Gene expression: Nguni and Bonsmara cattle

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

Industry Sector: Cattle And Small Stock

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

Research Institute: Agricultural Research Council

Year Of Completion : 2019

Researcher: Dina Linde

The Research Team

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

Executive Summary

Introduction

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

Objective statement

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

Project Aims

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

Results

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

Conclusion

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

Popular Article

A low energy feedlot diet may favour our indigenous breeds

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

Introduction

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

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

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

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

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

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

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

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

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

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

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

Gene expression: Nguni and Bonsmara

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

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.

Footer And Tags And Categorisation

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

Genetic markers for Haemonchus contortus in sheep


Genome wide association study to identify genetic markers associated with resistance to Haemonchus contortus in sheep

Industry Sector: Cattle And Small Stock

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

Research Institute: Department of Agriculture Forerst and Fisheries (DAFF)

Year Of Completion : 2019

Researcher: Margeretha Snyman

The Research Team

TitleInitialsSurnameHighest QualificationResearch Institution
DrCVisserPhDUP
DrPSomaPhDARC
DrFCMuchadeyiPhDARC-BTP
DrADFischerBVScQueenstown PVL
MrNJDlamimiMScARC

Aims Of The Project

  1. Collect blood samples and data on resistance to H. contortus on a sheep flock on a farm with major Haemonchus anthelmintic resistance problems
  2. Analyse the data, estimate genetic parameters and develop a protocol for recording of resistance to H. contortus under SA conditions
  3. Conduct various genomic studies to identify genetic markers linked to resistance

Executive Summary

The objective of this study was to compare four commonly used growth promotants in a commercial sheep feedlot. The steroidal growth promotants chosen for this trial were Ralgro (zeranol), Revalor G (Rev G; TBA/oestrogen- 17β), Revalor H (Rev H; TBA/oestrogen- 17β) and Zilmax® (zilpaterol hydrochloride). The growth promotants were compared with one another and within three sex groups, namely ewe, ram and wether (castrates), to determine which molecule or combination of molecules, if any, had the most benefit and profitability when measured against a control group.  Sheep were stratified based on initial weights and then randomly allocated to treatment groups in a completely randomised control study. All sheep originated from the same farm, and they were of  similar age, breed,  transport method,  processing method, feed (the only difference being  the groups receiving Zilmax® during the last 18 days of feeding, making provision for 3 days withdrawal), weather conditions, housing and time on feed. A time constant termination date was used in this study, in order to measure the performance of lambs in treatment groups over time.

The issue of resistance of internal parasite species to worm remedies is widespread throughout South Africa and the world and affects all small stock farmers. Especially Haemonchus contortus causes major losses among sheep in the summer rainfall regions in South Africa. For some areas, farming with animals resistant to nematodes seems to be the only solution in the long run. Genetic variation in resistance to nematode infestation in sheep, based on faecal egg count (FEC) as a criterion, has been reported for various breeds. Successful breeding programs for resistance have been reported for Australian and New Zealand sheep. There are, however, no large scale active breeding programs for resistance in South African sheep.

Because of the difficulty of routinely collecting phenotypic data associated with resistance to internal parasites, suitable data sets for the estimation of genetic parameters for resistance against H. contortus are scarce in South Africa. The history of and recent selection practices followed in the Wauldby Dohne Merino flock makes it an ideal resource for research into resistance to H. contortus in South African sheep.

In 2011, a project aimed at selection for resistance against H. contortus was started on the Wauldby Dohne Merino flock. Apart from full pedigree information, data on faecal egg counts (FEC), Famacha© score (FAM) and body condition score (BCS) were collected annually on all lambs born since 2011. FEC, FAM and BCS of all lambs were recorded from the middle of January onwards. FAM was recorded weekly and FEC and BCS every 14 days until the end of June when Haemonchus challenge had decreased. Lambs were only drenched when they had a FAM of 2.5 or more, in conjunction with a BCS of less than 1.5. Any lamb that was drenched was recorded as “Dosed” and those lambs that did not require any drenching as “Not dosed”. Replacement rams and ewes were selected from the animals that did not need dosing on the basis of a selection index incorporating FEC, FAM and BCS.

Data were analysed to compile protocols for selection against resistance to H. contortus in SA sheep.

Objective

The objective of this study is to identify of genetic markers for resistance to Haemonchus contortus in SA sheep, which could be included in the selection plan. See aims for the objectives of the three phases of the projects.

Results

The Dohne Merino lambs at Wauldby were subjected to severe H. contortus challenge. This is evident from the very high maximum FEC values recorded, even at the last two recordings during June. FEC ranged from 0 to 54100 epg among recordings over the trial period. Despite the high FEC challenge, mean FAM was still low, which is indicative of the high resilient status of the Wauldby flock. Dosing status had a significant effect on FAM, BCS and FEC. The Not dosed lambs had lower FEC, higher BCS and lower FAM compared to the lambs that were dosed. FAM increased and BCS decreased as the number of treatments received increased.

During the first year of the trial, 33% of the ram lambs and 45% of the ewe lambs were not dosed throughout the annual recording period. These percentages increased annually until 77% of the ram lambs and 82% of the ewe lambs did not need any drenching in 2016. One of the most significant results of the trial to date was the increase in percentage offspring of the sires that did not need drenching. The best performing sire used during 2011 had 53% lambs that did not need drenching, while 74% lambs of the poorest sire needed anthelmintic treatment. In 2016, the best performing sire had 97% lambs that did not need drenching, while 37% lambs of the poorest sire needed anthelmintic treatment.

FAM had a high genetic correlation and moderate phenotypic correlation with FEC. The highest heritability and repeatability of the resistance traits were recorded for BCS, but BCS had a moderate genetic and a low phenotypic correlation with FEC. In this study, BCS of the lamb, in combination with FAM, was considered in the decision whether to treat the lamb or not. However, due to the low phenotypic correlation between BCS and faecal egg count, BCS of an animal by itself is not an accurate indication of the existing level of H. contortus infection. The low phenotypic correlation estimated between BCS and FEC in this study is also indicative that other factors apart from worm load influence BCS in growing lambs.

Body weight, fleece weight and coefficient of variation of fibre diameter had favourable genetic correlations with FEC, FAM and BCS, while fibre diameter and staple length were unfavourably correlated with FEC. Inclusion of FEC in the selection protocol should therefore not adversely affect body weight and wool production.

As far as the application of FAM as criterion for the selection of resilient or resistant sires and dams is concerned, it should be used in combination with other resistance indicators such as FEC. During the high challenge summer rainfall period FAM will be recorded weekly or bi-weekly, therefore more FAM recordings will be available for inclusion in a final selection protocol. Due to its favourable genetic correlations with FEC and the production traits, and the fact that BCS of the Not dosed lambs in this study was higher than BCS of the Dosed lambs, BCS could be included in the selection protocol to be used for selection against resistance to H. contortus. BCS and FEC can be recorded at the beginning (January), at the peak (middle to end of March) and towards the end of the H. contortus season (June). Lambs that did not require any anthelmintic treatment up until selection age could be selected on the basis of a selection protocol incorporating these FEC and BCS recordings, together with all the recorded FAM.

The following selection indices, including FEC with or without incorporating FAM and BCS, were compiled / suggested:

  • SI1 = (-1 x FEC169 -1 x FAM +1 x BCS169) +10
  • SI2 = (-1 x FEC169 -1 x FAM) +10
  • SI3 = (-1 x FEC169) +10

As far as the genomic study is concerned, there were definite genetic differences among the animals in the flock and three genetic clusters were observed. Animals in the most resistant cluster had significantly lower FEC, lower FAM and higher BCS than the animals in the other two clusters. The sires of the animals in the resistant cluster also had more favourable EBVs for FEC and FAM.

The results of the genomic study further indicated the possibility of selection signatures on the same chromosomes in the Wauldby Merino animals than those on which QTL for faecal egg count and H. contortus FEC are reported in the sheep genomic databases. These will be further investigated in a comprehensive GWAS study.

Conclusion

The results indicate that progress was made when selecting for resistance to H. contortus in the Wauldby Dohne Merino flock.
There is genetic variation in host resistance against H. contortus in the Wauldby Dohne Merino flock. Sires in one genetic cluster are highly resistant and can be used in a breeding program to develop sheep that are resistant to H. contortus infections.
Moderate heritabilities and genetic correlations were estimated for and among FAM, BCS and FEC in this flock. Except for the unfavourable genetic correlation with fibre diameter, no detrimental genetic correlations between the resistance and production traits were estimated.
These results were used to develop protocols for selection for resistance to H. contortus under South African conditions. The developed protocols need to be validated on various farms before they can be implemented on a wider scale.

Popular Article

PROTOCOL FOR SELECTION FOR RESISTANCE TO HAEMONCHUS CONTORTUS IN SOUTH AFRICAN DOHNE MERINO SHEEP

Authors: M.A. Snyman, Grootfontein Agricultural Development Institute, Private Bag X529, Middelburg (EC), 5900 GrethaSn@Daff.Gov.Za. A.D. Fisher, Queenstown Provincial Veterinary Laboratory, Private Bag X7093, Queenstown, 5320 Alan.Fisher@Awe.Co.Za

INTRODUCTION

The issue of resistance of internal parasite species to worm remedies is widespread throughout South Africa and the world and affects all small stock farmers. Haemonchus contortus is the most important parasite and causes the most losses among sheep in the summer rainfall regions of South Africa. For some areas, farming with animals resistant to nematode infestation seems to be the only solution in the long run.

Because of the difficulty of routinely collecting phenotypic data associated with resistance to internal parasites, suitable data sets for the estimation of genetic parameters for resistance against H. contortus are scarce in South Africa. The history of and recent selection practices followed in the Wauldby Dohne Merino flock makes it an ideal resource for research into resistance to H. contortus in South African sheep. The farm Wauldby is located in the Stutterheim district in the Eastern Cape Province in a high summer rainfall area (800 mm annually). Wauldby has a well-documented history of heavy H. contortus challenge and H. contortus resistance and in the past the farm was used for several trials relating to resistance of H. contortus to anthelmintics.

In 2011, a project aimed at selection for resistance against H. contortus was started on the Wauldby Dohne Merino flock. Data on faecal egg counts (FEC), Famacha© score (FAM) and body condition score (BCS) were collected annually on all lambs born since 2011. FEC, FAM and BCS of all lambs were recorded from the middle of January onwards. FAM was recorded weekly and FEC and BCS every 14 days until the end of June when Haemonchus challenge had decreased. Lambs were only drenched when they had a FAM of 2.5 or more, in conjunction with a BCS of less than 1.5. Any lamb that was drenched was recorded as “Dosed” and those lambs that did not require any drenching as “Not dosed”. Data on all lambs were recorded throughout until the end of June, irrespective whether they needed drenching or not.

Selection in the flock was aimed at increasing resistance to H. contortus, while maintaining reproductive performance, body weight, wool weight and fibre diameter and improving wool quality traits. Selection for the production traits was done on the basis of selection indices and BLUP of breeding values for the mentioned traits measured at 14 months of age. Selection for resistance to H. contortus was based on a selection index incorporating FEC, FAM and BCS.

A selection line, in which the most resistant ewes were mated to the most resistant rams, has been established in 2012 as part of the project. These animals were run together with the rest of the flock animals, except during mating. Only ram and ewe lambs that had never been drenched were considered for selection into the selection line. Three rams and about 20 young ewes were selected annually for the selection line since 2012. Currently the selection line consists of 120 ewes, which are mated in three groups of 40 ewes each to the three most resistant rams in single sire mating camps. All progeny born in both the selection line and the rest of the flock were evaluated together. Rams and ewes performing the best in terms of resistance could be selected for the selection line, whether their parents came from the selection line or the other flock animals.

RESULTS TO DATE

The data collected over the years were used to estimated heritabilities and genetic correlations among the traits. Moderate heritabilities for and favourable genetic correlations among FEC, FAM and BCS were estimated. It will be impractical and expensive to record FEC every second week under commercial farming conditions. A combination of FEC recordings at the beginning, at the peak (middle to end of March) and towards the end of the season, proved to be the best alternative for selection purposes.

FAM had a high genetic correlation with FEC. In this study on-going first stage selection was done by identifying animals unsuitable for inclusion in the selection line on the basis of FAM and BCS. Identifying animals that required anthelminthic treatment according to FAM will ensure that only truly susceptible animals are identified and destined to be culled. Resilient as well as resistant animals will not be targeted and will remain untreated and available for final stage selection. As far as the application of FAM as criterion for the selection of resilient or resistant sires and dams is concerned, it should be used in combination with other resistance traits such as FEC. During the high challenge summer rainfall period, FAM will be recorded weekly or bi-weekly, therefore more FAM recordings will be available for inclusion in a final selection protocol.

The highest heritability and repeatability of the resistance traits were recorded for BCS, but BCS had a moderate genetic correlation with FEC. In this study, BCS of the lamb, in combination with FAM, were considered in the decision whether to treat the lamb or not. However, due to the low phenotypic correlation between BCS and FEC, BCS of an animal by itself is not an accurate indication of the existing level of H. contortus infection. By the time BCS is affected by H. contortus per se, the animal would have shown other clinical signs of Haemonchosis. Due to the fact that BCS of the Not dosed lambs in this study was higher than BCS of the Dosed lambs, BCS was included in one of the selection indices. BCS and FEC can be recorded at the beginning (January), at the peak (middle to end of March) and towards the end of the H. contortus season (June), as mentioned above.

SELECTION INDICES (SI)

The following selection indices, including FEC with or without incorporating FAM and BCS, were compiled / suggested:

SI1 = (-1 x FEC169 -1 x FAM +1 x BCS169) +10

SI2 = (-1 x FEC169 -1 x FAM) +10

SI3 = (-1 x FEC169) +10

For all the animals on which data were collected to date in the Wauldby flock, these three SI options were calculated. These three selection indices were evaluated on the data of the Wauldby animals born in 2015, 2016 and 2017. When the data of all the available animals were evaluated, basically the same animals will be selected with SI1 and SI2. Where selection is based only on FEC (SI3), somewhat different animals were selected in some years than when FAM and BCS were included in the selection index.

When the data of only a selected proportion of 5% rams and 25% ewes were evaluated, again basically the same animals will be selected with SI1 and SI2. However, rather different animals will be selected when only FEC was used as selection criteria. What this implies is that selection should preferably be done on SI1 or SI2. FAM should be included together with FEC, but the inclusion of BCS is optional.

PROTOCOL FOR SELECTION FOR RESISTANCE AGAINST H. CONTORTUS

The following protocols can be followed for selection for resistance against H. Contortus in stud and commercial flocks respectively.

Stud animals

Follow the normal internal parasite control program before weaning, i.e. routine pooled FEC.If the lambs needed to be drench before weaning, FEC, FAM and BCS of all the lambs could be recorded before drenching. All lambs could then be drenched after data collection.After weaning, recording of individual ram and ewe lambs should take place.FAM should be recorded every 14 days until the end of June when Haemonchus challenge has decreased.Individual FEC and BCS should be recorded at the beginning (January) and twice during the summer season (March and May).Lambs should only be drenched when they have a FAM of 2.5 or more.Any lamb that was drenched should be noted and culled.Replacement rams and ewes should be selected from the animals that did not need dosing on the basis of one of the above selection indices incorporating FEC and FAM, with or without BCS.Adult ewes should only be drenched on FAM (Targeted selective treatment). Note and cull ewes that need repeated drenching.Evaluate existing sires on the performance of their offspring.If rams are bought, buy only rams resistant to internal parasites.

Commercial animals

Follow the normal internal parasite control program before weaning, i.e. routine pooled FEC.After weaning only ewe lambs should be recorded.FAM should be recorded every 14 days until the Haemonchus challenge has decreased.FEC should be monitored through monthly pooled FEC samples.Lambs should only be drenched when they have a FAM of 2.5 or more.Any ewe lamb that was drenched should be noted and lambs that needed 2 or more drenchings should be culled.Adult ewes should only be drenched on FAM (Targeted selective treatment). Note and cull ewes that need repeated drenching.Individual FEC of all adult rams should be recorded during the peak Haemonchus season. Before faecal sampling, the rams should not receive any anthelmintic treatment for at least 3 to 4 weeks. Cull rams with too high FEC.Buy only rams resistant to internal parasites.

CONCLUSIONS

Progress was made when selecting for resistance to H. contortus in the Wauldby Dohne Merino flock. These results were used to develop protocols for selection for resistance to H. contortus under South African conditions. The developed protocols need to be validated on various farms before they can be implemented on a wider scale.

 ACKNOWLEDGEMENTS

Mr Robbie Blaine and the personnel at Wauldby for their valuable contribution in the execution of the project and RMRD-SA for funding of the project.

Conclusions

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project –

Greta Snyman on GrethaSn@daff.gov.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

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

Landscape genomics in South Africa

Genomic technologies for the improvement of South African beef cattle

Industry Sector: Cattle and Small Stock

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

Research Institute: Agriculture Research Institute – OVI

Researcher: Dr. Pranisha Omduth Soma

Title Initials Surname Highest Qualification
Prof. A.N. Maiwashe PhD
Dr F.C. Muchadeyi PhD
Prof. E. van-Marle Koster PhD
Prof. M.M. Makgahlela PhD
Dr M. MacNeil PhD
Dr S.O. Makina PhD

Year of completion : 2018

Aims Of The Project

  • To estimate linkage disequilibrium within South African beef cattle
  • To perform a genome wide scan for signatures of selection in beef cattle
  • To sequence genomic regions targeted by selection in order to identify possible polymorphisms

Executive Summary

South African indigenous and locally developed cattle breeds possess adaptive traits that are usually associated with tolerance to various diseases, extreme temperatures and humidity, and to change in feed availability. These breeds are also adapted to low-input management systems and have shown the ability to survive, produce and reproduce under harsh environments. Thus, these breeds hold potential in the changing South African production environments. However, little is known about the nature or extent of the genetic variation underlying these breeds.

The aim of this study was to conduct a genome wide scan for signatures of selection among Afrikaner, Nguni, Drakensberger, Bonsmara, Angus and Holstein cattle breeds of South Africa using data generated from the Bovine SNP50k BeadChip. The Angus and Holstein breeds were included as reference breeds since they have been extensively characterized using similar tools.

Therefore, in this project, the Bovine SNP50 BeadChip was used to characterize the genetic diversity and population structure of SA cattle breeds, determine the linkage disequilibrium and conduct a genome wide scan for signatures of selection among the Afrikaner (n=44), Nguni (n=54), Drakensberger (n=47) and Bonsmara (n=46)., using the Angus (n=31) and Holstein (n=29) cattle reference groups.

The first experiment performed included the evaluation of the Bovine SNP50 BeadChip to determine its utility for genome wide studies of South African cattle. Results of this experiment revealed that over 50 % of the SNPs were polymorphic (eg. Nguni = 35 843), indicating that the Bovine SNP50 assay would be useful for genome wide studies among South African cattle breeds.

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. Genetic diversity within the cattle breeds was analyzed using three measures of genetic diversity namely allelic richness, expected heterozygosity and inbreeding coefficient. The genetic diversity and population structure analyses indicated that the Afrikaner cattle had the lowest level of genetic diversity (He=0.24) while the Drakensberger cattle (He=0.30) had the highest among indigenous and locally-developed breeds. As expected, the average genetic distance was the greatest between indigenous breeds and Bos Taurus breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. Clear genetic divergence between South African (indigenous and locally-developed cattle breeds) and Bos Taurus cattle breeds was observed which suggested distinct genetic resources in South African cattle breeds which should be conserved in order to cope with unpredictable environments.

The extent of linkage disequilibrium (LD) is important for determining the minimum distance between markers for effective genome coverage for genome wide association studies. It can also provide insight into the evolutionary history of a population. The analyses of the extent of linkage disequilibrium (LD) showed that Afrikaner, Angus and Holstein had higher LD compared to Nguni, Drakensberger and Bonsmara cattle at all tested genomic distances. The higher LD within the Afrikaner cattle suggested that this breed has experienced considerable selection forces in contrast to what is expected of indigenous breeds and would require lower marker (50 000) density relative to what will be required for the Nguni, Drakensberger (150 000) and Bonsmara (75 000) cattle for genome wide studies. New breeding strategies may be required for the Afrikaner cattle breed to ensure future fitness of the breed. The effective population size for the Nguni, Drakensberger and Bonsmara were above the FAO recommended level.

The detection of selection signatures among cattle breeds may assist in locating regions of the genome that are, or have been, functionally important and targeted by selection. In this study, two approaches were employed. The first was based on the detection of genomic regions for which haplotypes have been driven towards complete

Fixation within breeds. The second approach identified regions of the genome exhibiting elevated population differentiation (Fst). A total of 47 genomic regions were identified as harboring potential signatures of selection using both methods. Thirty three of these regions were successfully annotated to identify candidate genes. Among these, were keratin genes (KRT222, KRT24, KRT25, KRT26 and KRT27) and one heat shock protein (HSPB9) on chromosome 19 (BTA) at 41,447,971-41,926,734 bp in the Nguni that have been previously associated with adaptation to tropical environments in Zebu cattle.

Furthermore, a number of genes associated with nervous system (WNT5B, FMOD, PRELP, ATP2B), immune response (CYM, CDC6, CDK10), production (MTPN, IGFBP4, TGFBI, AJAPI) and reproductive (ADIPOR2, OVOS2, RBBP8) performances were detected to be under selection in this study.

Target probes for enrichment were designed from exome and 5’ and 3’ untranslated regions of the cattle genome. Many SNP’s were identified in regulatory regions, leading to conformational changes in factor-binding sites. Gene ontology enrichment and clustering, resulted in the enrichment of gene ontology terms involved in fertility-related categories. Taking advantage of the availability of the fully sequenced bovine genome, the South African beef breeds were sequenced to detect genetic variants, in particular, large-scale SNP’s, which may contribute to the beef cattle genomics in South Africa.

The results presented in this study, forms the basis for effective management of South African cattle breeds and provides a useful foundation for the detection of mutations underlying genetic variation in traits of economic importance in South African cattle breeds.

This study produced one PhD thesis, 12 peer reviewed scientific articles and one popular article.

Popular Article

Genomic technology for South African Beef Cattle

Makina¹, F.C. Muchadeyi², E. van-Marle Koster³, A. Maiwashe¹ and P. Soma¹
ARC-Animal Production Institute, Private Bag X2, Irene, South Africa; ²ARC-Biotechnology Platform, Onderstepoort, ³University of Pretoria, Department of Animal and Wildlife Sciences, Private Bag X20, Hatfield, Pretoria, South Africa.

Corresponding author, E-mail: Pranisha@arc.agric.za, Tel: +27 (0)12 672 9218

South African (SA) indigenous and locally developed cattle breeds possess adaptive traits that are usually associated with tolerance to various diseases, extreme temperatures and humidity and to change in the availability to feed. These breeds are also adapted to low-input management systems and have shown the ability to survive, produce and reproduce under harsh environments. Thus, these breeds hold potential in the changing South African production environments. Despite their large numbers and not endangered status, their adaptive traits are of importance and there is a worldwide drive for the effective management of indigenous genetic resources, as they could be most valuable in selection and breeding programs in times of biological stress such as famine, drought or disease epidemics.

The recent development in molecular genetics and bioinformatics has enabled the development of genome wide SNP DNA arrays for livestock species including cattle. These chips present opportunities to study South African cattle breeds in order to unravel population structure as well as the genetic potential of these breeds.

The Bovine SNP50 BeadChip was used to genetically characterize these breeds. The study populations comprised the Afrikaner, Nguni, Drakensberger and Bonsmara cattle breeds with the Angus and Holstein cattle as reference groups. Results of this study demonstrated that the genomic information generated from the BovineSNP50 has potential for application in South African cattle populations and allow for the unravelling of their genetic potential with regard to production, reproduction, disease resistance and adaptation.

There was a clear genetic divergence between South African (indigenous and locally-developed cattle breeds) and <em>Bos taurus</em> cattle breeds which suggested distinct genetic resources in South African cattle breeds that should be properly utilized in order to cope with unpredictable future environments. The level of inbreeding was relatively low across the study populations although the assessment of the inbreeding level should be done every five years to determine any unfavourable change in inbreeding levels, so that appropriate steps can be taken. The population structure analysis in the study revealed some signals of admixture and genetic relationship between Afrikaner, Nguni, Drakensberger and Bonsmara. Nguni cattle shared some genetic links with the Afrikaner cattle, with about 8% of its genome derived from the Afrikaner cattle.   This result may reflect co-ancestry regarding the origin of these breeds as both these came from the same migration route into Southern Africa (Scholtz, 2011).

On the other hand, the Bonsmara cattle shared limited genetic links (0.5%) with Afrikaner cattle, which was unexpected. This low relationship may be attributed to genetic drift or a small sample size. Information generated from this study forms the basis for future management of these cattle breeds. The effective population size appeared to have decreased in all the study breeds in recent generations. The lower effective population sizes for the Afrikaner, Angus and Holstein breeds compared to those of Nguni, Bonsmara and Drakensberger at more recent generations, could be due to intense selection, inbreeding and probably wide spread use of artificial insemination in South Africa and the use of relatively few elite sires after 1970 (Hayes et al., 1990). In order to maximise the net response in genetic gain, Food and Agricultural Organisation (FAO) (FAO 1998) recommended an effective population size of 50 per generation. The Afrikaner, Angus and Holstein were below the FAO recommended number.

This suggested that these breeds are endangered and close to critical stage therefore pointing out the need for implementation of appropriate conservation programs as well as new selection and breeding strategies to ensure long-term fitness of these breeds. These could include increasing the number of animals contributing offspring to each generation by increasing the cow populations. It is critical for food security and rural development because it allows farmers to select stock or develop new breeds in response to changing conditions, including climate change, new or resurgent disease threats, new knowledge of human nutritional requirements, and changing market conditions or societal needs (FAO, 2010).

A total of 47 genomic regions were identified including genes associated with immune response, reproductive performances, coat colour, tropical adaptation and nervous system were identified. For example, the keratin family and one heat shock protein in the Nguni cattle were associated with tropical adaptation. In addition to the role that the keratin genes play during epidermis development, they also play a role in the formation of the hair shaft (Wu et al., 2008). Skin colour and the thickness of hair directly influence the thermos-resistance of cattle living in the tropics. Nguni cattle have smoother and shinier hair coats compared to European cattle breeds. These characteristics provide Nguni cattle with a greater ability to regulate body temperature and to more efficiently maintain cellular function during heat as well as the ability to resist tick infestation (Marufu et al., 2009).

Several candidate genes directly or indirectly involved in reproductive pathways including oestrus process, ovulation rate, testis development and prostaglandin were found. The fact that the Afrikaner, Nguni, Drakensberger and Bonsmara cattle have the ability to produce and reproduce under harsh environment conditions and are considered excellent dam lines for crossbreeding (Scholtz, 2010), supports the strong selection on reproductive loci that is likely to have occurred in their adaptation to South African conditions. Genes involved in muscle organ development and skeleton development were also identified as being under selection in the Bonsmara and Afrikaner cattle populations. The results presented in the study forms the basis for effective management of South African cattle breeds. Furthermore, a genomic understanding of how and where natural selection has shaped the pattern of genetic variation among cattle breeds in SA was unveiled by identifying loci that are important to the development of SA cattle breeds.

Future studies should focus on expanding the breed level analysis through the inclusion of all major African cattle breeds (Gautier et al., 2009) together with cattle breeds of the world. This could further provide insight with regard to the genetic relationship shared among South African cattle breeds and cattle breeds of the world and shed more light on the genomic requirement for survival in African environments.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Pranisha Soma on pranisha@arc.agric.za