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

Slaughter conditions to optimise chevon meat quality

Determination of slaughter conditions to optimise chevon visual and eating quality

Industry Sector: Cattle and Small Stock

Research focus area: Animal Products, Quality and Value-adding

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Dr L Frylinck PhD

Title Initials Surname Highest Qualification
Prof PE Strydom PhD
Prof EC Webb PhD Animal Science
Dr P Pophiwa PhD Animal Science
Prof LC Hoffman PhD Animal Science
Ms GL van Wyk MSce (Registered for PhD)
Ms JD Snyman ND Histologie

Year of completion : 2018

Aims of the project

  • To determine the expression of genomic markers in five South African purebred genotypes – Bos indicus
  • To determine the optimum slaughter procedures (electrical stimulation for 15 – 60 seconds or delayed/step wise chilling – time determined by optimal pH) for carcasses from castrated and intact male goats of two breed types: Boer Goats and Indigenous Veld Goats (IVG, Eastern Cape Xhosa or Northern Cape Speckled Goats
  • To evaluate the tenderness and connective tissue characteristics in six different muscles m. longissimus thoracis et longissimus (LTL), m. semimenbranosus (SM), biceps femoris (BF), supra spinatus (SS), infra spinatus (IS) and semitendanosus (ST) in electrical stimulated carcasses of Boer Goats and IVG from castrated and intact male goats.
  • To evaluate the tenderness and calpain system ageing related characteristics in m. longissimus thoracis et lumborum (LTL) and m. semimembranosus (SM) muscles of electrical stimulated and non-stimulated carcasses of Boer Goats and IVG from castrated and intact male goats.
  • To evaluate sensory attributes and other meat quality characteristics of chevon from the respective post-slaughter treatments in m. longissimus thoracis et lumborum (LTL) and m. semimembranosus (SM) muscles of electrical stimulated and non-stimulated carcasses of the two breed types; Boer Goats and IVG from castrated and intact male goats.

Executive Summary

The demand for goat meat in South Africa is relatively low because of traditional perceptions of off smells, off flavours and expected toughness. Perceptions also exist that Indigenous Veld Goat (IGV) produce tougher meat than Boer Goat (BG) specially bred to be a meat producing breed. The name indigenous goat is perceived as being small and not suitable for meat production. It is now discovered that some Indigenous Eco-types of Southern Africa, compare well with the Boer goat in size, can also produce good meat products if good farming and rearing practices are followed. Except for the advantage to preserve the indigenous breeds for the future generations, these breeds are well adapted to the harsh climate conditions in Southern Africa and are hardy with minimum need for veterinary intervention. Production and slaughter procedures should be adapted to suit the characteristics such as the low glycolytic potential and low carcass fat of goat carcasses. There is therefore a need to optimise the pre- and post-slaughter procedures in order to optimise the chevon (goat meat) visual and eating quality.

The first aim were investigated by applying different pre- and post slaughter procedures such as castration or not, applying electrical stimulation for 20 and 30 seconds or apply stepwise chilling. The monitoring of the muscle pH and temperature, muscle energy, meat colour and tenderness showed that either controlled step wise chilling or electrical stimulation of at least 30 sec will prevent cold toughening and produce ideal conditions for the intra muscular proteolytic enzymes to optimally function. It was found that castrated animals produced more tender meat than intact carcasses, but that more subcutaneous fat were produced, which could be advantageous to its eating experience. Both breed types: Boer Goats and Indigenous Veld Goats (IVG, Eastern Cape Xhosa or Northern Cape Speckled Goats, showed the same advantage in tenderness and colour if slaughter conditions were optimised.

The intrinsic characteristics of the six different muscles m. longissimus (LTL), m. semimenbranosus (SM), biceps femoris (BF), supra spinatus (SS), infra spinatus (IS) and semitendanosus (ST) differed from each other as expected, but castrated muscles had an higher intramuscular fat content – up to 4% than that on intact carcasses – similar in both breed-types tested. Percentage collagen solubility did not differ between the different muscles, but the total collagen measured in each muscle type did differ. Thus is optimal cooking method important.

Evaluating the tenderness and calpain system ageing related characteristics in m. longissimus thoracis et lumborum (LTL) and m. semimembranosus (SM) muscles of electrical stimulated and non-stimulated carcasses of Boer Goats and IVG from castrated and intact male goats confirm that the breed types did not differ in tenderness, but castration do have an advantageous effect on tenderness. It is said for beef that sarcomere length (SL) longer than 1.7 µm does not influence tenderness, but in this project it was obvious that the shorter 1.8 µm sarcomere length compared to that of our first subproject of 2 µm could have influenced meat tenderness. It is said that the calpain system works more effectively when the SL length is longer.

Sensory panel evaluation showed attributes and other meat quality characteristics of chevon from the respective post-slaughter treatments in m. longissimus (LTL) and m. semimembranosus (SM) muscles of electrical stimulated and non-stimulated carcasses of the two breed types; Boer Goats and IVG from castrated and intact male goats. Overall it seems like the sensory panel found the LTL and SM muscles tough, although the shear force measurements was not exactly inline with their findings. As mentioned before, the slaughter conditions could have been chosen better, for instance the ES should have been 30 sec and not 20 sec. Delayed/stepwise chilling could have given better results. I do recommend though that if a future sensory panel study is being done, mutton should be included to remove the possibility of biasness. Although I have no reason to doubt the professionalism of the panel, I do think that there could be a possibility of a negativity towards goat meat.

The evaluation of carcass characteristics and yield of electrical stimulated and non-stimulated carcasses of the two breed types; Boer Goats and IVG from castrated and intact male goats (additional aim) showed more differences between castrated and non-castrated carcasses than between carcasses of the two breed types. The dressing percentages did not differ between the castrated breeds, but was a bit higher that that of the intact carcasses. There was no significant differences in the percentage meat yield between breeds, although the different commercial cuts could differ a bit in sizes, mainly because of different ratios and form of different parts of the carcass that is genotypic-ally expected.

From this project a better understanding is formed on how goat temperament differ from other farm animals, that pre and post slaughter conditions must be adapted to take their unique characteristics into account. A small change in slaughter practice can have a mayor impact on the end product. Information acquired from these and future research should be disseminated to the farmers, producers and specific abattoirs that apply to special slaughter facilities and management for chevon production.

.Development of the market for chevon in South Africa would offer more diversity of species for red meat producers and especially benefit emerging farmers who produce over 90% of the goats in South Africa. There are good indications that goats can yield chevon or kid of acceptable quality to consumers, providing that animals of an appropriate age and sex group are slaughtered, handled and fed well during production and slaughter so as to minimise stress and prevent cold shortening.

Popular Article

Karkaskwaliteit/opbrengs van intakte en gekastreerde Boerbok en groot raam inheemse eco-tiepe veld bokke (sg. Noord-Kaap Spikkel en Oos-Kaap Xhosa (IVB) bokke)

Dr Lorinda Frylinck, Senior Navorser, LNR-Diere Produksie, Irene.

Veertig gespeende Boer en veertig IVB bokkies, waarvan 20 elk gekastreerde en intakte rammetjies was is in die krale van die Landbounavorsingsraad-Diere Produksie, Irene grootgemaak. Hulle is dieselfde dieet gevoer nl. “Ram, Lam en Ooi” pille, lucerne, hooi en natuurlike gras totdat ‘n gemiddelde lewendige massas van ongeveer 35 kg bereik het (lam ouderdom/0 permanente tande). Die gekastreerde IVB bokke was gemiddeld 1 kg ligter as die ander diere.

Hierna is hul geslag en die karkasse is oornag in ‘n koelkas van ongeveer 4°C geplaas. Buiten die warm karkasmassas, is die verdere karkaskwaliteitsmetings die volgende dag geneem. Die koue karkasmassas was tussen 14 to 16 kg en daar was ‘n warm tot koue karkasmassa verskil van ongeveer 3.5%. Die uitslag % vir die gekastreerde diere (BB en IVB)(44.5%) wat ongeveer 2.5% hoër was as die van die intakte rammetjies (42.0%). Ons het die sogenaamde vyfde kwart nie bestudeer nie.

Oogspier omtrekke gemeet in mm2 van die intakte ramme van beide die BB en IVB het nie verskil nie, maar die gekastreerde BB se omtrekke was effens groter end die van die gekastreerde IVB was effens kleiner – te wagte a.g.v. die kleiner karkasse.

Die karkasse is in die volgende kommersiele snitte verdeel en geweeg: nek, dikrib, lies, blad, bors, lende, kruis, boud en skenkel. Elkeen van hierdie snitte is weer gedisekteer om die % been, % sigbare vet en % vleis vir elke snit te bepaal. Verskille wat uitgestaan het tussen die 4 proefgroepe is die hoër nek % en dikrib % van die gekastreerde BB, die groter % lies by die BB oor die algemeen en die hoër % lende en boud van die gekastreerde IVB. Die % kruis van die gekastreerde diere was effens hoër invergelyking met die intakte diere.

Uit bogenoemde massas is die % vleis, % been en % sigbare vet (insluitend onderhuidse vet) per karkas bereken. Verstaanbaar het die intakte ram karkasse ‘n 1 tot 2 % hoër been persentasie van ongeveer 23% gehad teenoor die van 22% van die gekastreerdes. Die gekastreerdes het weer ‘n 2 tot 4% hoër totale vet % gehad van 9 to 10% teenoor die van die intakte ram karkasse van 6% vir die IVB en 8% vir die BB. Teenoorgestelde is weer gevind dat intakte IVB ram karkasse ongeveer 1% meer vleis (71% van die karkasmassa) gehad het invergelyking met die van die BB karkasse (69% van die karkasmassa) en die gekastreerde IVB ‘n karkasvleis % van 67% gehad het. Niere en niervet is ook geweeg. Niervet (kg) in al die gekastreerde karkasse (0.4 kg) was meer as die van die intakte ram karkasse van ongeveer (0.3 kg).

Dit lyk asof IVB nie so goed reageer op kastrasie nie omdat hulle so effens ligter was as die ander toetsgroeps en verdere studies hieromtrent is nodig. Hierdie kan ook dalk toegeskryf word aan kompetisie vir kos en kompeterende diere behoort alpart gehou te word. Tog lyk dit nie of dit die gekastreerde Boerbokke gepla het nie. Die uitslag persentasies het egter nie verskil tussen die gekastreerde rasse nie en was effens hoër as die van die intakte ramme, hoofsaaklik a.g.v. hoër % sigbare vet.Daar was nie noemenswaardige verskille in die % vleis tussen die rasse nie. Die groottes van die verskillende snitte verskil a.g.v. bouvorm en dit is genotipies te wagte, maar oor die algemeen gee die Boerbok en groot raam Inheemse Veld Bokke dieselfde tiepe opbrengs onder dieselfde produksie omstandighede.

Hierdie studie is deel van ‘n groter projek wat deur die Rooi Vleis Navorsings en Ontwikkeling SA (verteenwoordiger van die rooivleisbedryf) en Landbounavorsingsraad befonds word.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Lorinda Frylinck on lorinda@arc.agric.za

Genomic markers in beef tenderness

The effectiveness of genomic markers in predicting the meat tenderness in pure beef genotypes under South African production and slaughter conditions

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 Institute

Researcher: Dr L Frylinck PhD

Title Initials Surname Highest Qualificaion
Prof PE Strydom PhD Animal Science
Ms A Basson MSc

Year of completion : 2018

Aims of the project

  • To determine the expression of genomic markers in five South African purebred genotypes – Bos indicus (Brahman), Sanga type (Nguni), British Bos taurus (Angus), European Bos taurus (Charolais) and the composite (Bonsmara) for genes associated with beef tenderness in meat.
  • To determine the relationship between the actual physiological tenderness characteristics under South African production and slaughter conditions of the meat from these five main South African genotypes and the known DNA-marker information.
  • To assess the phenotypic variation in meat tenderness within South African selected pure beef genotypes under the same environmental conditions and to build a tenderness prediction model.

Executive Summary

Purebred South African bulls of 5 breeds (n=166) were finished on a grain diet at the Animal Production Institute of the Agricultural Research Council (API-ARC), Irene. Breeds included Angus (n=27; representative of British Bos taurus), Brahman (n=35; Zebu type Bos indicus), Bonsmara (n=35; South African composite breed with large Sanga contribution), Charolais (n=34; European Bos taurus) and Nguni (n=35; Sanga type Bos taurus africanus). Animals were sampled over 3 slaughter periods in 2011 (50 animals), 2012 (50 animals) and 2014/2015 (66 animals). Bulls were sourced from breeders that are registered with the appropriate breeders’ associations and were progeny of registered pure breed bulls and cows. Bulls were ≃9 months old when entering the feedlot and reared under feedlot conditions for ≃120 days to ≃12 months old. Bullas were slaughtered to yield A2/3 carcasses (zero permanent incisors, lean to medium fatness). Bulls were penned overnight with access to water before slaughter following captive bolt immobilization at the abattoir of the API-ARC. All treatments and procedures were approved by the Ethics Committee of the Agricultural Research Council (ARC AEC-I 2010 001).

To determine whether the effects of genotype were additive to electrical stimulation, the right half of the carcass was electrical stimulated for 15 seconds at 500V peak, using 5 ms pulses at 15 pulses per second and directly chilled at 4 °C. The left half of the carcass was not electrically stimulated (served as a control), while chilling was delayed for 6 hours (at 10 °C) to allow for the full development of metabolic processes within muscle fibers before chilling at 4 °C.

Animal measurements included weights, recorded during the feedlot growth period to determine body weight gain (total gain and average daily gain) and liver body weight (BW) measured on the day before slaughter as a final weight. Carcass measurements included hot carcass weight (HCW; used to calculate dressing percentage), cold carcass weight (used to determine carcass mass loss), EMA (in the thoracic region at T9/10), pH and temperature (measured at the lumbar end of the LTL). Beef quality estimates measured from samples collected directly from the carcass or from LTL excised from the lumbar region (L6) up to the thoracic region (T9/10) included myofibrillar fragment length (MFL), Warner-Bratzler shear force (WBSF), calpain enzyme system activities, sarcomere length (SL), colour measurements, energy metabolites, collagen (content and solubility) and water-holding capacity (WHC). Colour was determined using the CIE L*A*b* colour convention with measurements of L*, a*, b*, C* and hab over the ageing period. Energy metabolites included the concentrations of glycogen, glucose 6-phosphate, glucose, lactate, creatine phosphate and ATP determined at 1 h, 3 h, 6 h and 20 h post‑mortem.

The genes that are most likely to affect beef quality, specifically tenderness, as those of the calpain enzyme system. Calpain-1, calpain-2, calpain-3 and calpastatin are all found in the sarcoplasm and are known to determine post‑mortem proteolysis. The genes for these proteins can therefore be identified as causative to proteolysis at least, but potentially also for beef tenderness. We therefore used the 114 SNPs located in these causative genes (capn1capn2capn3 and cast respectively) to determine their genotypic distribution, as well as the association of these genotypes with beef quality traits in order to determine the importance of these genes in determining the quality (tenderness) phenotype. These data were used to identify possible markers for genomic selection (GS), once they were validated for tenderness in South African beef breeds.

  • The capn1 gene (on BTA29) was validated for beef tenderness, with a large number of strong associations (relatively high correlations) with estimates of beef tenderness, found in both the ES and the NS treatment groups. It correlated especially with MFL as a measure of physical tenderness (r2= 0.07 to 0.15), with fewer SNPs explaining the phenotypic variation in WBSF (r2 = 0.09 to 0.10). Almost no associations occurred with calpain-1 enzyme activity itself, but the effects of the SNPs in capn1 was rather a change in the responsiveness of the enzyme to calpastatin inhibition, as shown by several relatively strong correlations (r2 = 0.07 – 0.12) to the relative calpastatin inhibition per calpain(-s).
  • The capn2 gene (on BTA16) was validated for beef tenderness, explaining the phenotypic variation in, especially, the activities of calpain-1 and calpain-2 (r2 = 0.07 – 0.11). Although effects on enzyme activities were evident, these changes only resulted in a few significant associations of the genotypes with physical tenderness MFL (r2 = 0.07 – 0.09).
  • The capn3 gene (on BTA10) exhibited very few associations with beef quality. The protein coded by this gene is responsible for background proteolysis and does not cause variation in tenderness. The lack of an effect of these SNPs on tenderness is therefore unsurprising.
  • The cast gene (on BTA7) is quite large (136,434 bp) and contained a large number of SNPs (63), of which only 4 exhibited extensive effects on tenderness. Many of the correlations with MFL ranged between 0.07 – 0.11, although a few SNPs exhibited strong phenotypic correlations with MFL (r2 = 0.12 – 0.16), while associations with WBSF were less common and less pronounced (r2 = 0.07 – 0.11). These differences in physical tenderness were only in part explained by differences in the total and /or relative inhibition of calpastatin of protease enzyme activities (r2 = 0.07 – 0.12).

Using SNPs of the Illumina Bovine HD SNP BeadChip the capn1capn2 and cast genes were verified for tenderness in SA purebred beef cattle. The amount of phenotypic variation in tenderness estimates explained by some of these SNPs were large, making them useful targets for genomic selection in these breeds. Both Nguni and Bonsmara exhibited high allelic frequencies for alleles that were favorable for tenderness, giving them the genetic potential to produce tender beef.

Popular Article

Inheemse rasse soos die Nguni en Bonsmara het die genetiese potensiaal om sagte vleis te produseer

Basson, A

Inleiding

Hierdie proef is onderneem om vleisbeesgenetika in Suid-Afrikaanse (SA) rasse te ondersoek. As deel van die proef is daar getoets of die rasse wat algemeen vir kruisteling in SA gebruik word, verskil in die verspreiding van voordelige gene vir sagtheid (en ander vleiseienskappe), met spesifieke fokus op die inheemse Bonsmara en Nguni. Die karkasse is gehalveer om die een helfte elektries te stimuleer en dadelik te verkoel, terwyl die ander helfte as kontrole gedien het. Hier is verkoeling vir 6 ure uitgestel om die normale perimortem prosesse soos energieverskaffing in metabolisme, genoeg tyd te gee om te ontwikkel, voordat hierdie nie-gestimuleerde karkas-helftes verkoel is.

Daar is verskeie vrae waarvoor ons antwoorde soek met hierdie navorsing. Ons weet dat die Nguni oor die genetiese en biochemiese potensiaal beskik om sagte vleis te produseer (Frylinck et al., 2009), maar hoe vergelyk dit met Bonsmara, Angus, Charolais en Brahman? Kan die Nguni onder die regte slagtoestande, sagte vleis produseer? Kan ons deur middel van genomiese seleksie (GS) die kwaliteit van beesvleis verbeter in die industrie, waar elektriese stimulering dalk die invloed van voordelige gene sou uitkanselleer, of is verbeterde genetika se positiewe invloed op kwaliteit steeds waargeneem na stimulering?

Die Proef

Vyf vleisbeesrasse is in die proef ingesluit; Angus en Charolais as Bos taurus rasse, Brahman as Zebu-tipe Bos indicus, Bonsmara as ‘n inheemse kruisbeesras met ‘n groot Sanga-tipe bydra en Nguni as inheemse Sanga-tipe Bos taurus africanus. Die stoetbulle is afgerond in die voerkraal tot naastenby 12 maande oud voor slagting, of ‘n karkasklassifisering van A2/3. ‘n Groot aantal monsters is versamel van die Longissimus lumborum et thoracis spier (lende) om die toestande rondom slagting te bepaal, asook lendeskywe wat vakuum-verseël is en verouder is vir 3, 9, 14 en 20 dae, om die invloed van veroudering op vleiskwaliteit te bepaal (met of sonder elektriese stimulering).

Vleis se Kwaliteitseienskappe

Vir kwantitatiewe eienskappe is daar ‘n baie groot aantal gene wat ‘n eienskap bepaal en elkeen van hierdie gene dra slegs ‘n klein proporsie by tot die uiteindelike resultaat, byvoorbeeld sagte vleis. Elkeen van hierdie gene kan honderde (selfs duidende) variasies toon op ‘n molekulêre vlak. Enkel-nukleotied polimorfismes (single nucleotide polymorphisms = SNPs) wat die verskil in een enkele DNA molekule is, kan soms ‘n relatiewe groot invloed op die fenotipe hê. Hierdie SNPs (uitgespreek “snips”) is wat ons geïdentifiseer en getoets het binne-in gene wat sagtheid behoort te beïnvloed.

Genetika en Fisiologie

Spier in die lewendige dier het ‘n baie rigiede proteïenstruktuur wat hoogs ge-orden is, terwyl die omskakelings na vleis in die karkas ‘n ontwrigting van hierdie orde behels – hoe meer die speirstrukture ontwrig word, hoe sagter is die vleis. Die kalpaïen ensiem-sisteem (spesifieke proteases) dra grootliks by tot die ontwikkeling van die finale sagtheid van vleis. Alhoewel kalpaïen‑1 en kalpastatien (die inhibeerder van kalpaïen) die grootste bydra lewer tot die degradering van die proteïene in vleis om dit sagter te maak, kan kalpaïen‑2 en kalpaïen‑3 dalk ook hiertoe bydra. Ons het dus diere met die Bovine-HD SNP BeadChip van Illumina genotipeer vir die gene van die ensieme kalpaïen‑1 (capn1 in chromosoom 29), kalpaïen‑2 (capn2 in chromosoom 16), en kalpaïen‑3 (capn3 in chromosoom 10), asook die ensiem-inhibeerder, kalpastatien (cast in chromosoom 7). Ons bepaal dus eerstens watter gene fisiologies belangrik is en analiseer dan al die geen-variante (of SNPs) om die korrelasie tussen hierdie variante en vleiskwaliteit van die diere te bepaal. ‘n Groot voordeel van hierdie navorsing, wat dit onderskei van ander werk, is dat ons ‘n baie gedetaileerde prentjie van die fisiologie van die vleis het, deur meting van verskeie eienskappe (met of sonder behandeling), gekoppel aan redelik indiepte inligting omtrent die genotipes van hierdie funksionele gene.

Resultate

Brahman bulle (rooi in die grafiek) het deurgaans die hoogste vlakke van kalpastatien per kalpaïene getoon, wat bygedra het tot meer intakte spierveselstrukture (langer miofibril fragment lengtes – MFL) asook verhoogde taaiheid (hoë Warner-Bratzler snyweerstande of WBSW gemeet in kg). In teenstelling het die Nguni (turquois in die grafiek) heelwat laer inhibering van ensiemwerking deur kalpastatien getoon, wat in sommige gevalle die laagste van al die rasse was, met ander woorde die Nguni was die ras met die mees voordelige biochemie. In die Bonsmara was die patroon vir biochemiese en strukturele veranderinge baie soortgelyk aan dié van Nguni’s en die sagtheid van die lendeskywe (verlaging in snyweerstande) het vinnig verbeter tussen dag 3 en 9 van veroudering. Teen 14 dae se veroudering het die snyweerstande gestabiliseer en Bonsmara bulle het nie dieselfde sagtheid as die Nguni bereik nie, inteendeel, hulle snyweerstande was soortgelyk aan Brahman en Charolais.

Kalpaïen-1 is die belangrikste protease wat sagtheid bepaal en die kalpaïen‑1 geen (capn1) behoort dus by te dra tot vleiskwaliteit. Die grootste invloed van capn1 was om die proteïenstruktuur te ontwrig, deur middel van laer relatiewe kalpastatien inhibisie per kalpaïen aktiwiteit. Ons het sterk korrelasies vir verskeie SNPs in hierdie geen geïdentifiseer waar veral MFL (maar ook party van die snyweerstande), sowat 15-20% laer was in die “voordelige” genotipe (voordelig vir sagtheid).

Die kalpaïen-2 ensiem is verantwoordelik vir die ontwikkeling van agtergrond-sagtheid en die geen (capn2) was ge-assosieer met sowat 12 – 15% hoër protease ensiemaktiwiteit, wat in sommige SNPs met soveel as 38% hoër ensiem aktiwiteit geassosieer was. Dit was egter tot ‘n kleiner mate met die bevordering van sagtheid en die ontwrigting van vesels geassosieer.

Kalpastatien aksie kan ‘n groot invloed op sagtheid hê. In die lewendige dier funksioneer dit om die kalpaïen protease ensiemaktiwiteit, wat sellulêre proteïene groot skade sou kon aanrig, in beheer te hou. In die prosesse wat spier omskakel na vleis toe, verhoed dit ook die afbraak van spierproteïene, maar in dié geval sal dit dan die ontwikkeling van sagtheid benadeel. In die kalpastatien geen (cast) was daar ‘n relatief klein aantal SNPs wat ‘n redelike groot invloed op die ontwrigting van spiervesel proteïene gehad het. Die MFL was nagenoeg 10 – 15% laer, terwyl sommige van die SNPs se “voordelige” genotipes tot  meer as ‘n 20% verbetering in die MFL gelei het (i.e. korter lengtes). Dit was gedeeltelik verduidelik deur ‘n verlaging in die totale eenhede kalpastatien werking, met soveel as 20% laer inhibisie vanaf kalpastatien, gekoppel aan ‘n redelike verbetering in die sagtheid van die vleis, veral in die vroeë tot intermediêre stadiums van veroudering.

Bespreking

Uit die 4 gene wat hier getoets is, is die kalpaïen‑1 en kalpastatien gene veral geskik vir genomiese seleksie in Suid-Afrikaanse vleisbeesrasse, terwyl ‘n paar van die SNPs in die kalpaïen-2 geen ook potensiaal toon. Rasverskille in sagtheidseienskappe (fisiese en biochemies) word gereflekteer in verskille in die verspreiding van genotipes tussen die verskillende rasse (sien tabel hier onder)..

Totale Aantal Voordelige Allele*
cast capn1 capn2
Angus (n=27) 189 146 220
Bonsmara (n=35) 270 209 174
Brahman (n=35) 237 39 141
Charolais (n=34) 217 147 215
Nguni (n=35) 256 233 241

* Die groen blok dui die ras met die grootste aantal voordelige allele vir sagtheid aan

Nguni’s hét die genetiese potensiaal om sagte vleis te produseer, maar die noemenswaardige ligter karkasse is geneig om te vinnig te verkoel wat beteken die vleis raak te koud vir metaboliese ensieme om energie optimaal te benut, terwyl die struktuur binne miofibrille ook sub-optimaal word vir die proteases se ensiemwerking. In hierdie proef het Nguni’s die “beste genetika” gehad en die allele wat voordelige is vir sagtheid in die gene wat hier getoets is, was volop in Nguni’s.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Lorinda Frylinck on lorinda@arc.agric.za

Marker detection in beef cattle II

Marker detection in beef cattle Phase II

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 Institute

Researcher: Dr A Maiwashe PhD

Title Initials Surname Highest Qualificaion
Dr B Dube PhD
Prof MM Scholtz DSc
Prof K Dzama PhD
Prof M MacNeil PhD
Dr L Frylinck PhD
Dr NO Mapholi PhD

Year of completion : 2018

Aims of the project

  • To establish a beef cattle genetic marker discovery population
  • To collect phenotypic data on tolerance to ticks, post-weaning growth and feed efficiency and carcass traits
  • To detect Quantitative Trait Loci for tolerance to ticks, post-weaning growth and feed efficiency and carcass traits

Executive Summary

The project aimed to detect genetic markers for traits of economic importance in the Nguni X Angus F2 crossbred population. The specific objectives of the project were to: (1) establish a beef cattle genetic marker discovery population, (2) collect phenotypic data on tolerance to ticks, post-weaning growth and feed efficiency and carcass traits, and (3) detect quantitative trait loci (QTLs) for tolerance to ticks, post-weaning growth and feed efficiency and carcass traits. Accordingly, a number of experiments were conducted to address these objectives.

Briefly, a total of 233 F2 animals were produced since the inception of the project. The following phenotypic data were collected on the 233 F2 crossbred animals: growth rate, feed intake, tick count, skin volatiles compounds, skin thickness and colour, hematology, skin hypersensitivity and carcass traits. Coat color was scored and skin thickness was also done since they are known to be correlated with tolerance to ticks. Artificial tick infestation was conducted using Amblyomma hebraeum. Each animal was infested with 100 larvae obtained from ARC-Onderstepoort Veterinary research.

Tick counts were also conducted on 586 Nguni cattle under natural infestation with the aim of developing a protocol for measuring tolerance to ticks using tick count procedure.

The results indicate extensive variability on ticks counts among the animals, ranging from 0 to 100 per animal. Tick counts were higher in the hot months and Amblyomma hebraeum was the most dominant tick species. Heritability estimates for tick count ranged from 0 to 0.89. High genetic correlations were observed between whole body count and the anatomical location counts, suggesting that it may not be necessary to conduct whole body counts. Counts from the belly and perineum were most suitable surrogate traits for whole body count.

In another experiment, feed intake and growth performance data were collected at the feedlot on 170 animals at the ARC-Animal Production campus in Irene. Average daily feed intake (ADFI), average daily gain (ADG) and feed conversion ratio (FCR) were computed and analyzed using SAS software. The findings showed a significant effect of genotype on ADFI and ADG (P < 0.05), while there were no differences (P >0.05) in FCR among the genotypes. The F2 Nguni-Angus genotype had the best feedlot performance with ADFI, ADG and FCR of 7.9 kg, 1.5 kg and 5.6, respectively. There was also some correlation between ADG and FCR, while ADG and FCR were not correlated with ADFI.

For genomic analyses, hair and blood samples were collected from 233 F2 animals and DNA isolation conducted on 170 animals. Ninety-six (96) F2 samples were genotyped using Bovine SNP150K assay. A genomic analyses was conducted to characterise genetic parameters of tick count and identify genomic regions associated with tick resistance in South African Nguni cattle. A genome-wide association analysis for tick count was performed using GenABEL. Heritability estimates for the tick count traits ranged from 0.04±0.04 to 0.20±0.04. Two genome-wide significant regions on chromosomes 1 and 19 were identified for total tick count on the perineum and for total body count for A. hebraeum ticks. Additional regions significant at the suggestive level were identified on most chromosomes for several other tick count traits.

This research provides the first line of evidence of association between tick count and SNP markers in beef cattle under South African condition. The results are consistent with results from similar studies conducted in Brazil. Further research should consider fine-mapping of the genomic regions identified to be harbouring genes for tolerance to ticks.

Popular Article

Marker detection in beef cattle

Nguni cattle are adapted to the harsh conditions of South Africa characterised by, among others, high levels of tick infestation. This adaptation may be due to the natural resistance of the Nguni, which may be attributed to their genetic make-up. On the other hand, the Angus cattle are exotic to South Africa and are susceptible to tick infestations. However, they have excellent growth, feed utilization and meat quality characteristics. Combining the characteristics of these breeds into one breed may be a sustainable of way of improving beef production in the tick-infested production areas of South Africa. The objective of the study was cross the Nguni and Angus cattle to produce a crossbred animal that potentially has characteristics of both breeds.

The project started in 2013 using 84 Nguni cows and five Angus bulls, and has so far produced 233 animals that have been evaluated for several traits related to resistance to ticks, growth performance and meat quality. After weaning the calves were individually fed under feedlot conditions and their performance recorded and analysed. Daily feed intake for each animal was recorded and weekly weights were taken. At the end of the growth test, each animal was artificially infested with ticks so that its level of resistance can be determined by counting the number of ticks that feed and survive on it. Chemicals on the skin produced by the animal that may be responsible for repelling or attracting ticks were collected. In addition, the ability of the animal’s immune system to respond to tick bites was measured by measuring the degree of swelling and the time taken for it to subside. The response of blood parameters responsible for the immune system to tick bites was also evaluated. Also measured was the thickness of the skin, which may also related to the ability of the ticks to attach to the skin. Hair samples were collected to determine the genetic make-up of the animal, which will later be correlated with the level of resistance to ticks, growth performance and meat quality.

After the 120 days in the feedlot, the animals were then slaughtered following the recommended South African Meat Industry Company procedures. Carcass were weighed after dripping free water after 24 hours. Then several meat quality characteristics were evaluated, which included tenderness, water holding capacity, fat content and moisture content.

The results show that there are differences in the level of resistance to ticks in the cross-bred animals. No relationship was observed in the level of resistance to ticks with growth performance and feed utilization. Skin thickness was not found to influence the ability of ticks to attach to the animal. Meat quality results indicate that the crossbred animals produce meat of commendable quality. Male animals produced heavier carcasses than their female counterparts, and were less fat compared to the females. On the other hand, meat from females was more tender than that from males. So far the results show that there is no relationship between meat quality and the level of tick resistance.  Therefore, resistance to ticks can improved by combining the Nguni and Angus breeds without compromising growth, feed utilization and meat quality characteristics. More studies on the genetic make-up will be done to relate it to the other characteristics.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Azwihangwisi Maiwashe on norman@arc.agric.za

Dairy ranching for beef and milk

Small scale Dairy ranching for the resource poor sector in South Africa

Industry Sector: Cattle and Small Stock

Research focus area: The economics of red meat consumption and production in South Africa

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Dr. Susanna Maria Grobler PhD

Title Initials Surname Highest Qualification
Prof MM Scholtz DSc
Ms V Leesburg MSc (USDA)

Year of completion : 2018

Aims of the project

  • To generate results from a dairy ranching system that can be used by existing and new emerging cattle farmers.
  • To benchmark the system of dairy ranching for the resource poor sector in comparison with a small scale dairy production and an ordinary beef cattle suckler (weaner calf) system.
  • To do on station characterization and benchmarking of different cattle genotypes for suitability to be utilized in systems of dairy ranching.
  • To measure the levels of methane emission between the different genotypes

Executive Summary

Dairy ranching is defined as the practice of keeping cows of relatively low milk yield, who are parted from their calves in the evenings, milked out in the morning, and spend the day with their calves at foot while the cows are usually not milked in the evening.

The objectives of the study was firstly to generate results from a project that imitate Dairy ranching that can be used by existing and new emerging cattle farmers; secondly to benchmark the system of Dairy ranching for the resource poor sector in comparison with small-scale dairy production and an ordinary weaner system; thirdly to do on station characterization and benchmarking of different cattle genotypes for suitability to be utilized in aDairy ranching system; and fourthly to measure the levels of methane emission between the different genotypes.

The project commenced with five purebred heifers each of the Bonsmara, Brahman, Nguni and Red Poll breed. The small-scale dairy at Roodeplaat, was used to produce milk from Jersey cows grazing natural veld under small-scale conditions with limited resources. The weigh-suckle-weigh technique was used to estimate milk production from all breeds except the Jerseys, which was milked daily.

When comparing the different breeds, the Nguni cows followed by the Brahman cows showed the highest potential income from a weaner production system. In the Dairy ranching system, the dual-purpose Red Poll cows had the highest potential income. The Jersey cows milked in a conventional dairy system potential income reduced by 24% when cows were milked once per day instead of twice per day. The Dairy ranching system produced the highest potential income compared to the weaner production system and conventional dairy milking once per day. The conventional dairy produced the highest potential income when milked twice daily.

With funding from rural development, another ARC-API project “Dairy value chain”, established small-scale milk production units in rural areas in Limpopo, KwaZulu-Natal and Eastern Cape by making use of the Dairy ranching project’s principles after the Dairy ranching project’s promising preliminary results. These small-scale farmers are producing milk now successfully for the past three years.

Understanding the differences in enteric methane production from cattle in different production systems is important for the productivity in the different sectors and for developing mitigation strategies in respect of the contribution of agricultural activities to methane emissions.

In the first study methane production was measured from, Bonsmara, Nguni and Jersey heifers, grazing natural sour veld, forage sorghum under irrigation, oats pasture under irrigation and a total mixed ration (TMR) were significant differences were found between breeds and feed sources. It was also found that individual animals emitted higher or lower quantities of methane irrespective of the feed source. The second study evaluated methane production from pregnant Bonsmara-, Brahman-, Jersey-, Nguni- and Red Poll heifers grazing natural veld and forage Sorghum under irrigation. Bonsmara heifers produced the highest amount of methane and the Jerseys produced the lowest amount of methane on both the natural veld and forage Sorghum.

POPULAR ARTICLE

The smallholder milk producers in South Africa have their own constraints ranging from poor access to support services, lower productivity, limited access to market outlets and low capital reserves. These farmers have the opportunity to make use of a dairy ranching system with lowered liabilities in relation to intensive milk production systems. This includes less infrastructure, lower production costs and relative resilience to rising feed prices.

Methane is one of the major anthropogenic greenhouse gasses, second only to carbon dioxide in its impact on climate change. Understanding the differences in enteric methane production from cattle in different production systems is not only important for the productivity in the different sectors, but also for developing mitigation strategies in respect of the contribution of agricultural activities to methane emissions.

Dairy Ranching can be defined as the practice of keeping cows of relatively low milk yield, who are parted from their calves in the evenings, milked out in the morning, and spend the day with their calves at foot while the cows are usually not milked in the evening. Beef cattle can be a viable option for small-scale farmers to complement other farm enterprises, such as milk production. In tropical countries, making use of the calf to stimulate milking is a popular practice and it was reported that this system is adopted by 95% of 289 farms surveyed in the State of Minas Gerais, Brazil. Advantage of this restricted suckling system include a reduction in milk let-down problems and improved milk production under good nutritional regimes, reduce stress in both cows and calves and the efficiency of milk utilization is higher in calves that are suckled than when they take the same amount of milk from a bucket. Other benefits of suckling calves in relation to bucket fed calves are a reduced incidence of diarrhoea and the elimination of naval suckling. Udder health and the incidence of mastitis also decrease with suckling due to small-scale farmers not being able to milk the cows from time to time due to labour and other personal constraints. When compared to a conventional dairy system, Dairy Ranching has lower input costs, labour requirements and limited infrastructure is needed. It is also the perfect opportunity to add value to small-scale beef production enterprises. Dairy Ranching development in the rural-based, small farmer-oriented cattle industry can therefor increase productivity, raise income, promote self-reliance, reduce malnutrition and therefor improve standard of living.

The ARC-API conducted a trial funded by RMRD-SA to firstly generate results from a project that imitate dairy ranching that can be used by existing and new emerging cattle farmers; secondly to benchmark the system of Dairy Ranching for the resource poor sector in comparison with small-scale dairy production and an ordinary beef cattle suckler (weaner calf) system; thirdly to do on station characterization and benchmarking of different cattle genotypes for suitability to be utilized in systems of dairy ranching; and fourthly to measure the levels of methane emission between the different genotypes measured with a Laser Methane Detector. Purebred Bonsmara, Brahman, Nguni and Red Poll heifers were used to represent a weaner production system and dairy ranching system. Jersey cattle was milked from natural veld in a small-scale dairy at the ARC-API Roodeplaat campus, with limited infrastructure and resources to represent a small-scale rural dairy production system. The weigh suckle weigh technique was used to estimate milk production from all breeds except the Jerseys which was milked daily.

When a small-scale farm has the carrying capacity to sustain 25 large stock units (LSU), the amount of animals that can be sustained on the farm will differ between breeds with different frame sizes and different weights. Therefore, results obtained from the project was converted to simulate a farm with the capacity to sustain 25 LSU which included 15 Bonsmara, 16 Brahman, 20 Nguni, 21 Red Poll and 21 Jersey cows.

When comparing these different breeds in different production systems, the Nguni cows followed by the Brahman cows showed the highest potential income from a weaner production system. In the Dairy Ranching system, the dual-purpose Red Poll cows showed the highest potential income. The Jersey cows milked in a conventional dairy system potential income reduced by 24% when cows were milked once per day instead of twice per day. The conventional dairy produced a higher potential income than a weaner production system from 25 large stock units but less than the Dairy Ranching system, even when compared to pure beef breeds being used for milk production.

With funding from the Department of rural development and land reform’s REID project, another ARC-API project “Dairy value chain” established small-scale milk production units within the resource poor sector in rural areas in Limpopo, KwaZulu-Natal and Eastern Cape as one of the project’s objectives. The uncomplicated, economical small-scale Dairy Ranching unit, showed promising results at Roodeplaat, which inspired the coordinator of the “Dairy value chain” project to implement the principles at the newly established small-scale milk production units in the mentioned three provinces. These small-scale farmers received pregnant heifers in 2013/2014. They are producing milk now successfully for the past two/three years with cows already in their second lactation.

The methane production trial evaluated methane production (g/day) from the pregnant Bonsmara-, Brahman-, Jersey-, Nguni- and Red Poll heifers grazing natural veld and forage Sorghum under irrigation.

The methane production was much higher when grazing natural veld (164.8g/day) than grazing forage Sorghum (130.4g/day). The tannin content in Sorghum may have contributed to lower methane production as tannin content reduce enteric methane production. A significant difference was found between different breeds methane concentration (P=0.0692). The large frame Bonsmara and Brahman cows produced the highest amount of methane, 159.6g/day and 170.5g/day respectively. The small frame Red Poll and Jersey cows produced the lowest amount of methane, 139.4g/day and 119.9g/day respectively. Methane production is linked to body weight and from this study, it is clear that small frame animals produce less methane than medium frame animals

From this study, it is clear that Dairy Ranching is a viable strategy to increase income, add value, increase cash flow, competitiveness and long-term survival of rural smallholder cattle farmers.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Dr Grobler on mgrobler@arc.agric.za

Discovery of single nucleotide polymorphisms

Genome-wide genetic marker discovery in South African indigenous cattle breeds using next generation sequencing

Industry Sector: Cattle and Small Stock

Research Focus Area: Livestock production with global competitiveness: Animal growth, nutrition and management

Research Institute: Agriculture Research Institute – Animal Production Institute

Researcher: Dr. Avhashoni Zwane

Title Initials Surname Highest Qualification
Prof. Azwihangwisi Maiwashe PhD
Prof Este Van Marle-Koster PhD
Prof Jerry Taylor PhD
Prof Mahlako Makgahlela PhD
Dr Ananyo Choudhury PhD
Dr Farai Muchadeyi PhD

Year of completion : 2018

Aims Of The Project

  • To conduct a genome wide search for new SNPs in local cattle breeds
  • To validate newly identified SNPs using Run 5 data from the 1000 Bull Genomes Project and perform functional annotation and enrichment analysis
  • To identify selective sweeps and a panel of SNP markers to discriminate between the three indigenous breeds

Executive Summary

South African (SA) livestock has played an important role in food security country’s sustainability. Due to the important role of indigenous cattle breeds in SA, it is crucial for these breeds to be included in the generation of genotypic and sequence data. Genomic data provide opportunity for various genetic investigations including identification of breed-informative markers, selective sweeps and genome-wide association studies (GWAS). In this study sequence data were generated and used in combination with genotypic data to conduct a SNP discovery in the three indigenous SA breeds (Afrikaner, Drakensberger, and Nguni) and study potential selective sweeps and identify panel of breed-specific markers. Commercial bovine SNP assays, (BovineSNP50 and GGP-80K) were used for identifying the breed-informative markers, while an approach of breed pooled samples were used for sequencing. Sequencing of the three breeds generated approximately 1.8 billion (184 Giga-bp) of high quality paired-end reads which 99 % reads mapped to the bovine reference genome (UMD 3.1), with an average coverage of 21.1-fold. A total of 17.6 million variants were identified across the three breeds with the highest number of variants identified in NGI (12,514,597) than in AFR (11,165,172) and the DRA (7,049,802). In total 89 % of variants were SNPs and 11 % were Indels. On average, 85 % of the total SNPs identified were also shared among the breeds from 1000 Bull Genomes Project data and the remaining 15 % of SNPs were unique to SA indigenous breeds. Novel SNPs were further annotated to identify genes enriched in novel SNPs. In total, 461, 478 and 542 genomic regions identified from the top (5%) windows were enriched for novel variants (p < 0.001). A total of 174 putative breed-specific SNPs were identified across the breeds and showed the overall 100% breed allocation using PCA and GeneClass 2. This study provides the first analysis of sequence data to discover SNPs in indigenous SA cattle breeds and the results provide insight into the genetic composition of the breeds and offer the potential for further applications in their genetic improvement.

POPULAR ARTICLE

IDENTIFICATION OF SELECTIVE SWEEPS IN AFRIKANER, DRAKENSBERGER AND NGUNI CATTLE USING GENOME-WIDE SEQUENCE DATA

A.A. Zwane1,2, A. Choudhury, M.L. Makgahlela1, E. van Marle-Köster2, A. Maiwashe1,5 and J.F. Taylor4
1Department of Animal Breeding and Genetics, ARC-API, P/Bag X2, Irene, 0062, 2Department of Animal and Wildlife Sciences, University of Pretoria, P/Bag X20, Hatfield, Pretoria, 0028, 3Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, P/Bag 3, Wits, Gauteng, 2050, 4Division of Animal Sciences, University of Missouri, 920 East Campus Drive, Columbia, MO 65211-5300, USA, 5Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein 9300, South Africa
#Corresponding author: zwanea@arc.agric.za

Background: Whole-genome sequencing now provides a suitable platform to examine the entire genome for the identification of selective sweeps. Indigenous South African (SA) breeds including Afrikaner (AFR), Drakensberger (DRA), and Nguni (NGI) are important genetic resources for SA cattle production. These breeds were subjected to strong selection leading to changes in their morphology, physiology and behaviour.

Aim: The aim of this study was to identify selective sweeps that shaped phenotypic diversity among indigenous SA breeds.
Methodologies: Whole genome sequencing of pools of DNA from AFR, DRA, and NGI was performed using an Illumina HiSeq 2000 and 17.6 million variants were discovered across the breeds. To identify the selective sweep regions, SNPs were used to calculate Z-transformations of the pooled heterozygosity (ZHp) in each of the three breeds using a 150 kb sliding window to compute the ZHp Z-scores in each breed. The results were used to plot the distribution of SNP counts within the windows. The regions of selective sweeps were represented by the lower ZHp Z-scores with the minimum threshold of -4. Animal QTL database was used to determine the gene ontology of the genes identified in selective sweep regions.

Results: In total 688 candidate selective sweeps, with the ZHp Z-score ≤ −4 were identified across the three breeds with 223 putative selective sweeps (ZHp Z-score ≤ -5). About 93 regions had extremely low ZHp Z-scores (ZHp scores ≤ −6). These are the regions subjected to selection segninatures. Using animal QTLdb, several genes were identified, e.g., ESM1, CNOT6, ASIC5, KIT and MITF, associated with phenotypic variation in livestock species (Zielak-Steciwko et al., 2014; Fallahsharoudi et al., 2016).

Discussion: The ability to detect selective sweep regions provided useful genomic information for these breeds, whereas functional analysis of these regions revealed the presence of genes of biological and economic importance.
Conclusions and recommendations: This study provides a broad insight into the events that happened during recent selection events and artificial selection processes that have shaped the livestock genome. More work is needed to characterise genomic regions and genes identified in this study.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project –  vhashoni Zwane  on Zwanea@arc.agric.za

Crossbreeding Afrikaner, Bonsmara and Nguni cows

Crossbreeding effects with specialized sire lines in Afrikaner, Bonsmara and Nguni beef cattle herds

Industry Sector: Cattle and Small Stock

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

Research Institute: Agriculture Research Institute – Animal Production Institute

Researcher: Dr. M Scholtz

Title Initials Surname Highest Qualification
Mrs. A. Theunissen MSc
Prof F W C Neser Ph.D.
Mr. L De Lange Nat. Dipl.
Mr. T Jonker M.Sc.
Mr. F J Jordaan M.Sc. (Agric)
Dr M D MacNeil Ph.D.
Mr. O Ntwaeagae B.Tech
Mr. W Pieterson Nat. Dipl.
Ms. M C Mokolobate M.Sc. (Agric)
Ms. G M Pyoos B.Sc. (Agric. Sci.)
Ms. M Mokgadi M.Tech

Year of completion : 2018

Aims Of The Project

  • 1. To estimate the genetic and phenotypic trends in the dam lines
  • 2. To evaluate crossbreeding systems and quantify the phenotypic progress made in economically important traits in crossbred cattle for beef production
  • 3. To characterize the additive and non-additive genetic effects for production and health traits in progeny of terminal sires and dam line breeding cows
  • 4. To validate an existing simulation model for the development of breeding objectives for specialized sire lines on Landrace breed cows for use in small scale and commercial farming that better meet commercial feedlot requirements
  • 5. To make recommendations with regard to future selection and management of beef herds in warm arid areas
  • 6. To evaluate alternative production systems in anticipation of global warming

Executive Summary

Climate has been changing and these changes are predicted to be highly dynamic. Increasing frequencies of heat stress, drought and flooding events are likely, and these will have adverse effects livestock production. It is therefore important that production systems utilizing local landrace and adapted breeds that are better adapted to warmer climates, be investigated.

In South Africa extensive cattle farming dominate primary cattle production systems, while more than 80% of all beef cattle slaughtered in the formal sector in South Africa originate from commercial feedlots. A total of 67% of feedlot animals are crossbreds, indicating that crossbreeding is playing a significant role in the commercial industry in South Africa. Well-structured crossbreeding systems allows producers to capture benefits from complementarity and heterosis.

The study is being conducted at Vaalharts Research Station. The aim is to use the Afrikaner, Bonsmara and Nguni as dam lines in crosses with specialized sire lines from British (represented by Angus) and European (represented by Simmentaler) breeds. In addition these dam lines were also mated with Afrikaner, Bonsmara and Nguni bulls in all combinations. This is producing 15 different genotypes.

It is anticipated that the information from five breeding seasons will be needed for the a more comprehensive study. Currently the information from three seasons are available and have been summarized. A protocol for Phase 2 of the study has been submitted.

The phenotypic trends in production traits of the three breeds over 25 years revealed an increase in cow productivity in all the breeds varying from 10% in the Bonsmara to 18.3% in the Afrikaner, where cow productivity was defined as kg calf weaned per Large Stock Unit mated. This also resulted in a decrease in the carbon footprint of up to 12%. The bottom line is that cow productivity can be improved if the weaning weight of the calf relative to the weight of the cow can be increased; and the inter-calving period reduced. Well-structured crossbreeding should have a much bigger effect on this and therefore the environmental impact, will be included in the final analyses of this study.

The simulation study indicated that breed, weaner and carcass price have an influence in the gross income from weaner and ox production systems. The simulation model in question can be used to quantify the benefits from the different crosses on completion of the study on condition that it is based on sound assumptions regarding weaner and carcass prices.

The information on 550 weaner calves and 125 feedlot bulls are currently available. The heaviest weaning weights are from Simmentaler sires on Afrikaner (220 kg) and Bonsmara (213 kg) dams, as well as Angus sires on Bonsmara (252 kg) dams. The lightest weaner calves were produced from purebred Ngunis (171 kg) and Angus sires on Nguni dams (173 kg). The severe draught and extreme heat of the 2015/2016 summer season had a big effect on the Angus and Simmentaler sired calves. The Sanga sired calves and Angus/Simmentaler sired calves had the same weaning weight (171 kg) in this season. In contrast, the 2016/2017 summer season was cooler and wetter, resulting in the weaning weight of the Angus/Simmentaler sired calves being 27 kg heavier than the Sanga sired calves (210 kg versus 183 kg). This demonstrates the importance of including the effect of climate on the pre- and post-weaning performance in Phase 2 of the experiment.

At the completion of the study all the information will be updated and this baseline information used to evaluate how effective the current crossbreeding systems in South Africa are and to quantify the direct and maternal heterotic effects, the possible/promising advantages of structured crossbreeding, as well as the effect of climate.

The very dry and hot 2015/2016 season also had an effect on the post weaning feed intake and growth. For example, the ADG of the Angus and Simmentaler types decreased by 17%, whereas that of the Sanga and Sanga derived types (Afrikaner, Bonsmara, Nguni) decreased by 9%, as a result of the heat waves experienced.

It is foreseen that indigenous and adapted beef breeds may become more important in South Africa as a consequence of climate change that will result in more challenging environments. The use of specialized sire and dam lines offer an opportunity to increase output by taking advantage of heterosis and complementarity. The effects of weather patterns on beef production in South Africa should also be estimated and thereafter, mitigation strategies developed in the era of climate change to ensure optimal production efficiency.

With the information collect from the GrowSafe system, it will be possible to study feed and water intake patterns as well as behavior of individual animals and different genotypes. This may give valuable information on the effect of climate on animal performance and behavior.

This study produced one M.Sc. thesis, 8 peer reviewed scientific articles, chapters in books and conference proceedings, as well as 8 popular articles.

Popular Article

The principles behind climate smart beef cow efficiency through utilization of structured crossbreeding

Theunissen1, M.C. Mokolobate2 & M.M. Scholtz2,3

1Northern Cape Department of Agricultural, Land Reform and Ruswral Development, Private Bag X9, Jan Kempdorp 8550, South Africa

2ARC-Animal Production Institute, Private Bag X2, Irene, 0062, South Africa

3University of the Free State, Bloemfontein, 9300, South Africa; South Africa

atheunissen@ncpg.gov.za (Corresponding author)

 Background and deliberations

With the ever swelling costs of production, beef cattle producers in South Africa have a sure challenge for sustainability. This is aggravated by the vagaries of climate change. The country’s most recent vulnerability was displayed during the 2015 drought, which was the warmest year ever recorded and was accompanied by extreme heat. The beef industry is one of the agricultural sectors that need to focus on both adaptation and mitigation strategies in response to  greenhouse gas (GHG) emissions and global warming.

The utilization of more hardy breed resources in a changing production environment is one of the alternative strategies to be considered. The most fundamental factor in this strategy will be the emphasis on a high reproductive rate of the selected breeds in the particular environment to increase the overall efficiency of the beef cattle enterprise.

Another alternate is the use of sustainable crossbreeding systems that pool indigenous and exotic breeds, but with retention of the genetic resources, which have shown to be an effective means to reduces GHG, as it has been shown to increase reproduction and production levels in overseas and in local studies. In this regard, a newly developed more sophisticated Large Stock Unit (LSU) calculator by Neser (2012) and Mokolobate (2015) and the measurement of cow efficiency (to calculate kg calf weaned/kg LSU of the dam); initiated an evaluation tool for “cross-bred” selection and breeding to improve cow efficiency; as long as the nutritional needs of animals are fully met.

This expression of cow efficiency is an improved replacement for the biological definition of kg calf weaned/kg mature cow weight that not only has two variables of which anyone or both in the ratio can change to have the same answer, but does not express beef production in terms of an assigned nutrient intake. The advantage of the new biological expression of cow efficiency is that the method increases output and reduces input, which will then support and facilitate the implementation of climate smart production, adaptation and mitigation measures.

Initially Meissner et al. (1983) defined a LSU on the basis of the nutrient requirement of a unit.  However, with differences in frame sizes there are differences in the voluntary feed intake between such animals although they have the same body weight. The LSU equivalents for beef cattle of different frame sizes also vary according to physiological phases, eg. heifers (over 12 months of age) and lactating cows. Table 1 shows examples of the refined estimations of LSU equivalents according to frame sizes of cows that was derived with the calculator.

Table 1: LSU equivalents for beef cattle of different frame sizes and physiological phases

Weight

Kg

Small Frame Medium Frame Large Frame
Heifer (>12 months) Cow &

Calf

Heifer (>12 months) Cow &

Calf

Heifer (>12 months) Cow &

Calf

150 0.37 X X X X X
175 0.42 X X X X X
200 0.47 X 0.50 X X X
225 0.52 0.83 0.56 X X X
250 0.57 0.89 0.61 X 0.67 X
275 0.61 0.95 0.66 X 0.72 X
300 0.66 1.00 0.70 1.05 0.77 X
325 0.70 1.06 0.75 1.11 0.82 X
350 0.73 1.11 0.80 1.17 0.88 X
375 0.77 1.16 0.84 1.23 0.93 1.48
400 0.80 1.22 0.89 1.29 0.98 1.55
425 0.83 1.27 0.93 1.34 1.03 1.61
450 0.85 1.32 0.97 1.40 1.08 1.66
475 X 1.37 1.01 1.45 1.13 1.72
500 X 1.42 1.05 1.50 1.18 1.78
525 X 1.47 1.08 1.55 1.23 1.83
550 X 1.52 1.12 1.60 1.28 1.88
575 X 1.57 X 1.65 1.33 1.93
600 X 1.61 X 1.69 1.38 1.98
625 X X X 1.74 1.43 2.02
650 X X X 1.78 X 2.07
675 X X X X X 2.11
700 X X X X X 2.15

Crossbreeding has proved to increase cow efficiency when it is measured and calculated with the LSU caculator. Table 2 demonstrates the results of a study that was done at Vaalharts Research Station that used mature cows of different breeds. The cow efficiency, estimated by kg calf weaned / cow LSU (KgC/LSU), for the Afrikaner (A), Brahman (B), Charolais (C), Hereford (H) and Simmentaler (S) breed types were calculated according to their different frame sizes and expressed as percentage deviation from the Afrikaner breed in brackets.

Table 2 The estimated cow efficiency (KgC/LSU) for the 29 different breed types and percentage deviation from the Afrikaner breed in brackets

  Sire Breed
 

Dam breed

Afrikaner  (A) Brahman  (B) Charoloais  (C) Hereford  (H) Simmentaler  (S)
A 142.6

(0.0)

144.2

(1.1%)

145.7

(2.1%)

151.2

(6.0%)

143.7

(0.7%)

B 142.0

(-0.4%)

C 124.9

(-12.4%)

H 149.3

(4.6%)

S 139.3

(-2.3%)

BA 148.9

(4.4%)

147.1

(3.1%)

155.6

(9.1%)

162.0

(13.6%)

160.1

(12.3%)

CA 152.3

(6.7%)

155.5

(9.0%)

154.5

(8.3%)

157.1

(10.1%)

158.4

(11.0%)

HA 155.7

(9.2%)

170.1

(19.2%)

175.1

(22.7%)

161.2

(13.0%)

176.8

(23.9%)

SA 155.9

(9.3%)

156.6

(9.8%)

161.1

(12.9%)

163.8

(14.8%)

162.1

(13.6%)

Table 2 shows that with the exception of the Hereford, purebred dams were less efficient than purebred Afrikaner dams under the particular environmental conditions. The purebred Charolais (C) dam was the least efficient dam out of all the genotypes. Crossbreeding the Afrikaner (A) dam line with Brahman (B), Charolais (C), Hereford (H) and Simmentaler (S) as sire lines indicated small effects (between +0.7 to +6.0%) on KgC/LSU above that of the purebred Afrikaner (A). However, the efficiency in the F1 cow increased relative to that of the purebred exotic cows. For example, the cow efficiency of the CA cow, compared to pure C cow increased with +14.5% (from -12.4% to +2.1%).

In the case of FI cows the HA was unsurpassed and increased cow efficiency on average by +17.6%, while the BA, CA and SA dam lines increased cow efficiency by +8.5, +9.0 and +12.1% respectively. Continental and Zebu sire lines mated to the most productive HA crossbred dam line in a three-breed system (S x HA, C x HA and B x HA) increased KgC/LSU on average by +22.7, +23.9 and +19.2% respectively, against that of the A x HA backcross with +9.2%.

The improvement demonstrated in the study concurs with that of Schoeman (2010), which indicated that crossbreeding improves calf/cow efficiency when measured as energy requirements or input costs per kg of equivalent steer weight. Although the effect of heterosis on individual traits is normally relatively small, the cumulative effect on composite traits, such as weight of calf weaned per cow exposed are immense which explains the superiority in kgC/LSU as a composite trait. Conversely, researchers cautioned on the attempt to extrapolate research results to all environments other than those similar to where the studies were conducted because of the presence of genotype x environment interactions.

While KgC/LSU as trait on its own can be used to rank productive cows in a contemporary group, it cannot be used to plan breeding strategies. Fertility, or the number of calves weaned in a cow group should certainly also be considered as a complementary factor that influences cow efficiency. In this study the net effect on weaning rate (WR) was that crossbred dams outperformed their purebred contemporaries by 8%.

Cow efficiency can then be estimated as follows: Y = WR x KgC/LSU

where Y = cow efficiency.

Since weaning rate has a low heritability and largely depends on the climatic and managerial (environmental) factors of a particular farm, this trait can contribute to large deviations in the estimated cow efficiencies that were obtained in Table 2. When weaning rate is included in the metioned Vaalharts study, it showed that when compared to the A, only purebred H and S cows have increased cow efficiency potential (+11.4 and 5.3% respectively). Two-breed progeny of the A dam line increased cow efficiency on average by +16.5%. All these increases are ascribed to the increased WR of the breeds compared to that of the A, B and C pure-breeds.

While A sire line backcrosses increased cow efficiency on average by +20.3%, three-breed progeny from B, C, H and S sire lines had average increases of +21.6, +24.4, +30.2 and 34.8% respectively. The S x HA showed the notable increase of 49.7%. Similarly, the BA, CA, HA and SA dam lines respectively had average increases of +24.1, +18.9. +36.6 and +25.2% on cow efficiency. All crossbred dam genotypes increased cow efficiency, the only exceptions being a trivial increase of +0.6% of the B x CA genotype. In this study the Pearson correlation between kgC/LSU (cow efficiency without WR included) and WR x kgC/LSU (cow efficiency with WR included) is 0.88%.

In the current Vaalharts crossbreeding project, the Bonsmara and Nguni are added to the Afrikaner as dam lines. These dam lines are mated to Angus and Simmentaler as specialized sire lines. In addition, the dam lines are also inter-mated in all possible combinations. The result is 15 different genotypes. The data will be analysed similar to that of the previous crossbreeding project.

Conclusions

A sophisticated Large Stock Unit (LSU) calculator can be used for the measurement of cow efficiency (to calculate kg calf weaned/kg LSU of the dam) of different frame sizes and without additional inputs. Cross-breeding has shown to increase cow efficiency; as long as cow frame sizes do not increase up to a point where the nutritional needs of animals are not fully being met. Increases in cow efficiency (weaning rate x kg calf/large stock unit) in two-breed and three-breed cattle was mainly derived from differences in frame size, fitness and relationships between calf weight and cow Large Stock Units.

The fact that there are large differences in cow efficiency in reproductive cows point to genetic differences and holds the potential for cow ranking and improvement through selection in contemporary groups. Optimum crossbreeding strategies may increase cow efficiency up to a notable 49.7%. This will support climate smart beef production, since it will reduce resource use and reduce the carbon footprint per unit of product produced.

Acknowledgement

This work is based on research supported in part by Red Meat Research and Development South Africa and the National Research Foundation of South Africa (NRF), under grants UID 75122, 75123 and 90097. The Grant-holder acknowledges that opinions, findings and conclusions or recommendations expressed in any publication generated by the NRF-supported research are that of the authors and that the NRF accepts no liability whatsoever in this regard.

References

Meissner, H.H., Hofmeyr, H.S., Van Rensburg, W.J.J. & Pienaar, J.P., 1983. Classification of livestock for realistic prediction of substitution values in terms of a biologically defined Large Stock Unit. Tech. Comm. No. 175. Department of Agriculture, Pretoria.

Mokolobate, M.C., 2015.Novelty traits to improve cow-calf efficiency in climate smart beef production systems. MSc. Dissertation. University of the Free State, Bloemfontein, South Africa.

Neser, F.W.C., 2012. http://www.rpo.co.za/documents/pptrpo/proffrikkieneser.pdf

Schoeman, S.J., 2010. Crossbreeding in beef cattle. In: Beef Breeding in South Africa. 2nd Edition. Agricultural Research Council, Pretoria. ISBN-13 978-1-86849-391-3 pp 21-32.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Michiel Scholtz on gscholtz@arc.agric.za

Genetic study on wet carcass syndrome

Detection of quantitative trait loci affecting wet carcass syndrome in sheep

Industry Sector: Cattle and Small Stock

Research focus area: Animal Products, Quality and Value-adding

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Lené van der Westhuizen

Title Initials Surname Highest Qualification
Prof M.D. MacNeil Ph.D.
Prof M.M. Scholtz D.Sc.
Prof M.D. MacNeil Ph.D.
Prof F.W.C. Neser Ph.D.
Prof A. Maiwashe Ph.D.
Mrs A. Theunissen M.Sc.
Ms M. le Roux M.Sc.

Year of completion : 2018

Aims of the project

  • To map quantitative trait loci affecting wet carcass syndrome.
  • To identify specific loci affecting the predisposition to wet carcass syndrome (detection of a major gene).
  • To develop a diagnostic test for the genetic predisposition to wet carcass syndrome (if a candidate gene can be identified as the cause).
  • If a major gene is not responsible for wet carcass syndrome the second phase of the project will have the aim to develop a polygenic prediction equation for the predisposition of sheep to wet carcass syndrome.

Executive Summary

Wet carcass syndrome (WCS) is a condition predominantly found in sheep, which negatively affects the quality of their carcasses. During the pre-slaughter period, the animal appears to be clinically normal, showing no symptoms of an abnormality. However, after the removal of the skin during the slaughter process the carcass appears to be “wet”. When the description and results of prior research are taken into account, no physiological, environmental or management system was conclusively identified as the causative agent of WCS. Previous research has also not considered a potential genetic basis for WCS or the potential for an interaction of genotype with the environment (stress). Furthermore, the tentative breed-specificity, i.e. Dorper sheep breed, of the condition lends some credence to a potential genetic basis for it. The current study employed the Ovine Infinium® HD SNP BeadChip and a genome-wide association analysis approach to scan the genomes of both afflicted- and unafflicted sheep in search of putative quantitative trait loci associated with the WCS phenotype. This study was not only one of the first in Southern Africa to make use of this specific BeadChip but also the first to investigate the role of genetics as a causative factor of WCS. Muscle samples from sheep carcasses (33 afflicted and 36 unafflicted) were collected from three different abattoirs.

Using a candidate gene approach it was possible to map genetic loci, RYR1 (Chromosome 14) and PRKAG3 (RN¯; Chromosome two) causative of phenotypically similar conditions such as porcine stress syndrome and red, soft and exudative meat to the ovine genome, respectively. The positions of these loci mapped to the ovine genome were not in accordance with the loci showing significant association with the WCS phenotype; and no relationship was found between single nucleotide polymorphisms located within these genes and WCS. Furthermore, along with the latter approach, the test of runs of homozygosity presented similar results as well as providing plausible evidence that WCS is not a recessive inherited condition.

To test for an association between the phenotype (WCS) and a genetic marker(s) i.e. SNPs, a case-control study design was implemented. Given the relatively small sample size of the current study, the results obtained from the GWAS attested strong evidence of at least two loci, oar3_OARX_29903534 and oar3_OARX_113973214 positioned within the non-homologous region of the X chromosome for WCS carcasses. All afflicted animals, both males and females, carried at least one allele for marker oar3_OARX_113973214, which was shown to be related to the WCS phenotype. On the contrary, some of the unafflicted animals also carried this specific allele.  Given the apparent influence of stress on WCS, these unafflicted males and females in all likelihood did not experience adequate levels of stress to manifest the condition post-slaughter. The results of the current study also indicated that WCS may possibly be a rare X-linked inherited condition, provided only female individuals are considered. Finally, two possible major loci involving two major genes, HTR2C and DMD, positioned on the non-homologous region of the X chromosome have been identified as novel positional and functional candidate genes for WCS in sheep.

Popular Article

Wet carcass syndrome (WCS) is a condition mainly found in sheep, which negatively affects the quality of their carcasses. It has been identified in both sheep and cattle breeds, however, the frequency of WCS seen in cattle is substantially less than in sheep. Despite long-standing knowledge of the condition and research, little more is known about wet carcass syndrome and its causes than when it was discovered some three decades ago. Furthermore, it is very difficult to simulate the condition and in some years it is almost absent. Possible causing factors of WCS included the over-hydration of thirsty sheep on arrival at abattoirs, transport distances to abattoirs, allergies, compulsory dip, washing of carcasses in abattoirs under high pressure, condensation in coolers and provision of feed blocks during the pre-slaughter phase.

However, research could not find any link between these factors and the occurrence of WCS. Therefore, when the description and results of prior research are taken into account, no physiological-, environmental- or management system was conclusively identified as the causative agent of WCS. However, stress experienced by the animals during the pre-slaughter period has been identified as a possible contributing factor. Some prevention strategies have been proposed, but the problem still appears from time to time and is more severe in some years.

Wet carcass syndrome is mainly observed in hairy-type Dorper sheep and crosses of Dorper with indigenous and locally developed breeds of South Africa and Namibia, and largely seen in A0 / A1 carcasses (very low fat content with poor conformation). The Dorper breed is greatest in numbers in the studied areas (geographic regions where WCS occurs most frequently) of the Northern Cape Province in South Africa and the southern part of Namibia (Kalahari dunes and sandy veld). Unofficial slaughter statistics from WCS afflicted areas, reveal that certain abattoirs have higher numbers of WCS carcasses, whereas other abattoirs in the same region will have no recorded incidences. Communication between the researcher and abattoir management exposed the seriousness of the condition to communities in the Northern Cape. The condition is found widespread across areas where the grazing quality is poor, although the quantity is often abundant. WCS is also more frequently observed during autumn and winter, especially after droughts or after periods of above-average rainfall during spring, followed by low rainfall during the rest of summer.

During the pre-slaughter period, the animal appears to be physically normal, showing no symptoms of an abnormality. However, after the removal of the skin during the slaughter process, the carcass appears to be “wet”. An uncoloured, slightly sticky, jellylike fluid gives the carcass the shiny and wet appearance. The areas most affected on the carcass are the brisket, flanks, hindquarters, sides, and back. Affected carcasses do not dry off with overnight cooling. Consequently, WCS carcasses are not accepted, with two of the main reasons being appearance and a reduced shelf life. The most sensible explanation for the reduced shelf life is that the surface of the meat is a favourable environment for the growth of microorganisms. In addition, there is an occupational hazard associated with cutting wet carcasses in that a band saw pulls more on the meat which may result in injury to the operator. These observations further illustrate how potentially detrimental WCS is to the sheep meat industry in South Africa.

Lamb producers are very concerned about this condition and are actively participating in research to find solutions for this condition and to identify management procedures to alleviate their economic losses which may collectively rise to 10’s of millions of Rand annually. Carcasses that show WCS characteristics are generally rejected at the abattoir and not sold for human consumption. Taking carcass prices and inflation into account, the loss due to WCS can be estimated at a minimum of R 45,696,774 and during 2010 alone at R 27,010,387.

The literature review showed both promising results in terms of research opportunities and the identification of possible candidate genes for WCS. These candidate genes are the ‘genetic foundation’ of animals that will produce meat with characteristics of being pale, soft and exudative- (PSE); red, soft and exudative- (RSE) and dark, firm and dry (DFD) meat. These conditions are primarily observed in pork meat, but show phenotypic (visual) characteristics that are similar to WCS. All three of these meat characteristics are ‘trigged’ by stress. PSE/RSE meat will be the result of short term stress. Short term stress will cause a rapid decline of glycogen reserves within the muscle and finally result in meat with a low pH. The opposite occurs with DFD which is caused by long term stress. Long term stress causes severe muscle glycogen depletion, which in return causes the meat to have higher than normal pH levels. Selecting swine for leaner and heavier muscles resulted in some animals having greater susceptibility to stress and meat that is of poor quality. High vulnerability to stress in pigs is today referred to as porcine stress syndrome (PSS), and results in PSE meat. PSS can be described as acute death caused by stressors such as exercise, fighting, high temperatures, birth, stocking density, loading, transport, overcrowding at abattoirs, the use of electric prodders and abuse.

From a genetics perspective, PSS and RSE are caused by mutations within genes. PSS is caused by a single recessive inherited gene, ryanodine receptor 1 (RYR1), located on Chromosome 6 of the pig genome. There have been reports on PSE meat in other species including cattle, ostriches, turkeys and chickens. The Rendement Napole (RN¯) gene is a dominant inherited gene and located on Chromosome 15 of the pig genome and will result in RSE meat. RSE meat will result in meat having a high drip loss.

The most recent research, finished in 2018, was the first study to examine the role of genetics as the leading cause of WCS. Three scientific methods were used to identify regions within the sheep genome that may contribute to the development of WCS. These methods are termed comparative genomics using candidate genes, runs of homozygosity (ROH) and a genome-wide association (GWAS) using a case-control study design. The first two methods did not provide the research team with any positive results. Firstly, the mutations within genes causing PSS and RSE in pigs most likely do not cause WCS. Secondly, an individual with identical long stretches of DNA that are inherited from parent lines is called runs of homozygosity. The research team searched for these ROH within the DNA of WCS affected carcass, but could not find any positive results.

The final phase of the study, i.e. GWAS, compared the DNA of both affected (WCS) and unaffected (normal) carcasses in search of DNA markers, named single nucleotide polymorphisms (SNPs), that might be associated with the WCS phenotype. When using the GWAS methods, an SNP will be associated with the condition when this specific genotype (genetic make-up of the animal) is more common in affected- than in unaffected carcasses. The results from this part of the study however, provided strong positive results that at least two of these DNA markers positioned on the X chromosome of the affected carcasses are most likely associated with WCS. However, these DNA markers were also found within the genotype of some of the unaffected or normal carcasses. Now to summarize the important results, some sheep carcasses that were normal also carried the same DNA markers than WCS affected carcasses. One possible explanation could be that these unaffected animals did not experience high enough levels of stress before slaughter to cause the WCS condition after slaughter.

These two DNA markers that were identified by the research team were then further linked to two genes, 5-hydroxytryptamine (serotonin) receptor 2C (HTR2C) and Duchenne muscular dystrophy (DMD). As a result, these two genes were identified as candidate genes for WCS. Many biological functions of these genes exist, however, only a few functions could be connected to WCS. Assuming the HTR2C gene causes WCS, a disruption in cell homeostasis will occur, either during before the slaughter process by means of stress and anxiety; or after the slaughter period has been completed, through the calcium ion homeostasis mechanism within the cells of WCS affected muscles. Similarly, assuming the DMD gene causes WCS, the phenotype could be due to an increase in porousness of the cell membranes of muscles causing the typical shiny wet appearance of WCS. A novel or new porcine stress syndrome was, also identified in 2012 that is also caused by the DMD gene. Both of these genes explained in more modest words, will cause the cells within the muscle to act abnormally and fluid will move out from the cells onto the surface of WCS carcasses. However, this is only a theory and the precise biological mechanism causing WCS is presently unknown.

Future studies will first attempt to determine the exact position of the DNA marker(s) that cause WCS. Under the condition that WCS is caused by a single mutation, the development of a diagnostic test to identify live carrier animals of wet carcass syndrome, will enable sheep farmers to use this information in an attempt to eradicate the condition from their flocks. It is entirely possible that previous research attempts in search of environmental ‘triggers’ or causing factors for WCS were unsuccessful due to the unintentional sampling of mostly non-genetically susceptible or normal animals. Therefore, given the information provided and modern research techniques, nutritional studies will have the ability to make use of the genetically susceptible (WCS) animals to optimistically mimic WCS.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Lené van der Westhuizen on PienaarL@arc.agric.za

Lamb and Mutton Quality Audit

South African Retail Lamb and Mutton Quality Audit

Industry Sector: Cattle and Small Stock

Research focus area: Animal Products, Quality and Value-adding

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Dr Michelle Hope-Jones

Title Initials Surname Highest Qualificaion
Dr PE Strydom Ph.D Animal Science
Dr L Frylinck Ph.D Biochemistry
Dr SM van Heerden Ph.D Home Economics
Prof A Hugo Ph.D Biochemistry
Ms J Anderson N D Analytical Chemistry
Mrs JD Snyman N D Food Technology

Year of completion : 2018

Aims of the project

  • To measure the instrumental/physical quality (shear force tenderness, water holding capacity/cooking loss, fat and muscle colour, collagen properties, oxidative status (rancidity)), sensory qualities and chemical composition of lamb and mutton rib or loin chops (M. longissimus dorsi) from various retail outlets (including brand names and generic products).
  • To determine the reasons for variation in quality by chemical, histological, physical and biochemical tests.
  • To use the information from 3.1 and 3.2 to arrive at a list of factors needed to be addressed in research and/or technology transfer to improve meat quality in South Africa.

Executive Summary

Twenty three products (lamb loin chops) were identified and collected from the shelves of five major retail outlets and twelve smaller butcheries on 14 different dates over a three month period (n=306, certain products where not always available due to drought conditions). Products varied in type, namely Karoo lamb (lamb valued for it unique flavour attributes due to grazing on herbaceous bushes and shrubs from a particular region of South Africa), free range or feedlot. Products also varied in packaging (Modified atmospheric packaging: MAP, PVC overwrap, to openly displayed on shelves) and retailers and butcheries were spread over various socio-economic areas. Price was recorded and shear force tenderness, sensory evaluation (tenderness and flavour), colour of meat, drip loss, cooking losses and meat/fat/bone ratios were measured as properties valued by consumers at or after purchase. Physical, histological and biochemical measurements (proximate and fatty acid analyses, lipid oxidation and collagen) were performed in an attempt to explain variations in consumer related properties.

  • Both instrumental and sensory evaluations showed tenderness to be at a high level of acceptance across the board. The Karoo samples were the most tender with the free-range samples performing the worst especially with regard to sensory tenderness.
  • Karoo lamb stood out for ‘barnyard’ aroma and flavour while free-range samples stood out for ‘Karoo bossie” aroma and flavours meaning they could be distinguished from the other samples and from each other. In both cases however, the scores were of a low intensity. Karoo and free-range lamb are purchased for their distinctive flavour.
  • Karoo and free-range samples lost less drip during cooking compared to the remaining products. Thawing loss was very low in general for all the products.
  • Karoo and free-range products have more loin muscle and less fat per chop compared to feedlot products.
  • Colour of all products was at an acceptable level with no distinct pattern showing for any particular product.
  • Lipid oxidation was at a good level over all products and fatty acid profile were consistent with free-range vs. grain-fed products. This makes the lack of free-range and Karoo flavours more perplexing.
  • Karoo and free-range products were more expensive. Regarding the remaining products, price correlated more with socio-economic area and butchery vs. retailer.
  • In general lamb is of a good quality except for drip loss which needs to be attended to. This could be due to incorrect abattoir practices. Karoo lamb is sold at a premium and its lack of flavours is of concern. The consumer however is able to consistently buy tender loin chops at any retailer or butchery.

Popular Article

Quality audit of South African lamb

Dr Michelle Hope-Jones, Researcher: Animal Production Institute, Food Science and Technology Department

Meat tenderness and other quality traits are influenced by a combination of pre-harvest, slaughter and post-harvest conditions and interventions. Research addresses these factors in order to ensure maximum satisfaction for the consumer.

However, the success rate of various sectors of the meat industry to use these technologies may vary depending on factors like technical skills, knowledge, market sector, financial viability and others.

While new projects are designed to address quality challenges, very little is known about the quality of red meat offered to the consumer at various outlets. To this end, a lamb audit was recently conducted to determine the variation in quality (tenderness, colour, water properties and others) within and between different types of outlets, and also to attempt to verify the reasons for variation in quality, so that research or technology transfer can address specific problems.

Product auditing process

The fact that meat in general is distributed all over the country from various production and processing plants, and considering that much of those operations are in Gauteng and distribute to Pretoria outlets, the study was limited to proper sampling and testing within the Pretoria metropolis. All the selected outlets receive meat from different operations, assuring a reliable sample of the industry.

Twenty three products (lamb loin chops) were identified and collected (when available) from the shelves of five major retail outlets (R) and twelve smaller butcheries (B) on 14 different dates over three months (n = 306). Products varied in type, namely Karoo lamb (valued for its unique flavour attributed to grazing on herbaceous bushes and shrubs from a particular region of South Africa), as well as free range and feedlot lamb.

Products also varied in packaging, from modified atmospheric packaging (MAP), where high levels of oxygen are pumped into packages in order for the meat to maintain the desirable red colour that consumers prefer, to PVC overwrap, and also open products displayed on shelves.

Retailers and butcheries were spread over various socio-economic areas.

Evaluation of palatability

The palatability of meat is determined by a combination of tenderness, juiciness and meat flavour.

Tenderness and juiciness

Tenderness is the most variable quality characteristic and is also rated by consumers as the most important sensory attribute. Figure 1 shows that purchasing from retailers vs. butcheries had little effect on tenderness, with instrumental test levels (Warner Braztzler Shear Force, WBSF) being at an acceptable level across all outlets. All of the Karoo products however were more tender. This could be attributed to the use of growth promotants in feedlots.

There was a strong correlation between sensory tenderness (rated by a trained panel) and WBSF. Two of the Karoo products, R2K and B6K, stood out as being more tender.

One of the free range products, R5FR, performed poorly on tenderness, but also scored lower for juiciness. This could probably be attributed to abattoir processes. Increased juiciness can give the perception of a more tender product and the relationship between the two attributes can clearly be seen in the figure. Most of the products which scored low for sensory tenderness (tougher), scored low for juiciness too.

Hoewever, the overall good level of tenderness is good news for the industry.

Flavour and aroma

In the case of lamb, flavour and aroma can play as an important role as tenderness. This is especially the case when comparing free range lamb to feedlot lamb (grass-fed vs. grain-fed) and even more so with Karoo lamb, which has a very specific flavour and aroma. As expected, the three Karoo samples scored higher (a more intense aroma) for ‘barnyard’ aroma, although interestingly not for ‘Karoobossie’ aroma, except for one Karoo product. The opposite was found for the two free range products, which had higher ‘Karoobossie’ aroma when compared to the Karoo products, but did not have a strong ‘barnyard’ aroma.

When looking at the flavour profiles, once again the three Karoo samples stood out as having a stronger ‘barnyard’ flavour. The Karoo samples did not really stand out as having a ‘Karoobossie’ flavour. As Karoo lamb is sold at a premium for its very distinct flavour, it would therefore be expected for this flavour to come out strongly. Instead, the taste panel identified the Karoo samples more as grass-fed meat.

Drip loss

All the free range products, as well as two of the Karoo products (R2K and B6K), had much less drip loss (the liquid you would find in the tray) compared to the other products. In fact, they had just over half the drip loss compared to the product with the most drip (R4).

Colour

All products across the board fell into the distinctly brown category. It was expected that packaging, or whether a sample was cut fresh or was on display, would make a difference to the colour of the meat, but not even the MAP packaged samples were of a desirable colour. This is of concern as consumers rely on visual appearance at the point of purchase and meat with a bright cherry red colour is associated with freshness.

Fat and meat (muscle) ratio, price

Figure 2 shows the average percentage of fat and the actual muscle for loin chops from the various outlets. All the Karoo (K) and free range (FR) products had more meat (a greater percentage of loin muscle), compared to the other products. It was however slightly unexpected, as feedlot meat production employs beta-adrenergic agonists, which should increase muscle yield and decrease fat percentage.

However, the feedlot lamb still had a higher percentage of fat compared to Karoo and free range samples, which could overshadow the increase in muscle yield of feedlot samples. Fat percentage followed a pattern of decreasing with an increase in loin muscle, with the Karoo and free range samples having less fat.

Price

There was a strong correlation between price and loin muscle, with a larger percentage of loin muscle resulting in an increase in price.

The Karoo and free range products were markedly more expensive, except for R2K (which was sold at a lower level retail store which was more accessible to the bulk of the public). All other Karoo products were sold at butcheries in areas of increased socio-economic status. The area in which the products were bought and the type of retailer/butchery that it was bought from, seem to be more of an indicator of price, than the percentage loin muscle, with stores in higher income areas charging more.

Problems to be addressed

With lamb being an expensive product, it is good to see that the consumer can consistently buy a tender product. There are, however, a few problems which were identified.

  • Karoo lamb, which is sold as a speciality product, does not consistently stand out from other free range products.
  • Colour as a whole is also a problem, with lamb meat not having the cherry red colour that the consumer associates with freshness.
  • Generally only 50% of a loin chop consists of meat and price alone does not seem to be a very accurate indicator of how much meat the consumer will get, except for the more specialised Karoo and free range products, which have a much better meat to fat ratio.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Michelle Hope-Jones on hopejonesm@arc.agric.za