Exploring the financial implications of bovine babesiosis

The financial implications of endemic stability as a control strategy for Bovine babesiosis in veld grazing beef production systems of the KwaZulu-Natal Midlands

Industry Sector: Cattle and Small Stock

Research focus area: 

  • Animal Health & Welfare

Research Institute: University of Pretoria

Researcher: Francis Edwardes

Research Team

Title Initials Surname Highest Qualification Research Institution
Doctor W Hoffmann PhD Stellenbosch University
Title Initials Surname Highest Qualification Research Institution
Prof H Hogeveen   WUR

Completion: 2020

Aims of the project

  • Develop a model which can provide an estimate of the economic impact and financial implications of bovine babesiosis has at the herd level of a typical farm in the KwaZulu-Natal Midlands with the available data and existing research efforts.
  • Financially compare the established dipping strategies of the KwaZulu-Natal Midlands as a result of the developed model highlighted in point above.
  • Establish factors in which data relevant to the research problem is scarce or non-existent encountered through the development of the model as in the points above.
  • Establish the need for correct data collection by farmers when confronted with an infected animal in relation to point above.
  • Suggest methods of data collection in relation to Points 3 and 4 and further research opportunities in order to develop more accurate estimates of cost-effective management options.

Executive Summary

In South Africa, cattle production has increased by 46% in 2014 compared with 2005. Local consumption trends indicate that the country is a net importer of bovine meat products, due to the supply not capable of meeting demand requirements. The country’s projected population growth of 1.2% and the expected rise in beef consumption by 24% over the next ten years will require farmers to produce at greater efficiencies to meet local demand and to reverse the trade role it currently finds itself in. However, agricultural production comes with many challenges. Production diseases, such as the myriad of tick-borne diseases, are partly responsible for the challenges agriculturalists face. Amongst these, bovine babesiosis is considered as one the greatest economically important tick-borne diseases in South Africa.

Pathogenic parasites, such as Babesia bigemina and Babesia bovis, are responsible for the cause of this disease. The distribution of the parasites are directly related to the distribution of their vectors; B. bigemina has a greater distribution than that of B. bovis. Primary transmissions of B. bigemina in cattle older than nine months are less virulent when compared with B. bovis. Production losses can occur in the form of mortality, weight loss and abortions by varying degrees for either parasite. These losses coupled with treatment and prevention expenditure can result in significant costs for a farmer.  A prevention strategy that has long been discussed is to apply the concept of endemic stability. This means that the cattle are provided the opportunity to take advantage of their non-specific immunity through less aggressive tick eradication methods in order for herd resistance to develop over time.

Bovine babesiosis is considered a globally important disease and is one of South Africa most economically pertinent tick-borne diseases. However, no conclusive literature has been published regarding the economic impact caused by bovine babesiosis in South Africa and is known to be a problem since at least the early 1980’s. If bovine babesiosis is regarded with such high economic importance, why has there been little economic or financial research conducted internationally? Furthermore, why has South Africa not conducted exploratory economic or financial research studies in the last 35 years in an attempt to address this concern? The concept of developing a state of endemic stability through less aggressive acaricide applications is an intervention which has been suggested and is slowly implemented by the countries farmers, but no economic and financial insight is provided to those who implement this method of control.

The main research question for this study is; what is the value of adopting a strategic dipping option in an attempt to promote the development of endemic stability compared with an intensive acaricide treatment routine? By doing so, this study asks a question pertaining to the economic impact and financial implications of developing endemic stability by implementing a strategic dipping intervention. The study will be conducted at the herd level within the KwaZulu-
Natal Midlands and is compared with an intensive dipping approach.

Results

Preceding model development and the definition of various scenarios, simulations were run and results were analysed. For the sake of this executive summary, only the production, financial and economic analyses are presented.

The production effects of B. bigemina and B. bovis were translated into an economic impact assessment and a financial analysis of each dipping strategy per parasite prevalence.

The economic impact and financial analyses of either dipping strategy and respective scenario were compared. The economic impact assessment included the sum of all discounted costs as a result of disease prevalence and severity after a primary infection had occurred in either the breeding cows, weaners and calves in each one of the fifteen simulated years. The financial analysis included all the cash in- and outflows directly related to the production of beef weaners in the face of a bovine babesiosis challenge respective of the parasite prevalence and resulting disease severity. In light of a B. bigemina infection, the economic impact in Scenario 2 to 4 was greater for strategic dipping but less than intensive dipping in Scenario 1.

The economic consequences for intensive dipping decreased by an average of R21 115.34, with a range from R15 925.43 to R23 954.69, for each decrease in seroprevalence as per the respective scenarios. Adversely, the economic impact of strategic increased with a decrease in seroprevalence. Scenario 1 incurred the lowest impact of R82 082.86 and the greatest consequence of R95 679.96 was achieved in Scenario 4. The greatest component of the economic cost in each strategic dipping scenario was the value of weight lost consisting an average of 76% in each year. Dipping and treatment costs consisted of 10% and 9% in each year. The balance consists of recovery feed and compensatory growth costs. The value of weight lost cost component for an intensive dipping programme was greatest in Scenario 1, 2 and 3 consisting 67%, 63% and 53% of the total economic impact, respectively. This is followed by the dipping expenditure component which made up 21%, 25% and 36% of the total economic cost in each year. Dipping expenditures in Scenario 4 are greatest at 66% of the total economic cost followed by the value of weight lost at 29%. Treatment costs for Scenario 1 to three comprised 9% of the economic costs in each year and 5.0% in Scenario 4. The balance of the economic impact consists of recovery feed and compensatory feed costs. Results of the financial analyses for either dipping strategy and the respective scenarios indicate that the intensive prevention is a better financially viable option regardless of the parasite seroprevalence, and is indicated by the larger NPV and IRR values achieved.

The economic consequences of B. bovis are greater than that of the impacts realised due to B. bigemina. In all scenarios, the total economic cost of B. bovis is greater for strategic dipping when compared with the respective scenarios of intensive dipping. The largest cost component in strategic dipping is the value of weight lost as a result of a greater number of acute deaths and the longer duration of a recoverable infection. The value of weight lost held at an average of 95% of the total economic impact per year for either scenario of strategic dipping followed by treatment costs at 2.0%. The mean value of weight lost for intensive dipping in Scenario 1 to 3 made up 94% of the total economic cost while in Scenario 4 it is 8.0% less. Treatment costs outweighed dipping expenditures in Scenarios 1 and 2 whereas the latter component is greater than the former in Scenario 3 and 4. The economic impact realised in intensive dipping decreased by an average of R320 418.40, with a range from R244 736.00 to R362 558.30, with each decrease in seroprevalence as per the respective scenarios. Adversely, the economic impact increased from R1 255 592.16 to R1 492 277.39 with each respective decrease in seroprevalence. Despite the larger economic impact realised in all scenarios of strategic dipping, the financial analysis indicates that strategic dipping is more financially viable in Scenario 1 where a greater NPV is achieved. The conflict between NPV and IRR is resolved by identifying a cross-over rate of 7.89%. This indicates that strategic dipping is the more profitable prevention programme to choose while the interest rate remains below or equal to the cross-over rate and the seroprevalence of B. bovis is at 90%. In Scenario 2 to 4, intensive dipping is the more financially viable option to choose due to the greater NPV and IRR values realised.

Conclusion

The objectives of this study have been achieved. A dynamic stochastic model was developed to simulate the economic impact of bovine babesiosis a typical beef farm of the KZN Midlands would encounter where one of two dipping strategies are applied. A financial analysis of the cash in- and outflows was performed for either dipping strategy based on the data generated by the simulations. However, the model is limited in its performance due to various assumptions that were specified. Assumptions were made due to data collection difficulties.

Considering the limitations of this model, the overall results indicate that intensive dipping realises greater benefits. These benefits are increased as the seroprevalence decreases towards a 0% situation as demonstrated when NPV results are compared with those of a healthy farm. This suggests achieving a disease-free situation by means of parasite eradication. This study does not attempt to offer economic or financial insight as to the attainment of this state. Eliminating disease through eradication will contribute to an increase in animal welfare since fewer animals will have to undergo clinical infections in order for the farmer to achieve the state of endemic stability. Current results indicate that the concept of creating endemic stability as a control strategy is not a financially viable option. It is imperative to understand that these results are inconclusive due to the lack of available data as well as the limited research efforts concerned with various production effects of the disease. Emphasis is thus placed on the need for more stringent data collection routines and research efforts in order to effectively analyse the impact of various control strategies of bovine babesiosis from an economic perspective. The economic cost component of the model in this study has been developed as a foundation for future economic research in the realm of bovine babesiosis.

Objective Statement

The objective is to establish a set of principles enabling further economic and financial research to be pursued by primarily exploring the value of adopting a strategic dipping option in an attempt to promote the development of endemic stability compared with intensive acaricide prevention. This exploratory research should provide estimates identifying the economic consequences and financial implications of bovine babesiosis at the herd-level for either dipping strategy.

POPULAR ARTICLE

The economic impact of redwater and the need for data associated with the production effects of the disease

WFI Edwardes; Dr W Hoffmann

Bovine babesiosis, more commonly known as redwater in South Africa, is considered as one of the country’s most economically important tick-borne diseases. This is certainly not new information since the disease has been tagged with a label of economic importance for at least 35 years. Despite this dangling red tag of economic threat, little is known about the actual costs incurred by various stakeholders in the South African beef industry. The most recent economic impact estimate is reflected in an average annual expenditure of R5.1 million on babesicides. But how does this information help those that are affected the most by the disease; perhaps the producers? Furthermore, why has there been little to no economic research conducted to shed a little more light on this economically important disease?

A masters research study from Stellenbosch University was established to explore the economic consequences of redwater in veld grazing beef production systems of the KwaZulu Natal Midlands. For producers, research concerning the economic impact of disease is important so that a benchmark cost is known in order to compare the feasibility of other disease mitigation strategies with a current management strategy. Estimating the cost of redwater comes with difficulties due to the scarcity in data concerning the production effects of this disease in various management systems. The lack of data is a regular constraint in other economic impact assessments of disease. To cope with data scarcity, the first objective of our research was to develop a simulation model in which can provide cost estimates of African and Asiatic redwater at the herd- and cow-level based on available data and existing research efforts. The second objective was to establish factors in which data relevant to the research problem is scarce or non-existent encountered through the development of the model, in turn emphasising the need for greater data collection efforts.

A typical farm model was developed for the design of this exploratory research. An intensive dipping management strategy was chosen since it has long been the approach to manage tick populations, and therefore the transmission of the Babesia parasites, before the more recent approach of strategic dipping in order to promote the development of endemic stability. Other prevention measures such as blocking and blooding were excluded due to the lack of data. The chosen factors in which redwater affected production were the cost of mortality, weight loss, compensatory growth. The cost of recovery feed, treatment and dipping is also included. Four seroprevalence scenarios for Babesia bigemina and Babesia bovis, the respective parasites responsible for the cause of African and Asiatic redwater, were simulated. The scenarios included seroprevalence levels of i) 10% as per a situation of minimal disease; ii) 40% as per an endemically unstable situation; iii) 70% as per a situation approaching endemic stability, and iv) 90% as per an endemically stable situation. Using the seroprevalence and the average age of the herd the inoculation rate could be estimated. The inoculation rate is defined as the daily probability that an animal may receive a Babesia infection.

Simulation results, summarised in Figure 1, prove that Asiatic redwater is cause for greater concern. A comparison between the Babesia seroprevalence levels show that the economic cost of Asiatic redwater per breeding cow is on average ten fold that of African redwater. The value of weight loss either as a result of acute deaths or reduced weight gains following an infection is responsible makes up the largest cost component in all scenarios for both diseases, results are summarised in Table 1. Further investigation identified which animal cohort – cow, calf and weaner – yield the greatest economic cost given the inoculation rate for each simulated seroprevalence scenario. As illustrated in Figure 2 the economic impact is greatest in cow cohorts for lower seroprevalence levels. In higher seroprevalence scenarios the economic impact is felt greatest in weaner cohorts. This may be due to the calves being weaned where too few of them have received a primary infection before the age of nine months, resulting in too few attaining a non-specific immunity, but enough such that a risky population of Babesia parasites are harboured in the newly formed weaner cohort. Thus, more weaners receive a primary infection in which a non-specific immunity can no longer be attained. In our research, we attempted to simulate the economic impact of a strategic dipping strategy for the same herd. However, it was quickly discovered that results would not be reliable since there was not enough data to serve as input for this prevention strategy.

The objectives of this research were achieved in which a model was developed to explore the economic impact of redwater at the herd- and cow-level. Through the process of conducting this study, many constraints were encountered. These were largely in the form of scarce or non-existent data. Data concerning the production effects of redwater on Bos indicus cross Bos taurus breeds are not enough. Research efforts have investigated effects of the disease on certain variables such as weight loss, compensatory weight gain during recovery and are more concerned with Bos taurus breeds. Therefore, studies as such should be continued but more focus should be placed on the cross breeds. No studies were available concerning the effect that redwater had on milk production – and the subsequent effects it would have on calf growth, fertility, abortion and replacement. This gap in the literature should be addressed by livestock scientists and veterinarians. Greater knowledge pertaining to the effects of these production variables will lead to better cost estimates and the promotion of various cost-effective intervention strategies. Babesia bovis should continue to be the primary researched parasite due to its greater impact on production. The collection of data by farmers encountering such production effects should also be documented more strictly. Most farmers acknowledge the presence of the disease but do not document it and the resulting production effects; such data can aid research. This, however, is a challenging task as it requires the farmer to know the current seroprevalence amongst his/her heard and to continuously check its status throughout the year, to maintain strong relationships with the veterinarians in the area in order to correctly diagnose a sick animal and to communicate the data between the actors effectively. This may be costly for a farmer and lead to further economic studies researching the economic value of continuous Babesia seroprevalence monitoring in a herd.

In conclusion, this research has laid down the first stepping stone in the path of exploring the economic impact of redwater. Estimating the economic impact of redwater may only tell us something we already know, but without a cost estimate of redwater research can not compare the costs of alternative management strategies to a “norm”. Therefore, the need for more data associated with the production effects of redwater is emphasised. With the collective efforts of those in practice and research with an aim to collect data, more light will be shed on redwater for the benefit of the beef industry.

Please contact the Primary Researcher on the project if you need a copy of the comprehensive report – franco.edwardes@gmail.com

Detection of Mycobacterium spp. in slaughter cattle at Gauteng abattoirs

Prevalence and characterization of Mycobacterium spp. in slaughter cattle at Gauteng abattoirs: Food safety implications for meat consumers-A pilot study

Industry Sector: Cattle And Small Stock

Research Focus Area: Animal Health & Welfare

Research Institute: ARC – Onderstepoort Veterinarary Institute

Researcher: Dr Tiny Hlokwe

Team:

Title Initials Surname Highest Qualification Research Institution
Mrs V Mareledwane MSc ARC-OVR
Title Initials Surname Highest Qualification Research Institution
Prof AA Adesiyun PhD University of Pretoria
Prof P Thompson PhD University of Pretoria

Year of completion : 2020

Aims Of The Project

  • To isolate and identify Mycobacterium spp. from granulomatous/tuberculous lesions, lymph nodes (i.e. mesenteric, supra-mammary, retropharyngeal and internal iliac) and lungs of slaughter cattle
  • To determine the prevalence of bovine tuberculosis in slaughter cattle in selected abattoirs (high throughput, low throughput and rural/informal by using cell-mediated immune assays.
  • To characterize the isolates of Mycobacterium spp. recovered from cattle regarding their species identification and genotypes.
  • To obtain demographic information on farm management (feedlot, cow-calf or communal); animal information (age: adult or young, sex: male or female; and breed) by linking abattoir data back to the farms of origin and to visit farms from which seropositive animals originated to assess the existing risk factors for infection.

Executive Summary

Tuberculosis is a disease that is caused by a group of acid-fast gram-positive bacteria belonging to the Mycobacterium tuberculosis complex. Tuberculosis has a wide species range but not all species are equally susceptible and are divided into maintenance hosts and spillover hosts. M. tuberculosis is mostly the causative agent in humans while M. bovis is the predominant causative agent of tuberculosis in animals. In animals, cattle and buffaloes are the reservoirs of the disease in South Africa. TB is a zoonotic disease with great economic impact estimated to billions of dollars annually. This is because, for many farmers, cattle are a source of income. The impact is greatly felt in productivity. The zoonotic potential of the disease is a very big concern to public health. In addition, the interference of non-tuberculous mycobacteria in the diagnosis of BTB cannot be underestimated.

Globally, abattoirs are used for passive and active surveillance of diseases of both economic and public health significance such as tuberculosis. Surveys by serological and bacterial culture assays of slaughter animals may be used to detect newly introduced disease agents and in monitoring disease control and eradication programmes. Information generated from abattoir surveillance could provide an early warning system for impending epidemics or failures of intervention programmes such as vaccination of livestock against certain diseases, thereby allowing early intervention efforts to prevent epidemic loss of animals. Losses may result from mortality in animal population, cost of quarantine, isolation and treatment and in some cases loss of international trade. The usefulness of data obtained from abattoirs during surveillance for selected diseases is however dependent on the accuracy of the data obtained, data analysis and interpretation. Data generated from abattoirs could also be used to measure the potential health risk to farm workers, veterinarians or veterinary assistants attending to such animals, abattoir workers and consumers of products from the live animals, such as milk. The risk of zoonotic diseases, such as tuberculosis to workers who are exposed to infected animals pre-, during and post-slaughter, cannot be over-emphasized. Abattoirs in any country, if properly managed, are invaluable facilities for ensuring that only safe meat reaches the consumers, as well as preventing or reducing the potential health risk posed by infected or diseased animals to workers at these facilities.

Developed countries usually run efficient abattoirs and slaughterhouses and have effectively used them in the surveillance of diseases like tuberculosis and brucellosis in the USA, leptospirosis in New Zealand, and cystic echinococcosis in Spain. Reliable data obtained from abattoirs and slaughterhouses are used pro-actively to drive, monitor, change or formulate policies. In South Africa slaughterhouses are registered by government and closely inspected and audited for hygienic slaughter practices. Use of data obtained from these abattoirs for surveillance and diseases control purposes is however limited. The same applies to most other developing countries where, in most cases, slaughter practices in the abattoirs are not closely monitored by government and livestock diseases data are not captured and adequately used for surveillance and disease control.

In South Africa, as in most developing countries, there are also a number of unregistered informal slaughterhouses and small butcheries where virtually no hygiene monitoring, meat inspection or record keeping take place, thus creating a potential health risk to consumers. Records on zoonotic disease including Tuberculosis may be available at some abattoirs or laboratories country-wide, and these need to be accessed and analysed by researchers or veterinary officials as part of disease surveillance. This useful information may also be used for policy formulation on disease control. Furthermore, although some published reports exist on the detection of tuberculosis in livestock and wildlife diseases, the prevalence of the infections is largely unknown, particularly in communal livestock

Objective Statement

The current study was conducted at selected abattoirs in the Gauteng province, South Africa and the main objective was to determine the prevalence of livestock TB in slaughter livestock in these abattoirs using a cell-mediated immune assay (IFN-γ) and culture based methods.

Results

A total of 410 fresh blood samples were collected from slaughter livestock (369 cattle and 41 sheep) from 15 abattoirs, and analysed using Bovigam® test kit.

Of the 369 cattle sampled, valid IFN‐γ results (i.e. test samples passed quality control checks) were obtained in 318 (86.2%) of the cattle. The estimated prevalence of cattle positive for bTB was 4.4% (95% CI: 2.4-7.3%) (Table 1). Of the eight variables analysed, seven (animal species, sex, breed, district, municipalities, origin of animals and abattoir throughput) were not associated with the estimated prevalence of bTB. However, prevalence varied significantly between abattoirs (p=0.005), ranging between 3.6% (95% CI: 0.09-18.3%) in abattoir I to 23.1% (95% CI: 8.9%-43.6%) in abattoir B. The estimated prevalence of avian reactors was 5.9% (95% CI: 3.6-9.2%) (Table 2), also varying significantly between abattoirs (p=0.004), ranging from 3.6% (95% Cl: 0.09-18.3%) in abattoirs E and I to 20.7% (95% CI: 7.9-39.7%) in abattoir J. The prevalence of avian reactors in cattle was not significantly different to that of bTB. The estimated prevalence of cattle tested reacting to Mycobacterium spp. (combined bTB and avian reactors) was 10% (95% CI: 7.0-14%) (Table 3). In the univariate analysis, prevalence varied by sex of animal (3.0% in females and 11.9% in males) and by breed (5.4% in Jersey, 13% in Bonsmara, 0% in other breeds), but these differences were not significant after adjusting for confounding using exact logistic regression. Of the 41 sheep sampled, valid IFN‐γ results were obtained in 22 (54%) of the animals and none were positive for bTB nor were there any avian reactors (95% CI: 0-15%) (Table 1-3). No isolation was made from all the tissue samples cultured. However, non tuberculous mycobacteria were isolated from the environmental samples collected as confirmed by 16S rRNA gene analysis (see fig 1).

Conclusion

Meat inspection is a long-standing form of disease surveillance for both food safety and animal health. For diseases that produce slowly progressive but evident lesions, such as bTB, slaughterhouse inspection is an effective surveillance tool. The detection of positive bTB reactors in our study has, however, clearly illustrated the limitations of this method of disease surveillance, as the study also established that the abattoir source of the animals sampled significantly (p=0.005) affected the prevalence of bTB. The potential zoonotic risk of transmission to abattoir workers as well as food safety hazard to consumers, can therefore not be over-emphasized. Our study highlights the potential for the use of the IFN‐γ assay in reducing this risk. Studies have demonstrated that the use IFN‐γ assay in combination with other TB tests leads to a more accurate screening of bTB in cattle. Follow-up studies, with the intervention of the relevant area State Veterinarians, should be conducted to include using the animal information from the abattoir to trace back to the herds of origin and further testing of the whole herds.

Our study highlighted the inadequacy of meat inspection alone to detect bTB in cattle slaughtered for human consumption. It is therefore imperative to apply additional methods, such as the gamma interferon assay, to accurately determine the TB infection status in slaughter cattle from abattoirs. This approach will provide a true assessment of the risk of TB posed to abattoir workers and consumers of meat from infected cattle. Although we could not detect any Mycobacterium species by culture based method, we are not surprised by by these outcome, as all slaughtered livestock were cleared of having suspect lesions.

Popular Article

Inadequacy of Meat Inspection in the Surveillance of Bovine Tuberculosis: A Zoonotic and Food Safety Risk Concern

Authors: Vuyokazi Mareledwane1,2, Abiodun A. Adesiyun1,3, Peter N. Thompson1, Tiny M. Hlokwe4#

1 Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa. 2 Vaccines and Diagnostics Programme, Agricultural Research Council-Onderstepoort Veterinary Research, Private Bag X05, Onderstepoort, 0110, South Africa. 3 School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago. 4Diagnostic Service Programme, Agricultural Research Council-Onderstepoort Veterinary Research, Private Bag X05, Onderstepoort, 0110, South Africa.

Background

Bovine tuberculosis (bTB) is a zoonotic disease with serious consequences for the livestock and wildlife industries around the world. The causative agent, normally Mycobacterium bovis (M. bovis), has a broad host range (domestic and wild animals). Meat inspection represents a long-standing form of disease surveillance that serves both food safety and animal health.

Occurrence of bovine tuberculosis in cattle

Although test and slaughter programme reduced the prevalence in commercial cattle in South Africa, disease outbreaks in different regions of the country still occur. Bovine tuberculosis is a zoonotic disease with great economic impact estimated to be billions of dollars annually. This is because, for many farmers, cattle are a source of income. The impact is greatly felt in productivity.

Bovine tuberculosis as a zoonosis

Mycobacterium bovis is known to cause tuberculosis in both animals and humans, which makes this bacterium a potentially important zoonotic species. People are most commonly infected with M. bovis by drinking or eating contaminated and unpasteurised milk and milk products. Infection can also occur through direct contact with a wound of an infected animal during slaughter.

Use of abattoirs in the surveillance of bovine tuberculosis

Globally, abattoirs are used for passive and active surveillance of diseases, such as bTB, of both economic and public health significance. Our team, consisting of researchers from the University of Pretoria and Onderstepoort Veterinary Research recently conducted a study to investigate the prevalence of bTB in slaughter livestock at 15 abattoirs in Gauteng, South Africa. A total of 410 fresh blood samples were collected from slaughter livestock (369 cattle and 41 sheep) and analysed using Bovigam® test kit.

Outcome and implications

The estimated prevalence of the disease in cattle was 4.4% (95% CI: 2.4-7.3%), and varied among abattoirs, ranging from 0 to 23%; however, there were no significant differences among genders, breeds, municipalities, districts, origin of animal (feedlot, auction or farm) or throughput of abattoirs. None of the sheep sampled was positive for the disease. Results obtained clearly illustrated the limitation of disease surveillance using a meat inspection approach alone, considering that all the 410 slaughter animals sampled had passed visual abattoir inspection and therefore classified as free of bTB.

Zoonotic risk and food safety implications for meat consumers

Our findings therefore emphasize the zoonotic risk of transmission of bTB to abattoir workers and a potential food safety hazard to consumers. Furthermore, our study highlights the potential to use of the blood assay (Bovigam® test kit) for bTB surveillance at abattoirs.

Research Funding

The research was made possible through funds kindly provided by the Red Meat Research and Development (RMRD)-SA and the Gauteng Department of Agriculture and Rural Development (GDARD).

Figure 1 shows different ways in which bovine tuberculosis can be transmitted from cattle to people

Figure 2 show PhD students Vuyokazi Mareledwane and Maruping Mangena getting ready for abattoir sampling

Figure 3 shows a student analyzing test results in the laboratory

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project –
Nicholas Rivers-Moore on blackfly1@vodamailcom

Figure 1 shows different ways in which bovine tuberculosis can be transmitted from cattle to people
Figure 2 show PhD students Vuyokazi Mareledwane and Maruping Mangena getting ready for abattoir sampling
Figure 3 shows a student analyzing test results in the laboratory

Larvicide testing for blackfly control

Testing the blackfly organophosphate larvicide Abate® for viability in the Orange River Blackfly Control Programme

Industry Sector: Cattle And Small Stock

Research Focus Area: Animal Health and Welfare

Research Institute: University of KwaZulu-Natal

Researcher: Dr Nicholas Rivers-Moore PhD

Research Team:

Title Initials Surname Highest Qualification
Dr Helen Dallas PhD
Dr Robert Palmer PhD
Mr Shahin Naidoo BSc (Hons)
Ms Esther Ndou BSc (Hons)

Year of completion : 2017

Aims Of The Project

  • To confirm non-resistance to Abate in the Orange River pest blackfly populations;
  • To investigate the potential for re-activation of Abate as an alternative larvicide to Vectobac for control under high-flow conditions.

Executive Summary

Downstream flow alteration resulting from river impoundment or inter-basin transfer schemes, while improving water supply assurance levels, has been shown to have negative ecological consequences, including outbreaks in pest blackfly.  Outbreaks along the middle and lower Orange River have the potential to cause losses to livestock production estimated at US$13.3 million per annum (Rivers-Moore et al. 2014).  This figure is a conservative estimate as it excludes losses in the tourism and irrigated agricultural sectors through lost revenue and labour days.  Economic losses occur approximately 1200 km along the middle and lower reaches of the Orange River (Palmer 1997).  This is the river segment downstream of Van Der Kloof Dam, the major impoundment regulating flows in the Orange River.  The major pest species is Simulium chutteri, with more than 250 breeding sites (riffles) identified along the affected river sections, however S. damnosumS. nigritarse and S. adersi are also of concern (de Moor 1994, and citing others).

The Orange River Blackfly Control Programme, established in the early 1990s, was originally based on alternating use of two larvicides, viz. a bacterial larvicide (Vectobac®) and an organophosphate (Abate®; active ingredient is Temephos).  This programme extends over some 850 km of the middle and lower Orange River, where 148 rapids have been identified as optimal breeding habitat for pest blackfly species (Palmer et al. 2007).  The success of the control programme depends largely on correct timing of larvicide applications.  It is based on monitoring using a ten-point scoring system for larval and pupal densities developed by Palmer (1994), which is scientifically robust and user-friendly.  Larval density data are scored by the Department of Agriculture, Forestry and Fisheries (DAFF; Upington and De Aar regional offices) on a two-weekly basis, using the 10 point scale developed by Palmer (1994), reflecting seasonal changes of larval densities of the main blackfly pest complex comprising Simulium chutteri and S. damnosum.  The blackfly control programme along the middle and lower Orange River is based on aerial applications of larvicides to control the pest species Simulium chutteri.  Larvicides are generally applied three times in autumn and six times in spring (Palmer and Palmer 1995).  The two larvicides registered for blackfly control in South Africa are Vectobac® (produced from the naturally occurring bacteria Bacillus thuringiensis var. israelensis (Bti)and Abate® (organophosphate temephos) (Palmer and Palmer 1995).  However, wide scale application of the Abate larvicide, and blackfly larvae’s continuous exposure to it, has resulted in resistance being developed (Palmer and Palmer 1995).

Both larvicide options had advantages and drawbacks to their use.  In the case of Vectobac, the likelihood of pest blackfly developing resistance was low, but the higher viscosity and lower concentration of this larvicide in solution came with drawbacks including the need for more helicopter doses and clogging of nozzles.  While Abate does not result in these application drawbacks due to its more concentrated, lower viscosity formulation, its over-use was cautioned against because of the higher likelihood of resistance developing in Simulium chutteri.

By 2005, due to overuse of Abate, larvicidal resis been confirmed (Palmer et al. 2007), and a study completed in 2007 was unable to recommend any viable alternatives.  With ten years after the last use of Abate in the Orange River, it was hypothesized that larval resistance had diminished to the point where Abate could be used again.  During this period, where blackfly take 12-24 days to complete a life cycle, there is likely to have been at least 120-240 generations.  The purpose of this study was to establish whether blackfly larval resistance to Abate has subsided, thereby re-establishing a second larvicidal alternative for blackfly control on the Orange River.

Results

In the Great Fish River trials, larvae were a mixture of Simulium damnosum and S. chutteri in approximately a 3:1 ratio, while the reverse applied to pupae, and pupae dominated. Stock populations of blackfly larvae for the larvicide trials were low, with median values on the reeds sampled being 6.5 ± 1.4. Turbidity was relatively high, and flow rates were very low. Water was slightly alkaline, but with very high conductivity. In the Orange River, larvae were dominated by S. chutteri, with S. damnosum present, while pupal cases were almost exclusively S. damnosum with few S. chutteri present. Stock populations of blackfly larvae for the larvicide trials were higher than in the Great Fish River, with median values on the reeds sampled being 4.0 ± 1.4. Turbidity was relatively low, with prolific algal growth on rocks. Flow rates in the main river channel were normal; water was slightly alkaline, with conductivity comparable between river channel and irrigation canal.

Two concentrations of Abate were used: 0.3 mg.l-1 0.5 mg.l-1. Gutter trials of the efficacy of Abate on blackfly in the Great Fish River confirmed viability of the product, with mortalities of 95 and 97% respectively. Trials on Orange River populations showed similar trends at the same concentrations of larvicide. In all instances, declines in density classes were statistically significant (p < 0.05). In contrast, the class changes in the controls were not statistically significant (p < 0.05).

Conclusion

A downward change in density classes of blackfly larvae is expected to occur in both the control and trial gutter channels, due to a degree of downstream drift, where some larvae are dislodged and wash out of the gutters.  Despite this, there was a clear differentiation between changes in density scores between control sample populations and samples exposed to larvicide.  Not only was the viability of the Abate stocks confirmed after prolonged storage, but mortalities on the Orange River were significantly marked to indicate that larval resistance has subsided for concentrations of 0.3-0.5 mg.l-1.  In the project proposal, the original intention was to conduct larvicide trials on blackfly mortalities at a range of concentrations (0, 0.5, 1.0, 5.0 and 20.0 mg.l-1).  This range of concentrations was designed to range from the dosage concentration recommended by the manufacturers of Abate (0.10 ppm = 0.1 mg.l-1 or 30l per 100m3 where flows can be accurately determined), to higher concentrations to enable confirmation of larvicidal viability.  In this study, undertaking this full spectrum of trials was not possible due to the limited numbers of blackfly larvae available.  Additionally, it was demonstrated that Abate was effective at concentrations of 0.3-0.5 mg.l-1, which is within the magnitude of range recommended by the manufactures of Abate.

After a dormancy period of 10-15 years, blackfly larval resistance in the Orange River appears to no longer be a constraint in the use of Abate for blackfly control in the Orange River.

Objective Statement

  • Aim 1 (confirm non-resistance to Abate in the Orange River pest blackfly populations) has been successfully achieved.
  • Aim 2 (investigate the potential for re-activation of Abate as an alternative larvicide to Vectobac for control under high-flow conditions) will be an ongoing process. The Upington DAFF staff assisted with field trials. Further discussion will be required with DAFF (Upington and head office).

POPULAR ARTICLE

New hope for reintroduction of second larvicide to control muggies on the Orange River

Dr. Nick Rivers-Moore.

Red Meat Research and Development SA funded a recently completed study that tested a second larvicide for controlling pest blackfly on the middle and lower Orange River.  Mnr. Hoffie Joubert from KLK was also instrumental in assisting with project supplies.  While the larvicide is not new, it became ineffective in the mid-2000s for controlling pest blackfly here, because of a build-up of resistance to the product in the local blackfly population.  This means that only one larvicide, a bacterial larvicide called Vectobac, has been available for controlling blackfly for the past 10-15 years.  The Orange River Blackfly Control Programme, established in the early 1990s, was originally based on alternating use of two larvicides – a bacterial larvicide (Vectobac®) and an organophosphate (Abate®).  Both options had advantages and drawbacks to their use.  In the case of Vectobac, the likelihood of pest blackfly developing resistance was low, but the higher viscosity and lower concentration of this larvicide in solution came with drawbacks including the need for more helicopter doses, clogging of applicator nozzles.  While Abate does not result in these application drawbacks due to its more concentrated, lower viscosity formulation, its over-use was cautioned against because of the higher likelihood of resistance developing in Simulium chutteri.

By 2005, due to overuse of Abate, larvicidal resistance had been confirmed, and a study completed in 2007 was unable to recommend any viable alternatives.  With more than ten years after the last use of Abate in the Orange River, it was hypothesized that larval resistance had diminished to the point where Abate could be used again.  During this period, where blackfly take 12-24 days to complete a life cycle, there is likely to have been a few hundred generations, with resistance being bred out.

Dr Nick Rivers-Moore, an aquatic ecologist with fifteen years of research expertise on blackfly ecology, recently re-tested the efficacy of the larvicide Abate on pest blackfly.  This was first tested for product viability at a site about half an hour’s drive from Grahamstown on Great Fish River.  Here, the same species of blackfly which cause the outbreak problems on the Orange River have not been exposed to Abate.  Next, the gutter trials were repeated on the Orange River near Upington in the Northern Cape.  In all trials, larval mortalities were significant after application of the larvicide.  Dr Rivers-Moore said that “after a dormancy period of 10-15 years, blackfly larval resistance in the Orange River appears to no longer be a constraint in the use of Abate for blackfly control in the Orange River.”  These results were met with enthusiasm by the Blackfly Control Programme officers in the Upington DAFF office.  However, he says that “it is recommended that upscaling of these results is considered prior to re-introduction of Abate as a second larvicide for controlling pest blackfly on the Orange River.”

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project –
Nicholas Rivers-Moore on blackfly1@vodamailcom

Nick Rivers-Moore

TrichLabCheck – A voluntary trichomonosis inter laboratory comparison project

TrichLabCheck – A voluntary trichomonosis inter laboratory comparison project in South Africa

Industry Sector: Cattle and Small Stock

Research focus area: 

  • Animal Health and Welfare

Research Institute: University of Pretoria

Researcher: Dietmar Holm

Research Team

Title Initials Surname Highest Qualification Research Institution
Dr T Zangure BVSc University of Pretoria

Completion: 2020

Aims of the project

  • This study aimed to validate the accuracy of voluntarily enrolled private (n = 8) and state-owned (n = 5) laboratories that perform trichomonosis diagnostic tests by estimating the sensitivity (Se) and specificity (Sp) per laboratory. It was hypothesized that diagnostic laboratories in South Africa play an insignificant role in the inaccuracy of the diagnosis of trichomonosis.

Executive Summary

Trichomonosis is currently the most important venereal disease of cattle in South Africa with adverse economic implications to the beef production industry due to cow abortions, infertility and culling of carrier bulls. Once diagnosed in a herd, eradication is difficult due to financial and biological implications. Bulls are asymptomatic carriers and susceptibility increases with age. In infected females, clinical signs include embryonal death, abortion, pyometra, foetal maceration and uterine discharge.

Diagnostic accuracy is one of the major clinical problems preventing easy eradication of trichomonosis from a herd and can be influenced by biological variance in the occurrence of the organism, sampling errors, sample degradation during sample transport and diagnostic laboratory inaccuracies.

Objective Statement

The objective of the project was to determine the role that diagnostic laboratories play in the inaccuracies of trichomonosis diagnosis in South Africa.

Results

Laboratories performed either the culture method (n = 5), polymerase chain reaction (PCR) (n = 6) or a combination of culture and PCR (n= 2). Fresh preputial scrapings from four bulls with known negative status for trichomonosis were pooled in 200ml of phosphate buffered saline (PBS) to form the sample base for 12 subsamples of 13ml each. Duplicate subsamples were then contaminated with 2ml originating from four different laboratory cultures of Tritrichomonas foetus or 2ml of culture medium for four negative samples. Aliquots of the subsamples were transferred to an anaerobic transport medium, and the final concentration reached in these samples submitted to the laboratories, were categorised as follows: weak (30 organisms/μl). A total of 312 samples were sent by courier in two separate rounds: eight (4 duplicates) positive and four negative samples per round. Multiple logistic regression was performed on sensitivity, using sampling round, laboratory sector, diagnostic test type and sample concentration as independent variables, and removing variables in a stepwise manner based on the highest P-value.

Two public laboratories only reported on one round of sampling, and one batch of 12 samples was severely delayed in reaching another public laboratory. The sample identifications of a further two batches were not recorded by the respective private laboratories. The results from these 60 unreported samples were not included in the analysis. Laboratories that performed the PCR assay (solely, or in addition to culture) were grouped for data analysis. The overall specificity (Sp) was 100% and the sensitivity was 88.7% (95% CI 83.9% – 93.5%). Laboratories using PCR recorded higher sensitivity than those using the culture method (95.5%; 95% CI 91.0% – 99.9% and 81.3%; 95% CI 72.5% – 90.0% respectively, P < 0.01), and private laboratories recorded higher Se than public laboratories (96.4%; 95% CI 92.9% – 99.9% and 73.2%; 95% CI 61.2% – 85.2%, P < 0.01). For laboratories using PCR, weak positive samples recorded a lower sensitivity than strong positive samples (86.4%; 95% CI 70.8% – 101.9% and 100%; 95% CI 100% – 100%, respectively, P < 0.01). One public and six private laboratories obtained 100% accuracy during the two sampling rounds.

In the logistic regression model, private sector (compared to public), an increasing concentration of organisms in the sample and the second round of sampling (compared to the first round) were independent predictors of laboratory sensitivity for the detection of Tritrichomonas foetus.

Conclusion

It is concluded that inaccuracies in the diagnostic laboratory contributes to the deficiencies in diagnostic sensitivity for trichomonosis in South Africa, but does not influence diagnostic specificity. It is further concluded that diagnostic sensitivity was independently influenced by the sector in which the laboratory operates (private vs public) and the concentration of Tritrichomonas foetus organisms in the sample.

POPULAR ARTICLE

Trichomonosis: what role does the laboratory play in combating the disease?

Prof Dietmar Holm

INTRODUCTION

Trichomonosis is a venereal disease of cattle that results in significant losses to the beef industry in particular, due to a severe reduction in the reproductive potential of beef herds. The disease occurs worldwide and is currently widespread in South Africa. In many cases herds are infected without the knowledge of the farmer, because there are often no external signs visible in the cattle. This means that without knowing, farmers loose thousands of rands in potential income due to the loss of unborn calves.

The diagnosis of trichomonosis is done on bulls, and must be performed by a qualified veterinarian only. Incorrect sampling results in incorrect diagnosis, which means that a farmer will remain in the dark about the status of his or her cattle herd. After collecting samples, they are submitted to a laboratory for diagnosis. This diagnosis can be done using different types of tests and must also be done under strict controlled conditions. Several laboratories in South Africa perform this service for veterinarians.

The nature of the disease is such that the diagnostic test is not 100% accurate, even when done by the correct professionals. In a recent study performed by the Faculty of Veterinary Science at the University of Pretoria, the role of diagnostic laboratories in the accuracy of the diagnostic test for trichomonosis was investigated. The TrichLabCheck research team, led by Prof Dietmar Holm, found that indeed in South Africa, amongst the 13 laboratories that voluntarily participated in the research, several false negative results were reported. There were no false positive results reported in this study to date, which is in line with similar studies done elsewhere in the world. This is important information for veterinarians and farmers in South Africa, who need to consider that in some cases a bull that tested negative may in actual fact be positive and needs to be tested again to confirm his negative status. It was found in this study that the average diagnostic sensitivity of all participating laboratories to detect trichomonosis was 88.7%. This means that potentially for every 10 positive bulls tested in South Africa, at least 1 will provide a false negative test result.

The research emphasises the need to perform repeated samples on individual bulls to confirm their individual negative status, or to test a large number of bulls in a given herd to confirm the negative status of a herd. It also highlights the fact that a negative test result of a single bull in a positive herd must be interpreted with care, because it may just be that the particular bull gave a negative test result when in fact he may be infected with the disease.

“Trichomonosis has been an increasing problem in South African beef cattle over the past decades, and we are hoping that farmers and veterinarians will use this research to be more vigilant in their diagnostic approach towards the disease”, prof Holm stated.

The research further confirmed that the number of Trichomonas organisms in the sample contributes to the accuracy of the test. This emphasises the importance of using only a qualified veterinarian to perform this important task on farms. Dr Tinashe Zangure, the masters student and veterinarian involved in this study confirmed that he gained excellent knowledge not only about the disease, but also about the importance that bull sampling and laboratory techniques play in the effort to combat the disease in cattle herds.

The University of Pretoria, in collaboration with the Ruminant Veterinary Association of South Africa, will soon be publishing a list of laboratories with acceptable levels of accuracy for trichomonosis. The research will be ongoing, and the list will be updated in an effort to ensure that the veterinary industry strive towards diagnostic excellence in South Africa.

Please contact the Primary Researcher on the project if you need a copy of the comprehensive report – dietmar.holm@up.ac.za

STEC from feedlot to abattoir

Epidemiology of Shiga toxin-producing Escherichia coli in beef cattle from feedlot through to abattoir

Industry Sector: Cattle and Small Stock

Research focus area: 

  • Red Meat Safety, Nutritional Value, Consumerism and Consumer Behaviour

Research Institute: University of Pretoria

Researcher: Peter Thompson

Research Team

Title Initials Surname Highest Qualification Research Institution
Prof. A.A. Adesiyun PhD University of Pretoria
Prof. E. Madoroba PhD ARC-OVI
Dr. K. Keddy PhD NICD

Completion: 2020

Aims of the project

  • To determine the prevalence, dynamics and factors associated with shedding of Shiga-toxin producing Escherichia coli (STEC) in feedlot cattle; To determine the relationship between faecal shedding of STEC in the feedlot and on arrival at the abattoir, and carcass contamination at various steps in the slaughter process.

Executive Summary

Shiga toxin-producing Escherichia coli (STEC) has emerged as an important foodborne pathogen globally with a significant impact on public health. Healthy colonized cattle are major reservoirs of STEC and bovine “super-shedders” are considered to play a key role in the entry of STEC into the food chain. The public health relevance is determined by the pathogen’s low infectious dose and capacity to survive and be transmitted along different stages in the beef production chain. Of the over 470 different serotypes of STEC detected in humans, the O157:H7 serotype is the most frequently associated with large food and water-borne outbreaks. However, non-O157 STEC have been increasingly isolated from sporadic cases of haemorrhagic colitis and the sometimes fatal haemorrhagic uremic syndrome. In a recent RMRD-funded project a high prevalence of STEC contamination of beef products was detected in retail outlets in Pretoria, suggesting that STEC may pose a real food-borne disease threat and that further investigation of the epidemiology of the pathogen is required. Since the majority of beef consumed passes through the feedlot system, it is essential that we understand the dynamics of shedding of the organism in the feedlot in order to identify control measures to reduce the bacterial challenge resulting in carcass contamination in the abattoir.

Objective Statement

The specific objectives of the study were (i) to determine the frequency and dynamics of shedding of STEC in cattle in a feedlot; (ii) to longitudinally follow tagged study animals to slaughter to determine the frequency of STEC contamination pre-slaughter, during slaughter and post-slaughter; (iii) to characterize STEC isolates with respect to their serotypes and presence of virulence factors; and (iv) to to establish the genetic relatedness of the isolates between feedlot and abattoir.

Results

On arrival at the feedlot, 27% (29/106; 95% CI: 19-37%) of faecal samples were STEC-positive on PCR. Regarding virulence genes, 18 (17%) tested positive for stx120 (19%) were positive for stx212 (11%) were positive for eaeA and 23 (22%) were positive for hlyA. STEC prevalence during the longitudinal study indicated non-O157 STEC shedding in 92% (72/78; 95% CI: 84-97) of samples and non-O157 STEC super shedding (≥4llog10 CFU/g faeces) in 73% (57/78; 95% CI: 62-82) of samples.

The number of cattle available for follow-up varied for the months of October, November, December and February. There were only 16 cattle that were consistently negative and none was consistently positive for STEC O157 for the whole period. There was intermittent shedding of non-O157 STEC for the entire sampling event. There was a significant difference (P < 0.0001) between the proportion of non-O157 super shedders (92%) compared with the proportion of O157 super shedders. For the longitudinal study, the median STEC shedding level for non-O157 was 4.8log10 CFU/g, while the median for O157 was 3.4log10 CFU/g. Some cattle were consistent non-O157 STEC shedders throughout the 4-month period. Four cattle were super-shedders of non-O157 STEC persistently throughout the four sampling events and five were non-O157 super shedders for 3 consecutive sampling events. Four cattle were super shedders of both O157 and non-O157 STEC.

Only 8 animals were followed up at the abattoir primarily because of missing tags and sometimes due to the inability to keep up with fast processing lines. Overall, the prevalence of STEC based on the screening of carcass swabs using PCR was 32% (6/19; 95% CI: 13-57%), while STEC prevalence along the different stages of carcass processing was as follows: 22% (2/9), 17% (2/12), 25% (3/12) and 11% (2/19) for perineum hide, pre-evisceration, post-evisceration and post-wash swabs respectively (P = 0.688). There was no association between super shedding status (just before slaughter) and STEC carcass contamination for either O157 (P = 0.061) or non-O157 (P = 0.348). Likewise, there was no association between super shedding status (just before slaughter) and perineum hide swab STEC contamination for either O157 (P = 0.714) or non-O157 (P = 0.143) STEC.

The analysis of virulence genes and serotypes included isolates from the previous study together with this one. The distribution of virulence genes was highest in feedlot faecal samples (40%) compared with abattoir (33%) and retail outlets (28%) and this was highly statistically significant. Of the 86 STEC strains tested, the frequency of detection of stx1stxand a combination of both stx1and stx2 was 24%, 17% and 19% respectively. The eaeA gene was detected in 20 (23.3%) isolates in five different combinations; stx2+eaeA (2 isolates), stx1+stx2+eaeA (1 isolate), stx1+eaeA+hlyA (13 isolates), stx2+eaeA+hlyA (3 isolates), stx1+stx2+eaeA+hlyA (1 isolate). Of the 20 isolates carrying the eaeA gene, only two isolates (2/20; 10%) were found in mince beef, 3 isolates from abattoir carcass swabs (3/20;15%), and the remaining 15 isolates (15/20;75%) were found in feedlot cattle faeces. Of the 86 isolates recovered, only 39 could be serotyped, from which a wide range of serogroups (35) were detected.

On the pulsed field gel electrophoresis (PFGE) analysis, dendrograms of 55 isolates showed a high diversity with 45 distinct PFGE patterns. This diversity of PFGE patterns was observed in some isolates of the same serogroup that did not cluster together; these included serogroup O178 (feedlot environmental sample, feedlot cattle faeces, and supermarket boerewors). Also included were two isolates belonging to serogroup O20 (boerewors) and four serogroup O168 isolates (feedlot cattle faeces samples and abattoir perineum hide swab). Some patterns were observed in the dendrogram with varying band similarity percentages. At 100% banding similarity, eight band similarity patterns were identified. At 97.5% banding similarity, four closely related patterns were identified in eight isolates (7%): i. winter butchery boerewors and summer environmental feedlot faeces, ii. autumn supermarket boerewors and winter butchery boerewors, iii. summer cattle feedlot faeces and autumn butchery mince, iv. autumn brisket and mincemeat from the same supermarket. Analysis of the PFGE patterns at the 84.5% band similarity percentage or greater, revealed that most of the clades (7-clusters) belonged to isolates from different sources.

Conclusion

This study has established the presence of persistent and intermittent super-shedding of STEC O157 and non-O157 in cattle in a feedlot and at the abattoir just before slaughter. This results in continual environmental contamination and risk of re-circulation of the pathogen in the herds, which may lead to contamination along the food chain. In addition, the high count of non-O157, and the diversity of serogroups, shows that super-shedding is not limited solely to serogroup O157. We provide evidence of horizontal transmission and STEC strain recirculation along the beef production chain in Gauteng. All serogroups detected in this study have been previously implicated in STEC infections in human, with four considered as emerging serogroups. The high heterogeneity shown by PFGE and the difference in serogroups and virulence genes demonstrate the presence of a diverse but related STEC population in the beef production chain. There is need for further scientific investigation to advance the understanding of the dynamics of super-shedding in cattle, to sample a wider geographic region representing cattle-farming areas of South Africa, to conduct studies over a longer period to assess the impact of changes in climatic conditions and to promote epidemiologic surveillance for the clinically important STEC serogroups in public health laboratories in in South Africa.

POPULAR ARTICLE

Shiga toxin-producing Escherichia coli in beef cattle from feedlot through to abattoir

Dr LO Onyeka, Prof. AA Adesiyun, Dr KH Keddy, Prof. E Madoroba, Prof. PN Thompson

INTRODUCTION

Shiga toxin-producing Escherichia coli (STEC) has emerged as an important foodborne pathogen globally. Healthy colonized cattle are major reservoirs of this pathogen and cattle that shed STEC are considered to play a key role in the entry of the pathogen into the food chain. STEC causes a broad spectrum of disease from mild to intense bloody diarrhoea and in 5-10% of cases, haemolytic uremic syndrome (HUS). Globally Foodborne STEC have caused more than 1 million illnesses and 128 deaths. Of the over 470 different serotypes of STEC detected in humans, the O157:H7 serotype is the most frequently associated with large food and water-borne outbreaks. However, non-O157 STEC have been increasingly isolated from intermittent cases of haemorrhagic colitis and the sometimes fatal HUS.

The importance of the pathogen in South Africa and other southern African countries has recently been highlighted. STEC O157 was isolated in clinical stool specimens of diarrhoeic patients and environmental water samples in Gauteng, and recent reports from the Western Cape suggest STEC may be an environmental contaminant in informal settings and it is associated with diarrhoea in children under five years of age. Furthermore, in South Africa and other southern African countries, numerous clinical cases of diarrhoea in children and adults were reported between 2006-2013, in which a diverse range of STEC serogroups (O4, O5, O21, O26, O84, O111, O113, O117 and O157) were incriminated.

However, the poor surveillance and inadequate diagnostic techniques employed, almost certainly means that the occurrence of STEC-associated disease in humans is under-reported. Since the majority of beef consumed passes through the feedlot system, it is essential that we understand the dynamics of shedding of the organism in the feedlot and the characteristics of the pathogen in the beef production chain. This will help to identify control measures to reduce the bacterial challenge resulting in carcass and beef products contamination.

The present study aimed to determine the prevalence and dynamics associated with shedding of STEC in feedlot cattle and to characterise STEC isolates recovered at every stage along the beef production chain. The specific objectives were (i) to determine the frequency of shedders of STEC in cattle and associated animal factors in a feedlot in Gauteng Province through monthly sampling of a cohort of animals over a 4-month period; (ii) to longitudinally follow tagged study animals to slaughter and to determine the frequency of STEC contamination pre-slaughter, during slaughter and post-slaughter; (iii) to characterize STEC isolates with respect to their serotypes and presence of virulence; and (iv) to use pulse-field gel electrophoresis (PFGE) and serotyping to establish the genetic relatedness of the isolates between feedlot and abattoir.

MATERIALS AND METHODS

A six-month study from Sept 2016 to Feb 2017 was conducted at a commercial cattle feedlot located near Pretoria, Gauteng. The selected feedlot also owned a mechanized abattoir that slaughtered approximately 120 units per day. One hundred and six (106) cattle were randomly selected on arrival and tagged, and a minimum of 50 g of fresh rectal faecal grab sample was collected from each. Subsequently, over a period of 4 months, 26 cattle, including 15 animals identified as shedders and at least 11 non-shedders were selected, and sampled once a month until animals were sent for slaughter at the abattoir. At the abattoir, swab samples of tagged cattle were obtained from a 100 cm2 area using a sterile square metal template from each of four selected anatomical sites (4 x100 cm2 areas): rump, flank, brisket and neck, according to a standardized method.

Broth enrichment for processing of faecal samples was carried out and DNA Template from the broth enriched samples was investigated for the presence of stx1, stx2, eaeA and hlyA genes using multiplex PCR. 10-fold serial dilutions was plated on duplicate plates of two selective media known to target E coli O157 and non-O157 serogroups, incubated for 24 h at 37oC, after which typical colonies were selected and biochemically identified. Enumeration was performed by viable plate count method and expressed as CFU/g. Serotyping was conducted at the National Institute for Communicable Diseases (NICD). Pulsed-field gel electrophoresis (PFGE) of 55 isolates (including isolates from a recent study of beef products at retail outlets in Pretoria) was carried out to determine relatedness of strains.

RESULTS AND DISCUSSION

Samples collected on arrival at the feedlot indicated a STEC prevalence of 27% (29/106), with 19% and 11% being positive for stx2 and eaeA genes respectively. The longitudinal study showed that STEC non-O157 was shed at a significantly higher level than STEC O157. These results have several implications. Firstly, it demonstrates the presence of super shedding cattle in a feedlot herd. Secondly it shows that super-shedding is not limited to STEC O157, as described in recent reports from Europe. Thirdly, the higher prevalence of STEC non-O157 compared with O157 STEC is of public health significance, since non-O157 STEC have been increasingly linked to human disease in South Africa. Numerous clinical cases of diarrhoea in children and adults, as well as HUS, have been reported, in which a diverse range of STEC serogroups (O4, O5, O21, O26, O84, O111, O113, O117 and O157) was implicated.

It was also of interest that some cattle were simultaneous shedders of both STEC O157 and non-O157. In addition, several cattle shed ≥10,000 CFU/g non-O157 persistently throughout the study or for 3 consecutive sampling events. These cattle were identified as “super shedders”. Non-O157 STEC may be gaining importance in South Africa and such super shedders may pose an increased risk of contamination along the beef production chain, possibly leading to contamination of the food chain for human consumption.

PFGE has been used to track foodborne bacterial pathogens along the food production chain. In this study, PFGE analysis revealed a high diversity of 45 distinct PFGE patterns among 55 non-O157 STEC strains, which provides useful information on the genomic diversity of non-O157 STEC strains in the beef production chain in Gauteng. We observed eight PFGE-related patterns for 16 isolates originating from the same location and source but from different stages of the beef production chain, suggesting that the specific contaminating strain multiplied and spread at that point/stage of entry into the beef chain, such that once a pathogen is established at any production stage (farm, abattoir or retail processing) it may result in within-production-stage transmission. These data suggest evidence of epidemiological lineage, hence horizontal transmission of STEC strains along the beef production chain.

In this study, of the 86 STEC isolates only 17% carried the stx2 gene and 19% carried both stx1 and stx2. Of the virulence combinations, (23.3%) harboured the eaeA combinations. Epidemiologic studies have shown that the presence of stx2+eaeA gene combinations is important in the likelihood of developing HUS and with severe clinical symptoms. Of the 86 isolates recovered, only 39 isolates were serotypeable, from which a wide range of serogroups (35) were detected, including seven serovars of clinical relevance, namely O178, O174, O117, O101, O68, O8 and O2, considered to be emerging serogroups.

CONCLUSIONS

This study confirms that multiple different STEC strains are co-circulating in cattle in South Africa and further work needs to be done to establish whether these are clinically relevant in the human population. The high count of non-O157, and the diversity of serogroups, provides further evidence that super-shedding is not limited solely to serogroup O157. Also, we provide evidence of horizontal transmission and STEC strain recirculation along the beef production chain in Gauteng. There is need for active surveillance of STEC both in their reservoir host and in humans, and further studies to investigate effective methods to prevent contamination of the food chain.

Please contact the Primary Researcher on the project if you need a copy of the comprehensive report – peter.thompson@up.ac.za

Genotype imputation for genomic selection

Genotype imputation as a cost-effective strategy to increase genotype data for genomic selection in South African beef cattle

Industry Sector: Cattle And Small Stock

Research Focus Area: Livestock production with global competitiveness: Breeding,physiology and management

Research Institute: Agricultural Research Council

Year Of Completion : 2020

Researcher: Mahlako Makgahlela

The Research Team

ProfFWCNeserPhDUniversity of the Free State
DrMDMacNeilPhDDelta Genetics
ProfMMScholtzPhDAgricultural Research Council
MsSMdyogoloMScAgricultural Research Council
DrAAZwanePhDAgricultural Research Council

Executive Summary

The discovery of DNA polymorphisms (single nucleotide polymorphisms (SNP) or simply genomic data) and their cost-effective genotyping platforms have provided breeders and scientists in animal breeding additional tools to select young animals without performance records with much higher accuracies. Breeding programmes incorporating genomic information have achieved substantial increase in genetic improvement for cattle populations around the world. As a start, genotyping strategies are determined to identify individuals that are genotyped to increase the accuracy of predictions, and estimate relationships between candidates more reliably. Meanwhile, accuracy of genome-based schemes is a function of the reference population from which prediction equations for estimating genomic breeding values (GEBV) are developed. Setting up a sizable reference population is costly and remains a challenge for the uptake of genomic selection in South Africa.

Objective Statement

The aim of this research was to assess the accuracy of genotype imputation from low-density (7 931 SNPs or 7K) or medium density (150 000 SNPs or 150K) to high density (777 962 SNPs or 777K) panels using the reference population defined as influential animals explaining substantial genetic variation in the Afrikaner (AFR), Brahman (BRA) and Brangus (BNG).

Project Aims

  1. To evaluate whether the Celtic mutation on the POLL locus is the causative mutation for polledness in Bonsmara and Drakensberger
  2. To perform a genome wide association study of the Polled and Scur genes based on phenotypic data and genotypic data from the GGP Bovine 150K SNP bead chip
  3. To apply sequence data available from the Bovine Genomics Program to finemap the suspected regions for the Polled and Scur genes

Results

In identifying influential animals for the AFR, BRA, BNG and the other beef breeds (i.e., Limousine, Santa Gertrudis, Simbra and Simmentaler), it was found that only 100 ancestors explained approximately 50% of the genetic variation, and about 90% of the genetic variation was explained by 200 ancestors for all breeds. Genetic variation explained by top 1000 important ancestors was 95, 96 and 84% for AFR, BRA and BNG, respectively. Imputation accuracies within breed reference population, measured as the concordance rate, were 96.60, 91.39 and 89.91 using Beagle and 95.3, 92.8 and 96 using FImpute for AFR, BRA and BNG, respectively. Accuracies in multi-breed were lower (±80%) than within-breed reference populations. Furthermore, results demonstrated that accuracy tends to be greater when imputing from low-density 7K to medium-density 150K than bypassing the latter and impute from low-density 7K to high-density 777K. Higher accuracies were observed using Fimpute (93-97 %) versus Beagle (89-95%) and Impute (91-94%).

Conclusion

This study investigated the accuracies of imputation within breed and across breeds by masking actual genotypes in the Afrikaner, Brahman and Brangus breeds, and through genotype imputation from low density 7K or medium density 150K to high-density 777K in the Brahman cattle breed. The reference populations for imputation for all breeds were defined as influential animals with high marginal genetic contributions to young animals who were born in the last decade of the pedigree data, which were found to be few relative to the pedigreed population. Genotyped animals used in this study were few but promising accuracies were observed in within breed reference populations for AFR and BRA. Thus, imputation workflow established in this research could be integrated within the framework for implementation of genomic evaluations of GEBV and genomic selection in the Brahman and Afrikaner cattle breeds.

Popular Article

Genotype imputation: An essential, promising and cheap tool for assembling the reference population for genomic selection in the Afrikaner and Brahman cattle breeds of South Africa

Authors: Dr M.L. Makgahlela, Ms S. Mdyogolo, Prof F.W.C. Neser, Dr M. D. MacNeil, Prof M. M. Scholtz & Prof A. Maiwashe

The world will need to produce 100% more food in the next 40 years than currently produced (UNFAO, 2002). Accordingly, the demand for beef products, being the top valuable livestock product, will continue to increase significantly. Meanwhile, competition for resources will intensify, dictating that livestock systems must increase both productivity and efficiency. More than 60% of the additional food must come through technological innovations. Genomics is among technologies that will play a pivotal role in meeting the increasing demand while safeguarding natural resources and preventing environmental degradation. Genomic selection (GS) is the selection of genetically superior breeding animals based on genomic breeding values (GEBV) calculated from thousands of DNA markers or single nucleotide polymorphisms (SNP. Breeding programmes using GEBV have achieved substantial increase in genetic improvement for cattle populations around the world. The infrastructure for implementing GS within breed is a sufficient reference population of phenotyped (measured economic traits) and genotyped (SNP genotypes) animals. Setting up a sizable reference population requires substantial capital investments, and remains a challenge for the uptake of genomic selection in South Africa. There are several SNP genotyping panels of low-, medium- and high densities in terms of the number of SNP markers. Imputation is a method used to fill missing SNP on the low-density panel using medium- or high-density panel as reference population, without paying for the extra information. It provides an opportunity to achieve a sizable reference population for timely uptake of GS.

The aim of this research was to assess the accuracy of genotype imputation from low-density (7 931 SNPs or 7K) to medium density (150 000 SNPs or 150K) or high density (777 962 SNPs or 777K) panels using the reference population defined as influential animals explaining the genetic diversity in the Afrikaner (AFR), Brahman (BRA) and Brangus (BNG). In identifying influential animals for the AFR, BRA, BNG and the Limousine, Santa Gertrudis, Simbra and Simmentaler, it was found that only 100 ancestors explained approximately 50% of the genetic diversity, and about 90% of the genetic diversity was explained by 200 ancestors for all breeds. Genetic diversity explained by top 1000 important ancestors was 95, 96 and 84% for AFR, BRA and BNG, respectively. Imputation accuracies within breed reference population, measured as correctly imputed SNP, were 96.60, 91.39 and 89.91 using Beagle and 95.3, 92.8 and 96 using FImpute for AFR, BRA and BNG, respectively. Accuracies in multi-breed were lower (±80) than within-breed reference populations. Furthermore, results demonstrated that accuracy tends to be greater when imputing from low-density 7K to medium-density 150K than bypassing the latter and impute from low-density 7K to high-density 777K. Higher accuracies were observed using Fimpute (93-97 %) versus Beagle (89-95) and Impute (91-94). Genotyped animals used in this study were few but promising accuracies were observed in within breed reference population for AFR and BRA. Thus, imputation workflow established in this research could be integrated within the framework for implementation of genomic evaluations of GEBV and genomic selection in the Brahman and Afrikaner cattle breeds.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project on :mmakgahlela@arc.agric.za

Gene expression: Nguni and Bonsmara cattle

A gene-expression study on the growth performance of Nguni and Bonsmara cattle grown in a feedlot fed a high and low energy diet.

Industry Sector: Cattle And Small Stock

Research Focus Area: Livestock production with global competitiveness: Breeding, physiology and management

Research Institute: Agricultural Research Council

Year Of Completion : 2019

Researcher: Dina Linde

The Research Team

TitleInitialsSurnameHighest QualificationResearch Institution
DrM.M.ScholtzPhDARC-AP
ProfEvan Marle-KosterPhDUP
MrsA. Theunissen MSc Vaalharts Research Station

Executive Summary

Introduction

In South Africa, Nguni cattle are one of the breeds found predominantly in extensive production systems. The Nguni is an indigenous cattle breed and is widely used in crossbreeding systems due to their high fertility and mothering ability. Nguni cattle are also commonly used in communal production systems. The majority of beef in South Africa is produced in feedlots using commercially formulated high energy diets, where preference is given to medium and large framed later maturing cattle that include British types and composites such as the South African Bonsmara. Due to the Nguni’s small frame and low meat yield when compared to British types it is nor preferred as a feedlot animals, however studies have shown that Nguni cattle produce high quality meat. The veldt of South Africa has a varying degree of carrying capacity, however the occasional drought conditions have necessitated the use of alternative production systems such as feedlots for finishing cattle. The use of a lower energy diet in feedlots for indigenous cattle have been suggested and warrants investigation. Nutrigenomics is the study of the effect of nutrition on the genes of the animal by quantifying the gene expression. An improved understanding of the interaction between the nutritional environment and the genetics of the animal can lead to increased efficiency and production. Diets that are different in components or ingredients can result in different phenotypes in the animals. In this study the effect of two feedlot diets with different energy levels have been investigated using a transcriptome approach.

Objective statement

The objective of this study is to determine if there are gene expression differences between Nguni and Bonsmara cattle fed a low or a high energy diet. The gene expression of the cattle can determine the underlying differences in the reaction of the two breeds to the two different diets.

Project Aims

  1. To evaluate whether the Celtic mutation on the POLL locus is the causative mutation for polledness in Bonsmara and Drakensberger
  2. To perform a genome wide association study of the Polled and Scur genes based on phenotypic data and genotypic data from the GGP Bovine 150K SNP bead chip
  3. To apply sequence data available from the Bovine Genomics Program to finemap the suspected regions for the Polled and Scur genes

Results

Performance results showed a higher live weight, carcass weight and marbling score for all bulls fed the high energy diet compared to bulls fed the low energy diet. Only carcass weight and marbling score had significant difference in terms of diet (p < 0.05). Live weight, average daily gain, rib fat, rump fat and eye muscle area were only significant for breed. Diet had a greater effect on the Bonsmara compared to the Nguni according to transcriptomic and phenotypic values. Transcriptomic values showed 3584 differential expressed genes (DEG) between the Bonsmara fed the two different diets, while only a difference of 288 DEG were observed between the Nguni fed the two different diets. Phenotypic values show a difference of 20 kg between the Bonsmara groups and only a 6 kg difference between the Nguni groups. Most DEG were involved with cellular processes and metabolic pathways. A total of 73 differentially expressed genes were observed between the diets across breeds. The genes that were involved in intramuscular fat deposition (CRHR2, NR4A3, MMD) were expressed on a higher level in the bulls on the low energy diet compared to bulls on the high energy diet. Genes that were involved in muscle deposition (PITX2, Leptin, AVP) was expressed higher in the bulls on the high energy diet. Comparing the breeds revealed that 2214 genes were differentially expressed between the Bonsmara and the Nguni. At the end of the feedlot trial a higher expression of marbling genes (SIRT, ND, ADIPOQ) were observed in the Nguni, however this expression was not observed in the marbling scores recorded. Several genes (ASIP, MOGAT, SNAI3) that were involved in fat deposition were upregulated in the Bonsmara. This suggests that the Nguni was still growing at the end of the feedlot trial while the Bonsmara had reached physiological maturity. Little literature could be found on some of the gene showing the highest expression in the groups such as GSTA3, TEX28 and TUBB3. Glutathione-s transferase alpha 3 (GSTA3) is linked to steroidal genesis and could therefore have an influence on myogenesis, however no confirming literature could be found.

Conclusion

The diet had a smaller effect on the Nguni bulls compared to the Bonsmara bulls as observed in the DEG and the carcass weight of the bulls. This might indicate that the Nguni is more adaptable to a variation in feed quality. The Bonsmara bulls had a higher meat yield on the high energy diet, however it seems as if the bulls on the low energy diet had a higher expression of the marbling genes. This is in contrast to the phenotypically higher marbling score. Further research needs to be done as this study had a small sample size (n=40). An extended feedlot period for Nguni cattle should be considered in future studies. This study provides reference data for differentially expressed genes in muscle of South African feedlot cattle.

Popular Article

A low energy feedlot diet may favour our indigenous breeds

Dina Linde1,2, Michiel Scholtz1,3 & Este van Marle-Koster2

Introduction

The phenotypes of animals vary due to differences in their genetics and environment. The expression of the genes of animals can also be influenced by their diet. In South Africa, Sanga cattle (Afrikaner and Nguni) are adapted to various environments and production systems. However, these cattle are mostly found in extensive production systems that make use of natural grazing. They are not preferred in the feedlot, as their smaller frame sizes compared to Bos Taurus types and crossbreds will lead to smaller carcass sizes. The traditional diet fed in the feedlot is a high energy diet, that includes maize and maize by-products. There are however, farmers that believe that a high energy diet does not suite the genetics of Sanga cattle and that these breeds would do better on a lower energy diet.

A study was done to find alternative strategies for Sanga cattle in the feedlot. A diet low in energy (10.9 MJ ME/kg) or a high energy diet (12.5 MJ ME/kg) was fed to Nguni and Bonsmara cattle for a period of a 120 days respectively. During the feeding period the animals were weighed and real time ultrasound scanned for meat quality characteristics such as eye muscle area (EMA). At slaughter, muscle samples were taken to analyse the gene expression data.

In terms of the feedlot data, no significant difference could be found between the diets with regard to live weight, eye muscle area (EMA), rib fat and rump fat in the Nguni. Breed differences were however found. Carcass weight and marbling did however show significant difference as well as an interaction between breed and diet.

Breed had a much bigger effect compared to diet, with 2214 differentially expressed genes (DEG) and 74 DEG, respectively. Of the  genes found differentially expressed between the breeds, several genes known to be involved in marbling (SIRT, ND, COX, ADIPOQ, SERPINF2) was expressed higher in the Nguni compared to the Bonsmara. However, the phenotypic marbling score was higher in the Bonsmara compared to the Nguni.

This lead to the suggestion that the Nguni needed more time (a longer feedlot period) for the expression of the marbling genes to show phenotypically. This is in contrast to the industry that perceives that the Nguni deposits fat too early in comparison to exotic and crossbreds. Sanga cattle tend to first deposit fat intramuscularly, which might be an adaptation mechanism for the harsh conditions in which these cattle lived. It seems, however, that the Nguni only begins depositing muscle tissue after a sufficient layer of fat is deposited. This might be the reason for backgrounding, which is common practise in the Nguni breed.

Between the Nguni fed the high energy diet and the Nguni fed the low energy diet, 288 genes were differentially expressed. The different levels of energy in the diets seem to result in different components being deposited. Various genes (PITX2, PAX, Leptin, AVP, OXT) involved in muscle deposition were upregulated in the bulls that received the high energy diet, compared to the bulls fed the low energy diet. This is also seen in the phenotypic results with the carcass weight of the bulls fed the high energy diet being higher compared to the bulls fed the low energy diet.

The difference in carcass weight is very small between the Nguni fed the high energy diet and the Nguni fed the lower energy diet (6 kg). However, genes that influence intramuscular fat deposition (SPARC, CRNR2, CHRND, NR4A3, MMD) were elevated in the bulls that received the low energy diet compared to the bulls that received the high energy diet. This was also not shown in the phenotypic traits. Extending the period of feeding may result in the bulls that received the low energy diet to express the phenotype.

It seems that the low energy diet suite the Sanga cattle better, when compared to the traditional high energy diet fed in the feedlots. This should be further investigated as this study had a relatively small sample size (n=40). Furthermore, as these animals are ruminants, it would be also interesting to study the rumen microbiome in another study of this kind.

Dina Linde1,2, Michiel Scholtz1,3 & Este van Marle-Koster2

1ARC – Animal Production, Private bag X2, Irene, 0062, South Africa; 2Department of Animal and Wildlife science, University of Pretoria, Pretoria, 0002, South Africa; 3Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, 9300; South Africa;

Footer and Tags and Categorisation

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project on :mmakgahlela@arc.agric.za

Inheritance patterns of the Polled and Scur genes in South African beef cattle breeds

The genetic mechanisms and inheritance patterns of the polled and scur phenotypes in local South African beef cattle breeds

Industry Sector: Cattle And Small Stock

Research Focus Area: Animal Health and Welfare

Research Institute: Department of Animal & Wildlife Sciences, University of Pretoria

Year Of Completion: 2019

Researcher: E van Marle-Koster

The Research Team

TitleInitialsSurnameHighest QualificationResearch Institution
DrM.M.ScholtzPhDARC-AP
ProfEvan Marle-KosterPhDUP
MrsA. Theunissen MSc Vaalharts Research Station

Executive Summary

Introduction

It is standard practice to dehorn cattle at a young age by means of physical dehorning, but in most cases without the appropriate pain relief. The practice of dehorning has increasingly become a welfare concern and alternatives to dehorning are advocated worldwide. Breeding genetically polled cattle is a long-term, non-invasive and welfare friendly alternative to dehorning. Identification of genetically polled animals through a diagnostic test would therefore be advantageous, but a specific commercial diagnostic test for the polled phenotype is not currently available in South Africa.  The DNA tests that are available internationally are applicable to European Bos taurus breeds, which can give inconclusive results for indigenous South African and Sanga cattle breeds. Furthermore, the commercial diagnostic tests available for Taurine breeds can not identify carriers of either the scur gene or the African horn gene.

Over the past two decades commercial beef producers and feedlots in South Africa have indicated a preference for polled breeds, due to increased awareness of animal welfare and market preferences. In South Africa there are a number of polled breeds of European descent such as the Hereford, Angus, Charolais and Limousin, as well as a few local breeds, including the South African Bonsmara, Tuli and Drakensberger, that introgressed the polled gene. The Bonsmara breed requested research on the identification of homozygous polled bulls and the first research project in South Africa was performed at the Department of Animal and Wildlife Sciences, UP (Schmulian, 2006). This study was based on three Bonsmara families and the available microsatellite markers at that time were used. The study by Schmulian (2006) found linkage between the polled phenotype in the South African Bonsmara and alleles of nine microsatellite markers located on BTA1. Since the completion of this research project, the Bovine genome sequence has been completed in 2009 with high through-put molecular technology (Bovine HapMap Consortium, 2009), providing genomic information and high-density SNP chips.

The majority of previous research on the POLLED locus and polledness has been performed in European breeds, which does not provide a basis for identification of the causative mutation for polledness or scurs in indigenous South African cattle breeds. These breeds are genetically distinct from the European Bos taurus breeds (Makina et al., 2014) and besides the two main types of cattle, Bos taurus and Bos indicus, indigenous African cattle, such as the Sanga, are also found in South Africa.

Objective statement

This study focused on local South African beef cattle breeds to gain an understanding of the genetic basis and inheritance of the Polled and Scur genes by using pedigree data from phenotyped animals, as well as high density SNP data. The availability of DNA and high through-put molecular technology holds the potential to provide insight on the genetic mechanisms of polled and scurred animals with higher precision, compared to the microsatellite markers that were previously available.

Project Aims

  1. To evaluate whether the Celtic mutation on the POLL locus is the causative mutation for polledness in Bonsmara and Drakensberger
  2. To perform a genome wide association study of the Polled and Scur genes based on phenotypic data and genotypic data from the GGP Bovine 150K SNP bead chip
  3. To apply sequence data available from the Bovine Genomics Program to finemap the suspected regions for the Polled and Scur genes

Results

A total of 890 Bonsmara and 224 Drakensberger animals were screened for their status for the Celtic mutation at the POLLED locus using a PCR-based diagnostic test. It was possible to distinguish between heterozygous and homozygous polled individuals, but scurs could not be identified on a genotypic level based on the Celtic variant. The majority of animals screened, tested heterozygous polled, with homozygous polled animals occurring at a relatively low frequency. Based on the results of this Celtic screening, a total of 217 Bonsmaras (including homozygous polled, heterozygous clean polled and scurred animals) were genotyped using the GGP Bovine 150K SNP bead chip. Additional genotypes from the Bovine Genomics Program (BGP) were also included in this study.

Haplotype analysis of the POLLED locus revealed a reduced genetic diversity around the Celtic allele, with only two haploblocks (1.0-2.2 Mb) observed in the homozygous polled animals investigated. One of these haploblocks of six SNPs encompassed the Celtic mutation and presented only three distinct alleles with major differences in terms of frequencies. This result suggests that the Celtic allele was introgressed in the Bonsmara breed from a very limited number of founders. A low haplotype diversity combined with an intense selection on the polled phenotype in the Bonsmara breed can result in the selection of deleterious alleles linked with the Celtic mutation through a hitchhiking mechanism. Therefore, it is of primary importance to maintain some genetic variability around the Celtic allele.

Preliminary results of the GWAS study, based on 150k SNP chip data, indicated significant association for the scurs phenotype with three SNPs on BTA5, which contradicts previous findings that mapped the SCURS locus to BTA19. For the POLLED locus, preliminary results show significant association between the polled phenotype and BTA1, as expected. Of interest is another significant association with the polled phenotype that were observed on BTA28, which was not reported in previous studies. The significant SNPs that were identified in the GWAS analysis of the POLLED and SCURS loci will be annotated to identify candidate genes and to investigate the potential significant physiological pathways of these SNPs.

Conclusion

The POLLED Celtic variant was validated as the causative mutation of polledness in three South African beef cattle breeds and can be used as an efficient diagnostic test for polledness. This study also highlighted the current difficulties and limitations of accurate phenotypic recording of the horn status. It also confirmed that scurs cannot be identified on a genotypic level with the Celtic screening. Preliminary results of genotypic SNP data indicated significant association for the scurs phenotype on BTA5 in the Bonsmara, but these results need to be further investigated.

The following scientific output were achieved for the project:

Grobler, R., Visser, C. & van Marle-Köster, E., 2017. Accelerating selection for polledness in the South African Bonsmara using DNA technology. 50th South African Society for Animal Science (SASAS) Congress, Port Elizabeth, 18 – 21 September 2017.

Grobler, R., van-Marle-Köster, E., Visser, C.& Capitan, A., 2018. Haplotype variation at the POLLED locus in the South African Bonsmara cattle breed. World Congress on Genetics Applied to Livestock Production (WCGALP) 11-16 February, Auckland.

Grobler, R., Visser, C., Capitan, A. & van Marle-Köster, E., 2018. Validation of the POLLED Celtic variant in South African Bonsmara and Drakensberger beef cattle breeds. Livestock Science. 217, 136-139.

Popular Article

Introduction

Identifikasie van poena status in die Bonsmara met behulp van DNA tegnologie

Rulien Grobler (PhD Kandidaat)

Departement Vee- en Wildkunde, Universiteit van Pretoria

Inleiding

Die voordele van poenskop beeste vir die kommersiële vleisbeesindustrie is alombekend en wêreldwyd word die druk vir meer menslike praktyke in terme van dierebehandeling hoër, as gevolg van die impak op dierewelsyn. Alhoewel die opsie daar is om kalwers te onthoring, dui navorsing aan dat dit n pynvolle prosedure is, ten spyte van die tegniek of voorsorgmaatreëls wat gebruik word. Behalwe dat die onthoring van kalwers nie welsynsvriendelik is nie, is dit ook tydrowend en arbeidsintensief,en veroorsaak dit ook stres wat die groei van die kalf negatief kan affekteer. Hierdie faktore het dan ook ‘n verdere ekonomiese implikasie vir die boer. Dit is ook n opsie om poenskop beeste te selekteer gebaseer op fenotipiese rekords, maar hierdie proses is egter tydrowend en oneffektief, en veroorsaak stadige genetiese vordering. Deur gebruik te maak van DNA tegnologie om poenskop diere te identifiseer, kan seleksie vinniger en meer effektief plaasvind en genetiese vordering sal ook vinniger toeneem. Verder is dit ook ‘n welsynsvriendelike alternief, so wel as n langtermyn oplossing vir die onthoring van kalwers.

Poenskop oorerwing

Die Poena geen is outosomaal dominant en indien teenwoordig, sal die uitdrukking van die horing fenotipe onderduk word. Daar is twee allele teenwoordig by die Poena geen, P en p, en diere wat die dominante P alleel dra is fenotipies poenskop. Homosigotiese poenskop diere dra twee dominante P allele (PP), terwyl heterosigotiese poenskop (Pp) diere een dominante P alleel dra en een horing alleel. Dus, diere wat twee p allele dra het dan die horing fenotipe (pp). As gevolg van dominansie, kan daar nie onderskei word tussen die homosigoot en heterosigoot poena fenotipe nie. Dus is dit nodig vir n genetiese toets om draers van die poena en horing allele te identifiseer.

Afhangende van die poena status van die moer en vaar, word die poena allele in verskillende proporsies oorgedra na die nageslag (Figuur 1). Bv. Wanneer n homosigotiese poena (PP) bul, wat dan twee dominante poena allele dra, geteel word met n horing koei (pp), is daar ‘n 100% kans dat die nageslag fenotipies poenskop sal wees, omdat die nageslag een dominante P alleel kry van die vaar en een horing alleel van die moer. Maar wanneer n heterosigotiese poena (Pp) bul gebruik word, verminder die kans vir poenskop nageslag met 50% (Figuur 1).

Figuur 1 Die moontlike genotipiese proporsies vir verskillende paringsituasies van horing, hetero- en homosigotiese poenskop individue

Die oorerwing van die poena geen word verder gekompliseer deur die scurs fenotipe, as gevolg van epistatiese interaksie tussen die Poena en Scurs gene. Scurs is klein horingagtige vergroeisels wat op dieselfde plek as horings op die kop voorkom, maar hierdie abnormale vergroeisels is losweg aan die skedel geheg en is beweeglik (Figuur 2). Scurs is geslagsbeïnvloed en word gevolglik verskillend oorgeërf in manlike en vroulike diere. Dit is waargeneem dat scurs kan voorkom in diere wat heterosigoties poenskop is, en dat scurs meer in manlike diere as in vroulike diere voorkom.

Figuur 2 Die poenskop (A en B) en variasie van die scurs (C – F) fenotipes soos waargeneem in die Bonsmara

Die Poena Projek by UP

Die Poena geen is geleë op chromosoom 1 (BTA1) en minstens twee verskillende variante is verantwoordelik vir die poenskop fenotipe in beeste, naamlik die Celtic (PC) en Friesian (PF) variante (Allais-Bonnet et al., 2013).  Die Celtic (PC) variant is verantwoordelik vir die poenskop fenotipe in die meeste Bos taurus rasse van Europese herkoms, terwyl die Friesian (PF) variant hoofsaaklik voorkom in die Holstein Friesian ras.

In samewerking met ‘n navorser van Frankryk (INRA), is Bonsmara diere getoets vir beide die Celtic (PC) en Friesian variante (PF). Dit is vasgestel dat al die Bonsmara diere met n poenskop fenotipe, dra ten minste een alleel van die Celtic variant en geen diere is positief getoets vir die Friesian variant nie. Hierdie bevinding is in lyn met die geskiedenis en ontwikkeling van die Bonsmara vanuit n Europese Bos taurus ras. ‘n Groter groep Bonsmaras is getoets vir die Celtic variant (PC) en dit is bevestig dat die Celtic variant (PC) van die Poena geen verantwoordelik is vir die poenskop fenotipe in die Suid-Afrikaanse Bonsmara (Grobler et al., 2018).

Deur gebruik te maak van ‘n haarmonster, word DNA geëkstraeer uit die haarwortels. Die DNA word dan gebruik om die dier te toets vir die Celtic variant (PC) deur gebruik te maak van ‘n PCR-gebaseerde diagnostiese toets. Gevolglik kan draers van die PC variant geïdentifiseer word en sodoende kan diere ook as homo- of heterosigoties poena geïdentifiseer word op ‘n genotipiese vlak.

Bonsmara bulle en koeie, asook sekere kalwers, is uit spesifieke kuddes geselekteer om poenskop diere te identifiseer en tot dusver is n totaal van 890 Bonsmaras getoets vir die Celtic variant (PC) met die bogenoemde diagnostiese toets. ‘n Hoë frekwensie poenskop diere is waargeneem, waarvan die meerderheid diere heterosigoties poena getoets het (Figuur 3). Dit beteken dat hierdie diere slegs een PC alleel dra, asook een horing alleel, wat dan moontlik oorgedra kan word aan die dier se nageslag. Alhoewel homosigotiese poena diere wel waargeneem is, is dit waargeneem in slegs 12% van die diere wat tot dusver getoets is (Figuur 3). Die Bonsmara diere wat horing getoets het, is by n relatiewe hoë frekwensie van 42% waargeneem (Figuur 3). Dit is tog nodig om te noem dat die meerderheid van die homosigotiese poenas in een kudde waargeneem is wat vir meer as twee dekades al spesifiek selekteer vir die poenskop fenotipe. Alhoewel hierdie toets kan onderskei tussen homo- en heterosigote poenskop diere, kan die toets nie scurs op ‘n genotipiese vlak identifiseer nie en verdere navorsing is nodig vir scurs.

Figuur 3 Die genotipe frekwensie van die Celtic variant (PC) soos getoets in 890 Bonsmaras

Implikasies vir SA Bonsmara

Die diagnostiese DNA toets kan effektief gebruik word om heterosigotiese en homosigotiese poena diere te identifiseer op n genotipiese vlak. Hierdie toets kan egter nie gebruik word om scurs op n genotipe vlak te identifiseer nie, omdat beide poenskop en scurs diere genotipies heterosigoties poenskop toets (Pp). Dit is dan juis waarom dit belangrik is om die horingstatus van diere vroegtydig en akkuraat aan te teken. Die poenskop fenotipe is maklik om te observeer en verander nie tydens die dier se leeftyd nie. Die scurs fenotipe is egter moeiliker om aan te teken, omdat dit dikwels verwar word met horings of eers later uitgedruk word. Daarom word dit aanbeveel dat beeste ondersoek word by n jong ouderdom (gewoonlik tydens speen), asook tussen 18 en 24 maande.

Met behulp van hierdie DNA tegnologie kan die poena status van diere vroegtydig geïdentifiseer word, wat sodoende die genetiese seleksie van poena diere sal vergemaklik, asook versnel. Verder hou dit ‘n ekonomiese voordeel vir telers in wanneer gesertifiseerde poenskop bulle bemark kan word. Meer poenskop diere in die mark sal ook ‘n voordeel inhou deur arbeidskostes te verlaag en diere welsyn te bevorder omdat die onthoring van diere dan metteryd nie meer nodig sal wees nie. Die relatiewe hoë frekwensie van horing diere wat waargeneem is bevestig juis die belangrikheid van ‘n DNA toets, deurdat telers eers die poena status van diere op ‘n genotipiese vlak moet bevestig voordat vermeende poena diere ingesluit word in ‘n paringsprogram. Dit is veral belangrik vir bulle wat vir teeldoeleindes en veilings gebruik gaan word.

Erkennings

Dankie aan elke boer wat haarmonsters en inligting bygedrae het vir die Poena projek, en ook spesifiek vir Charl Uys vir sy hulp. Dankie aan Prof E. van Marle-Köster en Dr C. Visser; die studiepromotors op die PhD projek. Dank aan RMRD SA en die NRF vir befondsing.

Verwysings

Allais-Bonnet et al., 2013. PloS ONE. 8, 1-14.

Grobler et al., 2018. Livestock Science. 217, 136-139.

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Gene expression: Nguni and Bonsmara

A gene-expression study on the growth performance of Nguni and Bonsmara cattle grown in a feedlot fed a high and low energy diet

Industry Sector: Cattle And Small Stock

Research Focus Area: Livestock production with global competitiveness: Breeding,physiology and management

Research Institute: Agricultural Research Council

Year Of Completion : 2019

Researcher: Dina Linde

The Research Team

TitleInitialsSurnameHighest QualificationResearch Institution
DrM.M.ScholtzPhDARC-AP
ProfEvan Marle-KosterPhDUP
MrsA. Theunissen MSc Vaalharts Research Station

Executive Summary

Introduction

In South Africa, Nguni cattle are one of the breeds found predominantly in extensive production systems. The Nguni is an indigenous cattle breed and is widely used in crossbreeding systems due to their high fertility and mothering ability. Nguni cattle are also commonly used in communal production systems. The majority of beef in South Africa is produced in feedlots using commercially formulated high energy diets, where preference is given to medium and large framed later maturing cattle that include British types and composites such as the South African Bonsmara. Due to the Nguni’s small frame and low meat yield when compared to British types it is nor preferred as a feedlot animals, however studies have shown that Nguni cattle produce high quality meat.

The veldt of South Africa has a varying degree of carrying capacity, however the occasional drought conditions have necessitated the use of alternative production systems such as feedlots for finishing cattle. The use of a lower energy diet in feedlots for indigenous cattle have been suggested and warrants investigation. Nutrigenomics is the study of the effect of nutrition on the genes of the animal by quantifying the gene expression. An improved understanding of the interaction between the nutritional environment and the genetics of the animal can lead to increased efficiency and production. Diets that are different in components or ingredients can result in different phenotypes in the animals. In this study the effect of two feedlot diets with different energy levels have been investigated using a transcriptome approach.

Objective statement

The objective of this study is to determine if there are gene expression differences between Nguni and Bonsmara cattle fed a low or a high energy diet. The gene expression of the cattle can determine the underlying differences in the reaction of the two breeds to the two different diets.

Project Aims

  1. To evaluate whether the Celtic mutation on the POLL locus is the causative mutation for polledness in Bonsmara and Drakensberger
  2. To perform a genome wide association study of the Polled and Scur genes based on phenotypic data and genotypic data from the GGP Bovine 150K SNP bead chip
  3. To apply sequence data available from the Bovine Genomics Program to finemap the suspected regions for the Polled and Scur genes

Results

Conclusion

Performance results showed a higher live weight, carcass weight and marbling score for all bulls fed the high energy diet compared to bulls fed the low energy diet. Only carcass weight and marbling score had significant difference in terms of diet (p < 0.05). Live weight, average daily gain, rib fat, rump fat and eye muscle area were only significant for breed. Diet had a greater effect on the Bonsmara compared to the Nguni according to transcriptomic and phenotypic values. Transcriptomic values showed 3584 differential expressed genes (DEG) between the Bonsmara fed the two different diets, while only a difference of 288 DEG were observed between the Nguni fed the two different diets. Phenotypic values show a difference of 20 kg between the Bonsmara groups and only a 6 kg difference between the Nguni groups. Most DEG were involved with cellular processes and metabolic pathways. A total of 73 differentially expressed genes were observed between the diets across breeds. The genes that were involved in intramuscular fat deposition (CRHR2, NR4A3, MMD) were expressed on a higher level in the bulls on the low energy diet compared to bulls on the high energy diet. Genes that were involved in muscle deposition (PITX2, Leptin, AVP) was expressed higher in the bulls on the high energy diet. Comparing the breeds revealed that 2214 genes were differentially expressed between the Bonsmara and the Nguni.

At the end of the feedlot trial a higher expression of marbling genes (SIRT, ND, ADIPOQ) were observed in the Nguni, however this expression was not observed in the marbling scores recorded. Several genes (ASIP, MOGAT, SNAI3) that were involved in fat deposition were upregulated in the Bonsmara. This suggests that the Nguni was still growing at the end of the feedlot trial while the Bonsmara had reached physiological maturity. Little literature could be found on some of the gene showing the highest expression in the groups such as GSTA3, TEX28 and TUBB3. Glutathione-s transferase alpha 3 (GSTA3) is linked to steroidal genesis and could therefore have an influence on myogenesis, however no confirming literature could be found.

Conclusion

The diet had a smaller effect on the Nguni bulls compared to the Bonsmara bulls as observed in the DEG and the carcass weight of the bulls. This might indicate that the Nguni is more adaptable to a variation in feed quality. The Bonsmara bulls had a higher meat yield on the high energy diet, however it seems as if the bulls on the low energy diet had a higher expression of the marbling genes. This is in contrast to the phenotypically higher marbling score. Further research needs to be done as this study had a small sample size (n=40). An extended feedlot period for Nguni cattle should be considered in future studies. This study provides reference data for differentially expressed genes in muscle of South African feedlot cattle.

Popular Article – A low energy feedlot diet may favour our indigenous breeds

Dina Linde1,2, Michiel Scholtz1,3 & Este van Marle-Koster2

1ARC – Animal Production, Private Bag X2, Irene, 0062, South Africa; 2Department Of Animal And Wildlife Science, University Of Pretoria, Pretoria, 0002, South Africa; 3Department Of Animal, Wildlife And Grassland Sciences, University Of The Free State, Bloemfontein, 9300; South Africa;

The phenotypes of animals vary due to differences in their genetics and environment. The expression of the genes of animals can also be influenced by their diet. In South Africa, Sanga cattle (Afrikaner and Nguni) are adapted to various environments and production systems. However, these cattle are mostly found in extensive production systems that make use of natural grazing. They are not preferred in the feedlot, as their smaller frame sizes compared to Bos Taurus types and crossbreds will lead to smaller carcass sizes. The traditional diet fed in the feedlot is a high energy diet, that includes maize and maize by-products. There are however, farmers that believe that a high energy diet does not suite the genetics of Sanga cattle and that these breeds would do better on a lower energy diet.

A study was done to find alternative strategies for Sanga cattle in the feedlot. A diet low in energy (10.9 MJ ME/kg) or a high energy diet (12.5 MJ ME/kg) was fed to Nguni and Bonsmara cattle for a period of a 120 days respectively. During the feeding period the animals were weighed and real time ultrasound scanned for meat quality characteristics such as eye muscle area (EMA). At slaughter, muscle samples were taken to analyse the gene expression data.

In terms of the feedlot data, no significant difference could be found between the diets with regard to live weight, eye muscle area (EMA), rib fat and rump fat in the Nguni. Breed differences were however found. Carcass weight and marbling did however show significant difference as well as an interaction between breed and diet.

Breed had a much bigger effect compared to diet, with 2214 differentially expressed genes (DEG) and 74 DEG, respectively. Of the  genes found differentially expressed between the breeds, several genes known to be involved in marbling (SIRT, ND, COX, ADIPOQ, SERPINF2) was expressed higher in the Nguni compared to the Bonsmara. However, the phenotypic marbling score was higher in the Bonsmara compared to the Nguni.

This lead to the suggestion that the Nguni needed more time (a longer feedlot period) for the expression of the marbling genes to show phenotypically. This is in contrast to the industry that perceives that the Nguni deposits fat too early in comparison to exotic and crossbreds. Sanga cattle tend to first deposit fat intramuscularly, which might be an adaptation mechanism for the harsh conditions in which these cattle lived. It seems, however, that the Nguni only begins depositing muscle tissue after a sufficient layer of fat is deposited. This might be the reason for backgrounding, which is common practise in the Nguni breed.

Between the Nguni fed the high energy diet and the Nguni fed the low energy diet, 288 genes were differentially expressed. The different levels of energy in the diets seem to result in different components being deposited. Various genes (PITX2, PAX, Leptin, AVP, OXT) involved in muscle deposition were upregulated in the bulls that received the high energy diet, compared to the bulls fed the low energy diet. This is also seen in the phenotypic results with the carcass weight of the bulls fed the high energy diet being higher compared to the bulls fed the low energy diet.

The difference in carcass weight is very small between the Nguni fed the high energy diet and the Nguni fed the lower energy diet (6 kg). However, genes that influence intramuscular fat deposition (SPARC, CRNR2, CHRND, NR4A3, MMD) were elevated in the bulls that received the low energy diet compared to the bulls that received the high energy diet. This was also not shown in the phenotypic traits. Extending the period of feeding may result in the bulls that received the low energy diet to express the phenotype.

It seems that the low energy diet suite the Sanga cattle better, when compared to the traditional high energy diet fed in the feedlots. This should be further investigated as this study had a relatively small sample size (n=40). Furthermore, as these animals are ruminants, it would be also interesting to study the rumen microbiome in another study of this kind.

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Genetic diversity of landrace cattle breeds

Genetic diversity and relationships among seven South African landrace and exotic cattle breeds

Industry Sector: Cattle And Small Stock

Research Focus Area: Livestock production with global competitiveness: Breeding, physiology and management

Research Institute: Agricultural Research Council Animal Production (ARC-AP)

Year Of Completion : 2019

Researcher: Dr Lene van der Westhuizen

The Research Team

TitleInitialsSurnameHighest QualificationResearch Institution
DrM.M.ScholtzPhDARC-AP
ProfEvan Marle-KosterPhDUP
MrsA. Theunissen MSc Vaalharts Research Station

Executive Summary

Introduction

An existing 11 microsatellite marker database that resulted from parentage verification, was used to assess genetic diversity among nine breeds of cattle. These breeds were drawn from Bos indicus (Boran and Brahman), B. taurus (Angus and Simmental) and B. taurus africanus (Afrikaner, Bonsmara, Drakensberger, Nguni and Tuli). Due to the cost of genotyping, genetic variability and population structure studies using single nucleotide polymorphisms (SNPs) rely on relatively low numbers of animals to represent each of the breeds. However, large numbers of animals have been genotyped for parentage verification using microsatellite markers and this microsatellite information on large numbers of animals have the potential to provide more accurate estimates of genomic variability than SNPs.

The breeds in this study were characterized by unbiased heterozygosity, effective number of alleles and inbreeding. Ranges in estimates of these parameters were 0.569–0.741, 8.818–11.455 and -0.001–0.050, respectively. The analysis of population structure revealed descent from taurine, indicine, and Sanga types with K=3 and from unique progenitor populations with K=9. There are notable similarities between the results observed using a limited number of genetic markers and large numbers of animals with microsatellite markers.

The study revealed the southern African Sanga and exotic cattle breeds that are found in South Africa, are genetically distinct from each other. Therefore, using the Sanga and Sanga derived breeds in crossbreeding programs should be done with caution to ensure the conservation of genetic resources of these breeds. Furthermore, comparable genetic variability and inbreeding levels found in the present study demonstrate the genetic sturdiness of the Sanga and Sanga derived breeds. However, there is a notable similarity between the results observed in this study (using a limited number of genetic markers and large numbers of animals), with the results of studies with similar objectives which used substantial greater numbers of markers but much fewer animals.

The analyses revealed that the southern African, British and European breeds as well as the tropically adapted breed clustered separately. Therefore, exotic breeds in South Africa is expected to benefit from favourable heteroses effects due to crossing with Landrace breeds.

Objective Statement

The present study used existing microsatellite marker databases (provided by Breeders’ Societies) to estimate levels of heterozygosity and inbreeding of several southern African Sanga and exotic breeds, and quantify the genetic relationships between the breeds. To these ends, obtaining data from historical parentage databases allowed for use of substantially larger numbers of animals per breed to be studied than in previous investigations.

Project Aims

  1. To determine the level of genetic variation of each breed, therefore identifying the remaining resources of heterozygosity within the four South African landrace cattle breeds.
  2. To compare the level of genetic variation between the four landrace breeds.
  3. To determine the inbreeding for the breeds as whole.
  4. To determine the relation (genetic un-relatedness) between South Africa’s landrace breeds and Zebu, British and European breeds.

Results

From a genetic diversity perspective, all breeds had large numbers of alleles at each locus and high frequencies of heterozygous genotypes; and thus each locus had substantial polymorphic information content. The number of alleles per locus and frequency of heterozygotes found in the present study were both toward the lower ends of the corresponding ranges for the same loci that were previously observed in a substantially larger sample of Afrikaner cattle. Inbreeding is not currently at a sufficient level so as to be problematic in the South African segments of these breeds. From the present study, the number of Clusters found with the highest probability of membership, required to describe the between-breed genetic relationships, were two (K=2) and noticeably grouped the two taurine breeds separate from the Sanga and indicine (Afrikaner, Brahman, Boran, Nguni and Tuli) breeds. The second highest probability showed a total of three genetic Clusters (K=3) and grouped the taurine, indicine and Sanga breeds separately. When K=9 is used, breed individuality and admixture were clearly defined. Here, the Nguni was shown to be the most admixed with 31 % of membership belonging to the other eight Clusters. The Nguni is followed by Bonsmara and Drakensberger showing admixture from other Clusters up to 24 %. These results are in accordance with Makina et al. (2016), with the latter authors suggesting that the admixture within Nguni and Drakensberger have been involuntary, however, the admixture recognized within the Bonsmara was intentional given the breed history. Moreover, Angus showed to be the least admixed with significant membership within this Cluster with probability of 90 %. To demonstrate the genetic distances between the breeds, an NJ tree was generated. The tree illustrated the discrepancy between the three groups of cattle, with the southern African Sanga breeds grouping separately from the indicine and taurine cattle, but sharing a closer genetic background with the two indicine breeds. The NJ tree also supported the multi-locus clustering algorithm when K=2 is used with reference to Bonsmara and Drakensberger and again highlights the discrepancy between the present study and the results of Makina et al.  (2016).

Discussion

From a genetic diversity perspective, all breeds had large numbers of alleles at each locus and high frequencies of heterozygous genotypes; and thus each locus had substantial polymorphic information content. The number of alleles per locus and frequency of heterozygotes found in the present study were both toward the lower ends of the corresponding ranges for the same loci that were previously observed in a substantially larger sample of Afrikaner cattle. Inbreeding is not currently at a sufficient level so as to be problematic in the South African segments of these breeds. From the present study, the number of Clusters found with the highest probability of membership, required to describe the between-breed genetic relationships, were two (K=2) and noticeably grouped the two taurine breeds separate from the Sanga and indicine (Afrikaner, Brahman, Boran, Nguni and Tuli) breeds. The second highest probability showed a total of three genetic Clusters (K=3) and grouped the taurine, indicine and Sanga breeds separately. When K=9 is used, breed individuality and admixture were clearly defined. Here, the Nguni was shown to be the most admixed with 31 % of membership belonging to the other eight Clusters. The Nguni is followed by Bonsmara and Drakensberger showing admixture from other Clusters up to 24 %. These results are in accordance with Makina et al. (2016), with the latter authors suggesting that the admixture within Nguni and Drakensberger have been involuntary, however, the admixture recognized within the Bonsmara was intentional given the breed history. Moreover, Angus showed to be the least admixed with significant membership within this Cluster with probability of 90 %. To demonstrate the genetic distances between the breeds, an NJ tree was generated. The tree illustrated the discrepancy between the three groups of cattle, with the southern African Sanga breeds grouping separately from the indicine and taurine cattle, but sharing a closer genetic background with the two indicine breeds. The NJ tree also supported the multi-locus clustering algorithm when K=2 is used with reference to Bonsmara and Drakensberger and again highlights the discrepancy between the present study and the results of Makina et al.  (2016).

Conclusion

The study revealed the southern African Sanga and exotic cattle breeds that are found in South Africa, are genetically distinct from each other. Therefore, using the Sanga and Sanga derived breeds in crossbreeding programs should be done with caution to ensure the conservation of genetic resources of these breeds. Furthermore, comparable genetic variability and inbreeding levels found in the present study and Makina et al. (2014) demonstrate the genetic sturdiness of the Sanga and Sanga derived breeds. However, there is a notable similarity between the results observed in this study (using a limited number of genetic markers and large numbers of animals), with the results of studies with similar objectives which used substantial greater numbers of markers but much fewer animals. Thus, opportunities that arise to explore genetic diversity in both the livestock and wildlife industries in Southern Africa, may capitalize on microsatellite marker databases which remain cost-effective and accessible due to their continued use for parentage verification.

Both analyses revealed the southern African, British and European breeds as well as the tropically adapted breed clustered separately. Therefore, exotic breeds in South Africa is expected to benefit from favourable heterosis effects due to crossing with Landrace breeds. Opportunities that arise to explore genetic diversity in both the livestock- and wildlife industries may capitalize on microsatellite marker databases which remain cost-effective and accessible due to their continued use for parentage verification.

Popular Article

Genetic diversity and relationships among seven South African landrace and exotic cattle breeds

Genetic variability or genetic diversity is required for populations to be able to adapt to different environmental pressures. It can also be defined as the variation of alleles and genotypes present in a breed. This provides the basis for adaptive and evolutionary processes. The current level of diversity in livestock has been created by the combined forces of both natural- and artificial selection. These forces can be described as mutations, adaptations, segregation, selective breeding and genetic drift. Furthermore, genetic diversity in livestock species is essential for the adaptive responses needed in ever-changing farming conditions and ultimately to respond to the challenges created by climate change. Additionally, diversity also provides a reservoir for genetic variation to ensure that future market demands can be met through selection.

The indigenous cattle breeds of Southern Africa include the Sanga and Sanga derived cattle. Sanga cattle, especially those indigenous to southern Africa, are classified as Bos taurus africanus. The indigenous Sanga cattle of South Africa includes the Afrikaner, Nguni and Drakensberger, whereas the Tuli and Hugenoot are considered to be the Landrace breeds of Southern Africa. The Bonsmara is a Sanga derived composite breed. These breeds are extremely well adapted to the harsh climatic and other environmental conditions encountered under extensive ranching in South Africa. This will become even more important in the era of climate change.

Research has suggested that Sanga cattle, compared to European breeds are favourable with regard to meat tenderness. There has been speculation that the Landrace breeds may be closely related to other tropically adapted breeds (B. indicus) such as the Brahman due to their morphological similarities. However, several genetic studies have demonstrated a closer relationship between Sanga and B. taurus breeds.

In the early 1900’s there was a perception in South Africa that the indigenous breeds were inferior and this led to the promulgation of an Act in 1934 in which indigenous breeds and types were regarded as ‘scrub’ (non-descript). Inspectors were appointed to inspect the bulls in communal areas and to castrate them if regarded as inferior. Fortunately, this Act was applied effectively for only a few years, since it was very unpopular. However, the effect of this on especially the “purity” of the Nguni was never established. In addition, the Bonsmara is supposed to be 5/8 Afrikaner: 3/8 British composition. Through selection and subsequent upgrading, this composition may have shifted significantly. It is therefore important to also establish the relationship between the Landrace, Zebu, British and European breeds.

The Southern African landrace breeds are relatively poorly characterized at the genomic level in comparison to many taurine and indicine breeds. Using genotypes derived from microsatellite loci, several research projects have characterized contemporary populations of Bonsmara, Afrikaner, Nguni and the Tuli from Zimbabwe. Due to the cost of genotyping, substantially fewer animals (i.e., ≤ 50) have been characterized by single nucleotide polymorphism (SNP) arrays using approximately 50 000 DNA markers to estimate the diversity of Afrikaner, Bonsmara, Drakensberger, and Nguni cattle and to evaluate their relationship to other breeds worldwide. Bi-allelic markers such as single nucleotide polymorphisms (SNPs) are currently the subject of interest globally. However, in Southern Africa, microsatellite markers have been used routinely and are more cost-effective in the livestock, wildlife and aquaculture industries. Microsatellite markers have multiple alleles and are generally more informative than SNPs. However, the latter statement is largely dependent on sample size. Microsatellites have also been used over the years for relationship studies, inbreeding levels and breed differentiation.

The aim of this study was to use microsatellite marker databases (provided by Breeders’ Societies) to estimate levels of heterozygosity and inbreeding of nine Southern African Sanga and exotic breeds, and quantify the genetic relationships between the breeds. This allowed the use of substantially larger numbers of animals per breed to be studied than in previous investigations.

The breeds used in this study were Afrikaner, Angus, Bonsmara, Boran, Brahman, Drakensberger, Nguni, Simmental and Tuli. Animals were genotyped in response to requests from industry for parentage verification.  At least 300 animals were randomly chosen to represent each breed,

All breeds had large numbers of alleles at each locus and high frequencies of heterozygous genotypes. Inbreeding was found not to be at a level where it will be problematic in the South African segments of these breeds. While the present study used microsatellite data, another study, using SNP data, showed similar findings regarding the genetic variability and inbreeding levels of southern African Sanga cattle.

When provision was made for two ancestral populations (K=2), the two taurine (Angus and Simmental) breeds were separated from the Sanga and indicine (Afrikaner, Bonsmara, Brahman, Boran, Drakensberger, Nguni and Tuli) breeds. It was however noted that both Bonsmara and Drakensberger also showed some admixture of at least 30 % with the cluster belonging to Angus and Simmental. These results are consistent with the development of the Bonsmara breed with the B. taurus influence (5/8 Afrikaner, 3/16 Shorthorn, and 3/16 Hereford) and some uncertain or undefined breed origin of the Drakensberger.

When provision was made for three ancestral populations (K=3), it grouped the taurine (Angus and Simmental), indicine (Brahman and Boran) and Sanga (Afrikaner, Bonsmara, Drakensberger, Nguni and Tuli) breeds separately. When K=9 was used, breed individuality and admixture between the breeds could be clearly defined.

The study revealed the Southern African Sanga and exotic cattle breeds found in South Africa are genetically distinct from each other. Furthermore, comparable genetic variability and inbreeding levels found in the present- and other studies, demonstrated the genetic sturdiness of the Sanga and Sanga derived breeds.

There is a notable similarity between the results observed in this study (using a limited number of DNA markers and large numbers of animals), with the results of other studies, with similar objectives, which used substantial greater numbers of DNA markers but much fewer animals.

Both analyses revealed the southern African Sanga breeds, British and European breeds, as well as the tropically adapted Zebu breeds clustered separately. Therefore, exotic breeds in South Africa is expected to benefit from favourable heterosis effects, when crossed with Landrace breeds. Finally, the results from this study indicate that genetic diversity in both the livestock- and wildlife industries may capitalize on microsatellite marker databases which remain cost-effective and accessible due to their use for parentage verification.

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Please contact the Primary Researcher if you need a copy of the comprehensive report of this project. Lene van der Westhuizen lenevdwest@gmail.com