by strong selection based on scientific norms. Drakensberger has continuously been selected for economically important traits such as adaptability, fertility, milk production traits, longevity, growth ability, feed turnover conversion and carcass quality (Scholtz et al., 2010).

Bonsmara breed

Bonsmara was bred and strictly selected for economic production at Mara and Messina Research Station from 1937 to 1963 by scientists under the guidance of late Prof Jan C Bonsma (Bonsma, 1980). It is the only beef breed in South Africa created through a well-documented crossbreeding programme with the aid of objectively recorded performance data combined with visual evaluation according to norms of functional efficiency (Bonsma, 1980). It was bred to perform in sub-tropical environment, where British cattle had proved to be unsuccessful and Afrikaner struggled with calving regularly. Initially five bulls of British beef breed were used on Afrikaner cows after which the progeny were performance tested. After pilot trails it was decided to continue only with the better performing Hereford and Shorthorn cross breeds. Cross-breeding trails for 5/8 Afrikaner and 3/8 Hereford or Shorthorn blood provided suggestions that the calving percentage and weaning weights were higher, while calf mortality dropped. Through strict selection of breeding animals rapid genetic progress was made. Twenty years later a superior cattle breed, performing better than other breeds in the bushveld of the Northern Transvaal was established (Bergh et al., 2010). This breed was tested successfully in about 20 commercial herds in different areas of South Africa. In 1964 the breed society was formed by twelve breeders, since then this breed has expanded within the borders of South Africa to be the most prominent beef breed with over 100 000 registered Bonsmara cattle (Bonsma, 1980).

ACKNOWLEDGEMENTS
ABSTRACT
THESIS OUTPUTS
TABLE OF CONTENTS
LIST OF TABLES
LIST OF FIGURES
LIST OF ABBREVIATIONS
1. INTRODUCTION
1.1 Background and motivation
1.2 Aim and Objectives
2. LITERATURE REVIEW
2.1 Introduction
2.2 Historical overview of South African indigenous and local developed breeds
2.3 Genomic tools
2.4 SNP discovery and SNP array development
2.5 Applications of genomic tools in population genetics and diversity studies
2.6 Conclusion
3. EVALUATION OF THE BOVINESNP50 GENOTYPING ARRAY IN FOUR SOUTH AFRICAN CATTLE POPULATIONS
Published in South African Journal of Animal Science 2013, 43 (No. 1)
4. GENETIC DIVERSITY AND POPULATION STRUCTURE AMONG SIX CATTLE BREEDS IN SOUTH AFRICA USING A WHOLE GENOME SNP PANEL
Published in Frontiers In Genetics: published: 22 September 2014 doi:10.3389/fgene.2014.00333
5. EXTENT OF GENOME WIDE LINKAGE DISEQUILIBRIUM AND EFFECTIVE POPULATION SIZE WITHIN SIX CATTLE BREEDS IN SOUTH AFRICA
Prepared for submission
6. GENOME WIDE SCAN FOR SELECTION SIGNATURES WITHIN AND BETWEEN SIX CATTLE BREEDS IN SOUTH AFRICA
Prepared for submission
7. GENERAL DISCUSSION AND RECOMMENDATIONS
7.1 General discussion and recommendations
7.2 Future studies
7.3 Conclusions
8. ADDENDUM
GET THE COMPLETE PROJECT