STEC from feedlot to abattoir

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

Industry Sector: Cattle and Small Stock

Research focus area: 

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

Research Institute: University of Pretoria

Researcher: Peter Thompson

Research Team

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

Completion: 2020

Aims of the project

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

Executive Summary

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

Objective Statement

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

Results

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

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

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

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

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

Conclusion

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

POPULAR ARTICLE

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

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

INTRODUCTION

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

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

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

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

MATERIALS AND METHODS

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

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

RESULTS AND DISCUSSION

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

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

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

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

CONCLUSIONS

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

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

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

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

Industry Sector: Cattle And Small Stock

Research Focus Area: Animal Health and Welfare

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

Year Of Completion: 2019

Researcher: E van Marle-Koster

The Research Team

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

Executive Summary

Introduction

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

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

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

Objective statement

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

Project Aims

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

Results

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

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

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

Conclusion

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

The following scientific output were achieved for the project:

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

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

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

Popular Article

Introduction

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

Rulien Grobler (PhD Kandidaat)

Departement Vee- en Wildkunde, Universiteit van Pretoria

Inleiding

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

Poenskop oorerwing

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

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

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

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

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

Die Poena Projek by UP

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

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

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

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

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

Implikasies vir SA Bonsmara

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

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

Erkennings

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

Verwysings

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

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

Footer and Tags and Categorisation

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

Genotype imputation for indigenous beef cattle

Genotype imputation as a genomic strategy for the South African Drakensberger beef breed

Industry Sector: Cattle And Small Stock

Research Focus Area: Livestock Production With Global Competitiveness: Breeding,Physiology And Management

Research Institute: Department Of Agriculture Forest And Fisheries (DAFF)

Year Of Completion : 2019

Researcher: Carina Visser

The Research Team

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

Executive Summary

The SA Drakensberger is a medium-framed breed with a sleek, black coat. Considering its history as one of the oldest indigenous breeds, its prominent role in the present beef industry and its potential for improving the beef cattle gene pool in the future; there is value in characterizing the SA Drakensberger on the genomic level. There has recently been interest in incorporating genomic information into selection strategies for this breed. Apart from the fact that the implementation of genomic technologies relies on diligent phenotyping efforts, accurate and complete pedigree recording; genomic selection also requires adequate SNP genotyping profiles (Meuwissen et al., 2001). The SA Drakensberger meets the requirements for genomic selection with 100% participation in SA Stud Book’s Logix Beef performance recording scheme as well as an extensive recorded pedigree profile (SA Stud Book, 2017). Theoretically, current EBVs can therefore be enhanced with the use of genomics if financial resources allow the generation of adequate high-density genotypic profiles. Imputation is a statistical methodology that relies on the genomic segments shared within a breed, or a group of genetically similar breeds, to predict genotypic information for SNPs that were not physically genotyped (Marchini et al., 2007). The main advantage of this methodology is the reduction in genotyping costs by allowing genotyping to be undertaken using lower density SNP panels. The utility of such low-density panels for applications such as genomic selection will depend on the accuracy with which un-genotyped SNPs can be imputed to higher density from such lower density panels. Even though imputation is integrated into routine genomic evaluations internationally, the utility of this methodology has not been evaluated for indigenous cattle resources. Considering that these breeds often have admixed genomes, applying imputation requires optimization for such breeds and this includes the SA Drakensberger.

Objective Statement

The objective of this research project was to comprehensively study the validity of genotype imputation, from lower-density single nucleotide polymorphism (SNP) panels to higher density, for the economically-important SA Drakensberger beef cattle breed towards cost-effectively implementing genomically-enhanced breed improvement strategies such as genomic selection for this indigenous breed in the future.

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

Results generated from the first part of this study indicated that differences in genomic characteristics such as minor allele frequency (MAF), linkage disequilibrium (LD) and runs of homozygosity (ROH) exists between chromosomes. Mean genome-wide MAF was, for example, estimated to be 0.26 with chromosome-specific MAF ranging from 0.24 (Bos Taurus Autosome; BTA14) to 0.28 (BTA21). This was supported by the proportion of low-MAF (< 5%) SNPs estimated, which indicated 16.0% of SNPs to be classified as low-MAF SNPs on BTA14. The inter-SNP LD was generally weak, ranging from mean r²=0.11 (BTA28) to r²=0.17 (BTA14) for SNPs separated by≤1Mb and r²=0.20 extended only up to<30 kb. LD was weaker between SNP pairs including low-MAF SNPs. Consensus ROH segments were identified and the most prevalent of these occurred on BTA14 and was identified in ∼23% of the sampled population. The ROH length characteristics furthermore pointed towards more ancient inbreeding, reflecting known historic bottleneck events.

For the second and main object preliminary results were generated to understand the necessary dynamics, in terms of size and composition, of an appropriate sub-population to use as a reference for estimation of haplotypes to be imputed from. Initial results indicated that a larger reference population would improve imputation accuracy. For example, it was observed that a 4% increase in imputation accuracy could achieved when the ratio of reference:test population was 90:10 versus 75:25; imputation accuracy improved from 0.981 (range: 0.895-0.997) to 0.985 (range: 0.905-0.996) when the former versus the latter scenario was used. It was further observed that using a reference population consisting of animals with closer genetic relatedness to the test population would also improve imputation accuracy. A strong correlation of 0.817 (P<0.001) was observed between the mean genetic relatedness of animals in the test population, with animals in the reference population, and their resulting imputation accuracy.

This was supported by estimates showing mean imputation accuracy of 0.994 as opposed to 0.982 for animals that had both as opposed to no parents in the reference population. The influence of using different low-density SNP panels, consisting of varying density and SNP content, on more specifically animal-wise and SNP-wise imputation accuracy was then determined. Animal-wise imputation accuracy improved when the SNP density of the lower-density panel improved; correlation-based imputation accuracy ranged (minimum to maximum) from 0.625-0.990, 0.728-0.994, 0.830-0.996, 0.885-0.998 and 0.918-0.999 when 2 500, 5 000, 10 000, 20 000 and 50 000 SNPs when SNPs were randomly chosen. The variation between animals, as well as the degree of improvement in accuracy, became smaller with increasing SNP density. Improvements of 0.043 units were seen when SNPs were doubled from 2 500 to 5 000 SNPs, as opposed to an improvement 0f only 0.007 units when SNPs were (more than) doubled from 20 000 to 50 000 SNPs. Selection of SNPs based on both MAF and LD attributes proved to be the best selection strategy to maximize imputation accuracy and random selection produced the worst imputation accuracy. Mean imputation accuracy exceeding 97% (less than 3% errors) could be achieved by using only 5 000 SNPs when this method of selection was used; using other methods of selection this accuracy was only achieved when double the amount of SNPs (10 000) was used. In terms of SNP-wise imputation accuracy, accuracy estimates were lower for SNPs located on the chromosomal extremes and if the MAF of these SNPs was low. For chromosome 19, which was the chromosome with the worst mean imputation accuracy for most scenarios, SNPs located in the first (n=32), middle (n=42) and last (n=64) 1Mb of this chromosome, for example, had mean SNP-wise correlation-based accuracy measures of 0.640, 0.810 and 0.577. The difference in SNP-wise imputation accuracy moreover was 0.071 between SNPs in the highest (0.4<MAF≤0.5) and lowest MAF bins (0.01<MAF≤0.1); imputation accuracy was better for SNPs with higher MAF.

Results generated to achieve the final aim of this study are still preliminary and in the process of being analyzed. Preliminary results, however, shows strong correlations between conventionally-estimated EBVs and GEBVs, with the inclusion of genomic information being advantageous to breeding value estimation. The difference in GEBV accuracies estimated from true- versus imputed genotypes was small thus far, depending on the per animal imputation accuracy; the discrepancy is expected to be larger for animals with lower mean imputation accuracy.

Conclusion

The variation observed in genomic characteristics such as MAF and LD conformed to expectations and supported previous research suggesting that the SA Drakensberger is a composite breed with an admixed genome and heterogenous genomic architecture. This variation across the genome allowed variation in imputation accuracy between different chromosomes and genomic regions within chromosomes to be pre-empted. Genotype imputation is a valid genomic strategy for the SA Drakensberger breed and this study concluded that a genotyping panel consisting approximately 10 000 SNPs would suffice in achieving less than 3% imputation errors. Results presented further suggests that if such a panel were to be designed, that the SNPs considered for inclusion would have to be selected based on selection criteria, such as MAF and LD, specific to the SA Drakensberger breed. Considering that no Sanga-specific genotyping panel currently exists, it would be recommended that these SNPs be chosen from re-sequencing efforts, i.e. from a pool of SNPs that are identified as specific to the breed, and not necessarily from a pool of SNPs that are available on taurine- and/or indicine-derived genotyping platforms. The reason for this is that low MAF, because of ascertainment bias, was the most influential factor affecting  achievable imputation accuracy and therefore poses a concern. This study showed that it will be a valid strategy to integrate genotype imputation routinely into future genomic evaluation pipelines for the SA Drakensberger breed as imputation errors are expected to have a negligible effect on resulting GEBV accuracies. Finally, the inferences made from this study may be transferable to other Sanga breeds and may provide guidelines for consideration in future genomic endeavours for these breeds.

Popular Article

Genotype imputation as a genomic strategy for the South African Drakensberger beef breed by SF Lashmar, C Visser and FC Muchadeyi

The Drakensberger is a medium-framed breed of cattle with a sleek, black coat. It is believed to be one of South Africa’s oldest Sanga breeds and was developed from an ancestral population of cattle that was first sighted in 1659 in the Bredasdorp area of the Western Cape province. These cattle ancestors, also described as black in colour, belonged to native tribes and were crossbred with Dutch cattle of the Groningen breed, which were imported by European settlers in the 1700s. By this introduction of European Bos Taurus genetics, the development of the SA Drakensberger was initiated. The modern SA Drakensberger, as it is presently known, was however only recognized in 1947 when the SA Drakensberger Breeders’ Society was established. The breed therefore underwent a process of development that spanned centuries, whereby it withstood many harsh challenges in its history and this has led to the hardy breed it is today. Nicknamed the “profit breed”, the Drakensberger is both adapted and highly productive within SA’s beef producing environment and has a long history of diligent performance recording. In fact, it was the first breed to receive estimated breeding values (EBVs) using best linear unbiased prediction (BLUP) methodology, as performance testing was made compulsory to all breeders since 1980. Participation by Drakensberger breeders in SA Stud Book’s Logix Beef performance recording scheme is still at 100% today (SA Stud Book, 2017) and extensive pedigree records are available. Considering all of this, there has recently been interest in further enriching breed improvement strategies for the SA Drakensberger with genetic information in the form of genomic selection.

To implement genomic selection can significantly improve the efficiency of selection processes, and hence accelerate genetic progress, for the SA Drakensberger breed. This selection strategy, however, requires large numbers of animals to be “tested”, referred to as “genotyped”, for a high density of single nucleotide polymorphism markers (SNPs) in order to make reliable scientific deductions and to produce accurate genomic estimated breeding values (GEBVs) for farmers or breeders. From experience, international researchers have suggested 1 000 animals to be included in a training- or reference population to deduce the prediction equations that will be used in calculating GEBVs for selection candidates. Generating the amount of data to fulfill the number of genotyped animals necessary in the training population alone can become unfeasibly expensive, especially in developing countries, considering that the cost of genotyping an animal for about 150 000 SNPs is currently approximated at ZAR200 per animal. The cost of genotyping can, however, be alleviated by genotyping animals with SNP chips containing lower numbers of SNPs and “imputing” to higher density.

In statistical terms, imputation refers to the process of replacing missing data with substituted values. In the context of genomics, genotype imputation refers to a method of predicting SNP genotypes for SNPs that are either missing or were not physically genotyped. The genotypes are predicted based on patterns observed from a more complete data set of SNPs that are available for a group of animals that are representative of a specific breed. Consider for example that we have a young animal tested for 10 000 markers (which would be referred to as a “low-density SNP panel”) and the parents of this animal are tested for 100 000 markers (which would be referred to as a “high-density SNP panel”). Given the genetic relationship between the parents and the offspring, and the fact that these animals share large parts of the DNA, we can “impute” or infer the “missing” 90 000 markers for the young animal by making certain statistical assumptions using the principles of genetics. On a larger scale: if a “reference” population (consisting of older, high-impact animals with many offspring in the national herd) is genotyped for a high density of genetic markers (let’s say 150 000 SNPs) and a “test” population (younger, commercial animals in the national herd) is genotyped for a smaller subset of these SNPs (let’s say 50 000 SNPs), the 150 000-SNP genotype profile can be imputed for the “test” animals. The prerequisite is, however, that the animals in the reference- and test populations need to be related in some way, in other words they need to share underlying genetic patterns. These shared patterns can be used to fill in the gaps in SNP information. The imputed SNPs i.e. the 100 000 “missing” SNPs not included on the lower density panel, can however only be used in downstream application such as genomic selection if they were accurately imputed or assigned otherwise inaccurate scientific deductions will be made.

Imputation is now almost routinely included in genomic evaluation processes abroad because this methodology has been optimized, through trial-and-error and studying the factors influencing “imputability” of SNPs, for the most popular international breed. To be able to make use of this methodology within the South African beef industry, and more specifically for local breeds, requires a process of validation and this has not yet been performed for breeds such as the SA Drakensberger. The aim of the study was therefore to comprehensively evaluate genotype imputation for the SA Drakensberger breed so that it can be routinely applied in a GS pipeline.

The first step in the process of validation was to investigate the genomic characteristics of the breed. The genomic characteristics of SNPs have previously been shown to have an influence on the accuracy with which genotypes can be imputed. The genome of each animal is subdivided into different structures, called chromosomes, and on each of these chromosomes differences may furthermore exist between different DNA segments depending on the origin of these segments i.e. from which animal in the pedigree that part of DNA was inherited. As a result of the history of the SA Drakensberger, the genomes of animals belonging to this breed are expected to be composite i.e. containing genomic segments from both Bos taurus and Bos indicus. Certain parameters can provide more information on the SNPs within each of these segments and these include the minor allele frequency (MAF) and linkage disequilibrium (LD). The MAF gives an indication of the value of a specific SNP to the breed in question; if the MAF is high, it is an indication that both alleles of the SNP are present amongst the animals in the breed i.e. the SNP is informative. The LD provides an indication of the relationship between adjacent SNPs; if SNPs are in high LD, a “block” of SNPs can be inherited together and animals share larger parts of the genome with one another. This improves the ability of SNPs in these regions to be imputed. The software, Plink, was used to quantify these parameters on a per chromosome basis. Results showed that there was variation in these genomic characteristics between different chromosomes and this led us to expect differences in imputation accuracy between chromosomes.

The logical next step was to calculate the actual achievable imputation accuracy. The accuracy of imputation was calculated for imputation from several custom-derived low-density panels. To achieve this objective, different sets of SNPs were extracted from the SNP data available (150K SNP data) to mimic possible lower-density SNP panels. Panels containing 2 500, 5 000, 10 000, 20 000 and 50 000 SNPs were tested. The choice of SNPs to be included on each of these panels were based on certain SNP selection strategies i.e. different criteria were used to select the SNPs. The different strategies of selection included 1) selecting SNPs randomly, 2) selecting SNPs so that they were approximately evenly spaced, 3) selecting only SNPs with the highest MAF and 4) selecting SNPs based on a score combining its MAF and relationship to neighbouring SNPs (LD). Imputation was done using a software called FImpute and our findings suggested that a low-density SNP panel consisting of approximately 10 000 SNPs that were selected based on their MAF and LD information will be optimal. Using such a panel resulted in less than 3% imputation errors.

The final step was to determine the influence of mistakenly imputed SNPs on the accuracy of GEBVs and hence on genomic selection. The “single-step” approach to GS was tested using software called Mix99. Breeding values were calculated using 1) only pedigree information (traditional), 2) using true genotypic data (GEBV) and 3) using imputed genotypic data (imputed GEBV). These different breeding values were compared to determine whether imputation accuracy had an effect. Our preliminary findings suggest that the inclusion of genomic data is advantageous and that there is a minimal effect on GEBV accuracy estimates if imputation accuracy was good.

To conclude, results from this study indicated that imputation is a valid genomic strategy towards cost-effectively implementing GS for an indigenous breed such as the SA Drakensberger despite the uniqueness and complexity of its genome. The outcomes of this study may moreover be transferable to other Sanga breeds and may provide a set of guidelines for genomic studies requiring imputation in the future. Even though this study has shown that a more affordable lower-density panel can be developed from choosing SNPs with high MAF in indigenous breeds from currently available genotyping platforms, it would be invaluable for future genomic endeavours to develop a Sanga-specific panel using breed-specific SNPs identified from re-sequencing efforts.

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

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

Modeling veld production using MODIS LAI – Phase 3

Modeling the net primary production of arid and semi-arid rangelands in southern Africa using MODIS LAI and FPAR products – Phase 3

Industry Sector: Cattle and Small Stock

Research Focus Area: Sustainable Natural Resource utilisation

Research Institute: University of Pretoria

Year of completion : 2019

Researcher: Anthony R. Palmer

The Research Team

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

Aims of the Project

  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

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.

This project has continued upon earlier, RMRD-SA funded projects that evaluate the using of earth observation (remote sensing) to model net primary production in South African grazing systems. The final results of this research are included in several research papers, students completions (PhD and BSc (Hons)), as well as a popular article. An Android application (Smartphone only) has been developed to determine the grazing capacity from the Google Earth Engine database of Landsat and MODIS imagery. This application is in the process of being tested in on-farm situations and is available to individual smartphones and tablets onto which the application can be installed. A further extension of the app development is an MSc project at Stellenbosch University that has prepared a new map of the fractional cover of grass, trees, shrubs and bare soil across South Africa. There has been one scientific paper published on the project since the last report, and two conference proceedings. A mini thesis (Geo-informatics Hons) describes how the application works. This application has also been made available in the public domain in the Google Earth Engine environment: https://liezlvermeuln.users.earthengine.app/view/spacegrazer

The objective of this phase of the project was to further validate the production estimates being made using MODIS LAI and fPAR, and to develop an Android-enabled application that can convert these estimates into grazing capacity model that could be used by farmers.

Results

Aim 1  All MODIS LAI and fPAR data are now available via the Google Earth Engine (GEE) interface. It is no longer necessary to download and archive these data from the NASA Distributed Archive. A large number of Java scripts have been written to extract data for livestock farmers throughout the Eastern Cape from the GEE user interface. Ms T Zondani has been appointed on the project and has been trained to extract data from GEE. Through GEE, data acquisition has been extended to other MODIS products, including the enhanced vegetation index (EVI), net primary production (NPP), gross primary production (GPP) and evapotranspiration (MOD16). Water use efficiency maps (WUE) have been prepared for all the years 2000-2017.

Aim 2  During this phase of the project we held workshops with the farmers in several rural villages to determine their response to the climate change predictions for that region, particularly where it is predicted to become hotter and drier. The project has established a world-class scientific installation on a livestock farm in the Smaldeel. This part of the project has seen the establishment of two eddy covariance systems on a site that had experienced bush encroachment in the past 50 years (See attachment).  Each eddy covariance system measures the direction and amount of carbon and water that moves between the earth and the atmosphere, and is a major contribution to South Africa’s understanding of the dynamics of this exchange between the earth and the atmosphere. The installation provides the opportunity to explore the consequences of climate change on grassland and bush encroachment. The RMRD-SA contribution to this site has been the transport to and from the site.

Aim 3 Using data from an eddy covariance (EC) system in the Albany Thicket, the project assessed the C sequestration options for farmers in the thicket. Carbon sequestration rates for the thicket biome are in line with those predicted by Aucamp and Cowling and Mills (2013) of 0,13-0,15 kg C m yr-1. The EC system has been moved to the farm Endwell in the Adelaide District and the C sequestration benchmarks for this area, which is being invaded by Vachellia karroo, will be available during 2018-2019. The development of the grazing capacity of South Africa based on the NPP data from 2009 has been published in both the peer-reviewed (Meissner et al 2013) and popular media (Palmer 2013). Since 2014, we have tested the map against other estimates of carrying capacity.  This beta testing of this map showed that the estimates for grazing capacity were too high (50%) and this was most likely due to the high fraction of woody plants (trees and shrubs) in the Eastern Cape. The new MSc project to prepare a tree/shrub/grass/bare soil fractional cover map was therefore initiated. The climate change predictions for the West Coast (hotter and drier conditions) have been incorporated into workshops and grazing management recommendations for two rural communities.

For the east coast, the predictions are more promising, with an increase in rainfall predicted. The effect is already being experienced in this region, with an increase in grassiness and a general improvement in the net primary production being reported. In order to deal with this understanding and its implications for commercial livestock farmers, a new experimental site has been established at Endwell farm.

Aim 4.A BSc (Hons) project was completed using the relationship between Landsat NDVI and biomass production. The application accessed Landsat and MODIS databases via the Google Earth Engine portal (GEE). The student has registered for an MSc (Stellenbosch University). She developed an Android application called Land Suitability Index (LSI) using hybrid model technology. The application determines the geographic position of the farmer from the geo-location options on an Android smartphone. It uses GEE web-interface to collect data on the NDVI history of the specific site. This provides a long-term (19 year) summary of the photosynthetic performance of the site, and evaluates the current NDVI relative to the mean for the 18 years. This history is converted into the available biomass produced in the last 12 months. The farmer can then adjust his stocking rate based on the actual production. An improvement is the addition of proportion of vegetation that is grass, as this is the major one relevant to cattle and sheep. In order to achieve this, Ms Vermeulen, in her MSc, has developed and tested a new fractional cover map. The output is now available as a Google Earth Engine application called Spacegrazer.

https://liezlvermeuln.users.earthengine.app/view/spacegrazer

This application can be used by anyone to ascertain the grazing capacity of a site in southern Africa.

Ms Vermeulen conducted field surveys where she measured the fraction of grass, shrubs, trees and bare soil in pixel of a Sentinel scene. The results from this analysis will form part of her MSc thesis.

Conclusion

The project has made excellent progress since its inception in 2010. The has been exceptional growth in the understanding of the benefits and dis-advantages of using remote sensing to estimate net primary production. In commercial farmland, where farmers tend to leave standing biomass available for the dry season, the predictions of NPP provided by the MODIS products have been very useful, and can be used to predict the grazing available to the farmer. This certainty has been converted into two applications: 1) for an Android device and 2) on-line application in the Google Earth Engine environment. Both of these applications have been tested on several commercial livestock farms and on several game farms. Several farmers have been signed up to receive monthly predictions of the biomass available for their property. One of the big challenges when using remote sensing to predict production is the presence of woody species. This is being solved through a national map of fractional woody cover which has now been produced by the project through an MSc at Stellenbosch University. However, in communal rangelands, where most biomass is consumed as it is produced (the so-called continuously grazed systems), the MODIS products are not able to detect all of the net primary production. Fially, the project has also enabled us to establish, in collaboration with Rhodes University and the National Equipment Programme, two eddy covariance systems that measure the actual C sequestration and water use of  rangelands. This collaboration has resulted in the establishment of a world-class experimental facility on a commercial livestock farm. At this site we are computing the impact of woody encroachment on grass production and water use. This will feed into policy on how the state will deal with woody encroachment and its impact on the catchment water balance.

Popular Article

Using satellite imagery for climate smart adaptive planning of grazing in near real time by Weideman, CI and Palmer, AR 2019

Click on this link to download thea article which was published in the Wool Farmer Article LINK

Conclusions

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

Supplementation of ruminants on winter pastures

Supplementation of ruminants on winter pastures

Industry Sector: Cattle and Small Stock

Research focus area: Livestock production with global competitiveness

Research Institute: University of Pretoria

Researcher: Prof Willem.A. van Niekerk PhD (Agric) Animal Science

Research Team:

TitleInitialsSurnameHighest Qualification
ProfLourens. J.ErasmusPhD (Agric) Animal Science
DrA.Hassan
PhD (Agric) Animal Science
MrR.J.Coetzer
MSc (Agric) Animal Science
MrHMynhardtMSc (Agric) Animal Science

Final report approved: 2016

Aims of the project

  • To develop a cost-effective supplementation strategy for ruminants under low quality winter forage conditions
  • To maintain body weight during the wineter season by assessing different sources and levels of nutrients that enhances poor quality roughage utilisation
  • To investigate intake, fiber degradation and microbial protein production when various types and levels of nutrients are supplemented to ruminants kept at maintenance under extensive conditions

Executive Summary

A series of studies was conducted to evaluate differential energy and nitrogen (N) sources as supplemental feed to sheep grazing low quality winter grazing in the High veldt. Knowledge on supplementation under local conditions are limiting as the majority of supplementation studies are funded and performed in the more temperate areas. Results indicated that higher N and energy inclusion levels are necessary to optimize ruminant production under local conditions compared to temperate areas. In addition, the ratio of fermentable energy to available protein is an important parameter in optimizing supplementation programs. It is concluded that the supplementary recommendations from the current feeding tables does not describe the requirements and nutrient quality of the tropical grasses satisfactorily and as such, cannot be used to predict supplementation responses by the tropical forage fed ruminant.  del can be used for further sensitivity analyses and “what if” scenarios as well as a database to answer specific questions.

Popular

SUPPLEMENTATION OF SHEEP GRAZING LOW QUALITY GRASSES WITH UREA AND STARCH

BY:  *H. MYNHARDT, W. A. VAN NIEKERK AND L. J. ERASMUS, UNIVERSITY OF PRETORIA

Every year sheep might lose up to 30% of their summer body weight gain during the dry winter periods in the high veldt.  While these weight losses have an economic impact on its own, it also is associated with an increased susceptibility for diseases and parasitic infestations and decreased reproductive performances. It generally is considered that protein or non-protein nitrogen (NPN) supplementation is necessary to limit these weight losses during these periods. However, due to the type of grass found in the High veldt area of Southern Africa, data is limiting on the effects of supplementation of ruminants grazing these types of grasses (See box: Differences between C4 and C3 grasses). As such, supplementations recommendations derived from current feeding tables seldom satisfy the needs of the grazing ruminant in Southern Africa. Therefore, a series of studies was conducted at the University of Pretoria to determine and quantify the requirements of the ruminant grazing low quality Eragrostis curvula hay commonly found in the Southern Africa High veldt.

* References and correspondence can be obtained from the author: hermanmynhardt@yahoo.com


Box 1: Differences between C4 and C3 Grasses

The acronyms C3 and C4 refer to the first product of the photosynthetic processes in the respective grasses with the first product of photosynthesis in the C3 grass being phosphoglycerate (a 3 carbon structure) while for the C4 plant, the corresponding molecule is a 4 carbon molecule (oxaloacetate). C3 grasses are temperate grasses and are adapted to the temperate regions of the world where rainfall is more constant with maximum temperatures seldom topping 22 OC. In contrast, C4 grasses are more adapted to the subtropical and tropical climates with temperatures frequently topping 25oC during the growth period. These areas also are associated with seasonal droughts and the occasional frost. Due to these extremes in temperatures and seasonal droughts, C4 grasses contain more bundle sheath cells and less available nutrients compared to C3 grasses during all maturity stages. Ruminant production therefore in general is significantly lower in ruminants grazing C4 grasses compared to temperate C3 grasses, especially during the dormant stage of the grass where lignification of the C4 grasses reduces the availability of the nutrients even further. As such, supplementation requirements and responses differ between ruminants grazing these grasses. However, the majority of supplementation studies in the past have been conducted on C3 grasses as it is found more in the European countries where research funding is more available. As such, as more studies conducted on low quality C3 grasses are incorporated in the current feeding tables, supplementation requirements derived from these tables to the low quality tropical forage fed ruminant are not always accurate. As such, the need was established to conduct research through the financial support of the **RMRD-SA on the nutritional requirements of the low quality tropical forage fed ruminant in order to improve ruminant production in Southern Africa.


*RMRD -SA – Red Meat and Research Development, South Africa



Results and Discussion

Forage intake and digestibility was not influenced by either the level of urea or starch supplementation to the wethers. However, CP-balance, measured as CP intake – CP excretion in the faeces and urine, increased from 12.5 g CP/day in the LU wethers up to 70 g CP/day in the EHU wethers. Based on these observations, only the EHU treatment supplied sufficient protein to potentially satisfy the needs of the 50 kg wethers as they require 65 – 70 g CP for maintenance. These recommendations are significantly higher than the recommendations set in the current feeding standards, however, it is in alignment with the observations and recommendations set out by **Leng (1995) studying ruminants grazing tropical grasses in Australia.

Forage intake and digestibility was not influenced by either the level of urea or starch supplementation to the wethers. However, CP-balance, measured as CP intake – CP excretion in the faeces and urine, increased from 12.5 g CP/day in the LU wethers up to 70 g CP/day in the EHU wethers. Based on these observations, only the EHU treatment supplied sufficient protein to potentially satisfy the needs of the 50 kg wethers as they require 65 – 70 g CP for maintenance. These recommendations are significantly higher than the recommendations set in the current feeding standards, however, it is in alignment with the observations and recommendations set out by **Leng (1995) studying ruminants grazing tropical grasses in Australia.

HIGHER LEVELS OF PROTEIN AND ENERGY SUPPLEMENTATION IS NECCESARY TO OPTIMISE THE GRAZING RUMINANT IN THE S.A. HIGH VELDT DURING THE DRY WINTER MONTHS

An important parameter in ruminant nutrition is microbial protein synthesis (MPS) as it gives an indication of the efficiency of the rumen microbes. During the dry winter months, MPS generally decreases due to the lack of available nutrients in the roughages (Leng, 1990, 1995) which decreases the productivity of the animal which is experienced as weight loss by the farmer.  In this study, MPS increased almost 50% from 78 g MPS to 106 g MPS as the level of starch supplemented was increased from 200 (LS) to 280 (HS) g starch/day. This observation is in agreement with suggestions made by Leng, (1990; 1995) that energy is an important nutrient driving MPS in the tropical forage fed ruminant, provided that the protein requirements of the ruminant have been met. Interestingly, energy supplementation for the temperate forage fed ruminant is not always advocated as these grasses contain higher concentrations of water soluble carbohydrates compared to the tropical grass.

Based on the above results, higher levels of both protein and energy supplementation is necessary to optimise ruminant production during the dry winter months in the High Veldt. The question now was asked whether there was an “ideal” quantity of protein and energy to be supplemented to ruminants grazing low quality “tropical” forages.

Graph 1 is a schematic representation of MPS per unit CP intake (MNS: N intake) while Graph 2 represents the mean rumen ammonia nitrogen (RAN) concentration as influenced by the ratio of starch supplemented to available protein intake.

Graph 1

Urea supplementation across all three starch treatments affected the MPS: CP ratio similarly with the ratio decreasing from almost 3 to below 1 where the wethers were supplemented with the higher urea treatments (HU and EHU). It is important to note that alleviated MPS: CP levels (above 1) could be indicative of CP deficiency as more microbial protein was synthesized in the rumen compared to dietary CP intake. The additional CP required to produce the microbial protein under these circumstances is derived from body protein catabolism which in itself, is an inefficient process, resulting in an excessive body weight loss. As such, in this trial, it is suggested that the protein intake of the wethers supplemented with at least 26.4 g urea/day (HU) was sufficient to meet the requirements of the wethers.

Graph 2

An inverse relationship was observed between RAN and the ratio of starch: digestible protein intake (Graph 2) with RAN decreasing and plateau between 5 and 10 mg RAN/ dL rumen fluid as the ratio increased. An inflexion point was observed where RAN increased exponentially to levels as high as 25 and even 30 mg RAN/dL rumen fluid as the ratio decreased below 2: 1. This graph highlights the importance of supplementation of both rumen available energy sources (starch in this instance) as the supplementation of only RDP sources to the ruminant could lead to an increased risk of ammonia toxicity under these circumstances.

Conclusion

The results from this study suggest that the supplementation requirements of 50 kg wethers grazing low quality tropical forages (2.7% CP) differs to the current feeding standards as:

  • Higher levels of protein (urea supplementation up to 26.4 g urea per day per wether or 3% urea of the total DM intake) is necessary to optimise CP balance in the tropical forage ruminant.
  • Starch supplementation (up to 280 g/wether/day or almost 20% of the total DM intake) in addition to urea supplementation is necessary as tropical grasses not only are deficient in protein, but also in easy available energy.
  • For wethers grazing low quality tropical grasses, the ideal ratio of starch supplemented to digestible protein intake lies between 2 and 3: 1.
  • Additional research is necessary to study the effects of other energy sources and protein sources on rumen environment and the production parameters of the tropical forage fed ruminant as these sources might have different availabilities compared to urea and pure starch within the rumen.

The authors wish to thank the Red Meat Industry and Research Development (RMRD) for their financial support of this study.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project –
Willem van Niekerk on willem.vanniekerk@up.ac.za

Shiga toxin-producing Escherichia coli in beef

Prevalence and risk factors of Shiga toxin-producing Escherichia coli serotypes in beef at abattoirs and retail outlets in Gauteng

Industry Sector: Cattle and Small Stock

Research focus area: Red Meat Safety, Nutritional Value, Consumerism and Consumer Behaviour

Research Institute: Department of Production Animal Studies, University of Pretoria

Researcher: Prof. Peter Thompson Ph.D.

The Research Team

TitleInitialsSurnameQualification
ProfA.A.AdesiyunPh.D
DrE.MadorobaPh.D
DrL.O.OnyekaM.Sc

Year of completion : 2017

Aims of the project

  • To determine the prevalence O157 and non-O157 Shiga-toxin producing Escherichia coli (STEC) in beef abattoirs in Gauteng
  • To determine the prevalence O157 and non-O157 STEC in beef and beef products at retail outlets in Gauteng
  • To identify the important STEC serotypes present in beef and beef products in Gauteng
  • To identify risk factors for STEC contamination of carcasses and beef products in Gauteng

Executive Summary

Shiga toxin-producing Escherichia coli (STEC), particularly the O157 strains, are food-borne zoonotic pathogens of public health importance worldwide. Foods of cattle origin have been implicated in various outbreaks and epidemiological studies have revealed that cattle are major reservoirs of STEC. We conducted cross-sectional surveys from Nov 2015 to Nov 2016, to investigate the prevalence and molecular characteristics of O157 and non-O157 strains of STEC in beef and beef products in the Gauteng province of South Africa.

A total of 265 swab samples of beef carcasses from 12 abattoirs and 399 beef products from 31 retail outlets were screened for STEC using a multiplex PCR. The overall prevalence in abattoir samples was 37% (55/149) in summer and 34% (39/116) in winter. In beef products at retail outlets it was 20% (27/137) in autumn, 14% (18/130) in winter and 17% (22/132) in summer; the highest prevalence was detected in boerewors (35%) followed by mincemeat (21%). The predominant serotypes detected were O113 (19.4%) and O157 (14.9%) in beef products, and O113 (14%) from abattoirs.

Our results demonstrate that STEC is present in South African beef and beef products, and that this may pose a real food-borne disease threat. Further investigation of the epidemiology of the pathogen is required; it is proposed that this take the form of longitudinal studies to investigate the prevalence of shedding of STEC by cattle in the feedlot, following them through to the abattoir to determine factors associated with carcass contamination.

Additional Comments

As this is part of a PhD project, further molecular work is still to be done on the isolates, resulting in further planned publications. The samples also provided material for an MSc student (funded by UP research funds) to work on Salmonella contamination – these results will also be made available to RMRDSA once finalized.

Popular Article

Assessing the prevalence of shiga toxin-producing escherichia coli in beef at abattoirs and retail outlets in gauteng

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

Introduction

The production of safe and wholesome beef and beef-derived food products is the highest priority for the beef industry in South Africa. There are potential risks associated with the possible presence of harmful pathogens in the food production chain; however, clear guidelines and regulations have been implemented to reduce these risks to a minimum and ensure a safe product for consumers. Nevertheless it remains important to continually assess these risks and to ensure effective implementation of control measures.

Shiga toxin-producing Escherichia coli (STEC) are bacteria associated with food and waterborne diseases and have been recognized as causing public health problems worldwide. The WHO Foodborne Disease Burden Epidemiology Reference Group (FERG) reported that ‘Foodborne STEC’ caused more than 1 million illnesses and 128 deaths in 2010 (8).

Of the over 470 different serotypes of STEC detected in humans, the O157:H7 serotype is the most frequently associated with large food and water-borne outbreaks (7). However, non-O157 STEC have been increasingly isolated from cases of haemorrhagic colitis (severe GIT infection and bloody diarrhoea) and as well as some fatal kidney failure (HUS; haemolytic uraemic syndrome) cases.

Although the first report of the occurrence of HUS in South Africa dated as far back as 1968 (6), the causative agent was poorly understood at that time. The first clinically proven incidence of E. coli O157:H7 in South Africa was later linked with haemorrhagic colitis (3). The importance of the pathogen in South Africa and other southern African countries has, however, been highlighted by subsequent major outbreaks of bloody diarrhoea in which E. coli O157 strains were implicated (4). Of particular interest was a study in Gauteng province in 2011, in which 7.7% of children with diarrhoea were positive for E. coli O157 (5).

Epidemiological investigations have revealed that cattle are a major reservoir of STEC. Many outbreaks of E. coli O157:H7 have been associated with beef, in particular ground beef, and analyses of some cases have identified undercooked beef as a significant risk factor. However, the fact that E. coli-associated conditions in humans, such as HUS, are not as yet notifiable in South Africa may mean that the occurrence of STEC-associated disease in humans is under-reported. In addition, given the weight of evidence from elsewhere in the world, it is possible that contamination of beef products is also a risk factor in South Africa.

Research problem and objectives

There is a dearth of current information on the frequency of occurrence of O157 and non-O157 strains of STEC, and on the risk they pose to consumers of beef products, in South Africa. Hence, the objective of this study was to determine the prevalence and characteristics of O157 and non-O157 STEC strains in beef carcass and beef products sold at retail outlets in the Gauteng province of South Africa.

Materials and Methods

During a one-year period from Nov 2015 to Nov 2016, two independent cross-sectional surveys were carried out to determine the prevalence of STEC at abattoirs as well as at retail outlets where beef-based food products are sold.

Study 1: Twelve abattoirs (six high throughput and six low throughput) were selected and each was visited during summer and winter months for sample collection. Five animals were randomly selected in each abattoir and tagged for sample collection. Firstly, samples were collected by swabbing the skin of the perineal area immediately after slaughter. Thereafter, carcass swab samples were collected from different parts of the carcass at various stages during processing, including pre-evisceration, post-evisceration, post-washing and 24 hours post-chilling.

Beef carcass sampling and processing at the abattoir

Study 2: A total of 31 retail outlets including both large supermarket chains and smaller butcheries were randomly selected. Visits were made to each of these outlets during autumn, winter and summer months of 2016 for sample collection. Sampling of five types of popular beef products (brisket, boerewors, mince, cold meat, and biltong) was done at each outlet during each visit.

Each sample was analyzed for the presence of Shiga toxin-encoding genes (stx1and stx2) using conventional multiplex PCR. All samples positive for stx genes based on PCR were screened for the following O-serotypes: O26, O91, O103, O111, O113, O145 and O157 using a multiplex PCR assay.

Results and Discussion

Overall, the prevalence of STEC in beef carcass swabs collected from 12 red meat abattoirs across Gauteng province during summer and winter months was 35.5% (94/265). The highest prevalence (50%) was detected in perineal samples, which is hardly a surprise because cattle are an established reservoir of STEC; this may therefore reflect the prevalence of the pathogen in cattle arriving at abattoirs. Transportation stress is known to increase the shedding of enteric pathogens and could therefore be a contributing factor to the observed high prevalence in perineal samples. STEC was found in 39% of both pre-evisceration and post-evisceration carcasses, while washed carcasses and 24 hour chilled carcasses had a lower prevalence of 23% and 20% respectively. Therefore, although washing of carcasses at the abattoir removed much of the STEC contamination, the fact that the bacteria were still present on the surface of some chilled carcasses is of potential food safety significance, since cuts from these carcasses end up for sale in various forms at retail outlets.

Boerewors on display in a retail outlet

Of the 399 beef products sampled from 31 retail outlets, 67 (16.8%) were contaminated by STEC strains, an observation that is of food safety significance if such products were to be improperly cooked and consumed by highly susceptible individuals.

The highest prevalence of STEC was detected in boerewors (35%), followed by minced meat (21%). Ground beef ordinarily includes meat from many carcasses; consequently a few infected livestock could potentially contaminate a great quantity of ground beef. Biltong had the lowest prevalence of contamination (5%), while brisket and cold meat had 11% and 6% respectively. These results are in contrast to a previous study in South Africa, in 2009, involving biltong, cold meat and minced meat at retail outlets, which found that 2.8% of the samples were positive for E. coli O157 (1).

The prevalence of STEC in abattoir and retail outlet samples was somewhat higher during the summer months compared to the winter months. While many factors are believed to affect the prevalence of E. coli O157:H7, only season has been consistently shown to impact the shedding of this bacterium by cattle (2), and some previous studies have also observed a higher prevalence of shedding during the warmer months than the winter months.

The serotype analysis showed that O113 was the post prevalent serotype both on beef carcasses (14%) as well as in beef-based products (19%). This observation is of particular interest considering that O113 is an emerging serotype associated with human illness and sometimes with HUS in several countries including Spain, Belgium and Australia. Serotype O113 of STEC may therefore potentially be important in human diseases in South Africa and this requires further studies. Some of the other serotypes detected  have also previously been implicated in human diseases elsewhere in the world.

Unlike in abattoir samples where the prevalence of serotype O157 was very low (1%), a higher prevalence of 15% was detected in retail meat samples. This finding may be explained in part by the fact that the current study was cross-sectional by design (giving a “snapshot” at a particular point in time) and not a longitudinal study. Therefore serotype O157-contaminated beef products may have originated from abattoirs not sampled in the current study, and the prevalence may vary greatly between places and over time. There is also a possibility that it may partially also be a result of contamination from other sources at the retail outlet level.

Mince meat on display in a retail outlet

Conclusion

This study has shown that contamination of beef products with potentially harmful bacteria can occur during different processing stages. The low numbers of reported cases of food-associated disease in South Africa suggest that the risk to consumers is low; however, it is not known whether all cases are reported, or that all cases are correctly diagnosed. Therefore, further research is needed in order better understand the dynamics of foodborne pathogens in South Africa, to accurately assess the risk they pose, and to accurately inform control measures.

It is well known that efficient implementation of control measures during slaughter and processing procedures can greatly reduce meat surface microbial contamination and ensure the safety of the final product. The South African Meat Safety Act (2000) has addressed potential risk factors by adopting several internationally recognized preventive measures such as the Hazard Analysis Critical Control Point (HACCP) system and Good Manufacturing Practices (GMP) in order to promote safe meat for consumers. The application of GMP and HACCP principles during handling and processing of products, as well as the proper cooking of meat products before consumption, will effectively reduce the threat of food borne disease.

Acknowledgments

We thank Red Meat Research and Development South Africa (RMRD SA) for funding this research and the Gauteng Department of Agriculture and Rural Development for granting us access and assistance to carry out the cross-sectional survey at the abattoirs.

References

  1. Abong’o, B.O. and Momba, M.N., 2009. Prevalence and characterization of Escherichia coli O157: H7 isolates from meat and meat products sold in Amathole District, Eastern Cape Province of South Africa. Food Microbiology, 26(2), pp.173-176.
  2. Berry, E.D. and Wells, J.E., 2010. Escherichia coli O157: H7: recent advances in research on occurrence, transmission, and control in cattle and the production environment. Advances in Food and Nutrition Research, 60, pp.67-117.
  3. Browning, N.G., Botha, J.R., Sacho, H. and Moore, P.J., 1990. Escherichia coli O157: H7 haemorrhagic colitis. Report of the first South African case. South African Journal of Surgery, 28(1), pp.28-29.
  4. Effler, E., Isaäcson, M., Arntzen, L., Heenan, R., Canter, P., Barrett, T., Lee, L., Mambo, C., Levine, W., Zaidi, A. and Griffin, P.M., 2001. Factors contributing to the emergence of Escherichia coli O157 in Africa. Emerging Infectious Diseases, 7(5), p.812.
  5. Galane, P.M. and Le Roux, M., 2001. Molecular epidemiology of Escherichia coli isolated from young South African children with diarrhoeal diseases. Journal of Health, Population and Nutrition, 19(1), pp.31-38.
  6. Kiibel, P.J., 1968. The haemolytic-uraemia syndrome: a survey in Southern Africa. South African Medical Journal, 42(27), pp.692-698.
  7. Mora, A., Herrera, A., López, C., Dahbi, G., Mamani, R., Pita, J.M., Alonso, M.P., Llovo, J., Bernárdez, M.I., Blanco, J.E. and Blanco, M., 2011. Characteristics of the Shiga-toxin-producing enteroaggregative Escherichia coli O104: H4 German outbreak strain and of STEC strains isolated in Spain. International Microbiology, 14(3), pp.121-141.
  8. WHO [World Health Organization], 2015. WHO estimates of the global burden of foodborne diseases. Available at http://apps.who.int/iris/bitstream/10665/199350/1/9789241565165_eng.pdf

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Peter Thompson onpeter.thompson@up.ac.za

Evaluation of methane measuring techniques

Evaluation of different techniques to quantify methane emissions from South African livestock

Industry Sector: Cattle and Small Stock

Research focus area: Sustainable natural resource utilization

Research Institute: University of Pretoria

Researcher: Dr JL Linde du Toit

Title Initials Surname Highest Qualification
Prof WA van Niekerk PhD
Mr J van Wyngaard MSc
Mrs Z Goemans BSc(Agric)

Year of completion : 2018

Aims of the project

  • To measure methane emissions from livestock using the SF6 technique
  • To measure methane emission from livestock using the handheld laser methane detector (LMD) technique
  • To compare the results of the SF6 and the LMD techniques

Executive Summary

The need to verify greenhouse gas inventories demands the development of high throughput, economical yet accurate short-term measurement techniques, such as the laser methane detector (LMD). The aim of this project was to compare methane (CH4) emission rates as measured by the LMD to the sulphur hexafluoride tracer gas (SF6) technique from lactating dairy cows grazing pasture and to evaluate the practicality of the LMD measurement protocol under grazing conditions in the temperate coastal region of South Africa. Methane production was determined from six lactating Jersey cows on pasture using both techniques. The data generated by the LMD had a superior daily repeatability compared to the SF6 technique in the present study. A higher between-cow coefficient of variation (CV) (0.6 vs. 0.4) from the LMD compared to the SF6 technique was observed and this was ascribed to the sensitivity of the LMD to ambient conditions, animal movement while grazing and time of measurement. Methane production as measured by the SF6 technique (348 g/d) was higher (P<0.05) compared with the LMD technique (82.6 g/d).

Results from this study indicated that the LMD yielded approximately a 70% lower average daily CH4 production when compared to the SF6 techniques under the experimental conditions and daily CH4prediction models using the same animals and dry matter intakes. The lack of a third measuring technique and a standardized LMD methodology makes an accurate comparison between techniques and published data difficult. Both the SF6 and the LMD methods are viable methods to evaluate differences between mitigation options, for ranking of animals for selection purposes and to identify differences between dietary treatments. More research is needed before new techniques such as the LMD can be employed to determine absolute CH4 daily emissions which can be up scaled for inventory purposes.

Popular Article

Measuring methane from livestock

Recently, methane has been reported as the most abundant organic trace gas in the atmosphere. The radiative forcing of methane (CH4) is significantly higher than carbon dioxide (CO2) and it is estimated that CH4 has a global warming potential of 28 compared to CO2 with an atmospheric half-life of 12.4 years1. Enteric production of CH4 from ruminant livestock production systems is one of the major sources of agricultural greenhouse gas emissions globally. The relatively short atmospheric half-life of CH4 makes it the main target in livestock greenhouse gas mitigation protocols. Methane is also an important indicator of livestock productivity as it is associated with the conversion of feed into animal product i.e meat, milk or fibre.

Methane is produced in the rumen by methanogenic bacteria as a by-product of the fermentation process. Ruminal fermentation by rumen microbes result in the formation hydrogen (H2). Accumulation of excessive amounts of H2 in the rumen negatively affects the fermentation rate and growth of some microbial consortia which will reduce feed intake and production of animals. Methanogens therefore reduce carbon dioxide (CO2) to methane (CH4) and water (H20) thereby capturing available hydrogen and sustaining a favorable fermentation environment in the rumen2. Methane is exhaled or belched by the animal and accounts for the majority of emissions from ruminants. Methane also is produced in the large intestines of ruminants and is expelled in much smaller volumes compared to ruminal methane.

There are a variety of factors that affect CH4 production in ruminant animals, such as: the physical and chemical characteristics of the feed, the feeding level and schedule, the use of feed additives to promote production efficiency, and the activity and health of the animal1. Reductions in greenhouse gas emissions from livestock can be achieved through a range of CH4 mitigation strategies and more efficient livestock production systems through improved genetics and management.

Regardless of the mitigation strategy imposed, any reduction in enteric methane production must be quantified and for this to be achieved, accurate baseline emissions data are essential1. There are currently many techniques available to researchers to quantify CHemissions from livestock each with specific applications and challenges. These techniques vary from tracer and capsules for individual ruminants to whole farm systems. The development of baseline emission data can also be achieved through modeling, employing specific livestock and environmental activity data to estimate emissions. One of the main challenges of the majority of the measurement techniques is the lack of “real time” emissions from grazing ruminants under natural conditions. There is a need to develop measuring techniques and methods which can be standardized, is relatively low-cost and which can deliver reliable, feasible and repeatable assessments of emissions from grazing livestock.

The Sulphur hexafluoride (SF6) technique and spot sampling lasers are two of the techniques which shows promise to measure CHemission from grazing livestock. Researchers recently compared these two techniques in a pasture dairy production system in the Western Cape province of South Africa. It was found that the spot sampling with the laser could be useful for purposes such as selective animal breeding and comparing between different mitigation strategies, where the requirement is for relative emission data but not necessarily daily methane production. This trial highlighted the need to develop specific operational standards when employing methane quantification techniques under natural conditions in order to minimize variation and environmental interference when recording measurements.

Strategies to reduce greenhouse gas emissions and to increase farm productivity are likely to remain vague, random and possibly inefficient without the development of standardized, accurate and reliable CH4 measurement techniques1.

References

  1. Hill, J., McSweeney, C., Wight, A.G., Bishop-Hurley, G. and Kalantar-zadeh, K., 2016. Measuring methane production from ruminants. Trends in Biotechnology, Vol. 36 (1).
  2. Goopy, J., Chang, C. and Tomkins, N., 2016. A Comparison of Methodologies for Measuring Methane Emissions from Ruminants. In: Methods for Measuring Greenhouse Gas Balances and Evaluating Mitigation Options in Smallholder Agriculture. Editors: Todd S. Rosenstock, Mariana C. Rufi no Klaus Butterbach-Bahl, and Eva Wollenberg Meryl Richards. Springer International Publishing AG Switzerland.
Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Linde du Toit on linde.dutoit@up.ac.za

Methane and nitrous oxide from beef cattle manure

Direct manure methane and nitrous oxide emissions from a commercial beef feedlot in South Africa.

Industry Sector: Cattle and Small Stock

Research focus area: Sustainable natural resource utilization

Research Institute: University of Pretoria

Researcher: Dr JL Linde du Toit

Title Initials Surname Highest Qualification
Prof WA van Niekerk PhD
Miss K Lynch BSc(Agric)
Dr L Stevens PhD

Year of completion : 2017

Aims of the project

  • To identify the on-farm manure management system employed in a typical commercial beef feedlot in South Africa
  • To determine the methane emissions from manure in a commercial beef feedlot
  • To determine the nitrous oxide emissions from manure in a commercial beef feedlot

Executive Summary

Methane and nitrous oxide emission from pen surfaces in a commercial beef feedlot in South Africa

Global warming has become a worldwide concern in recent years.  The release of Greenhouse gasses (GHGs) have brought about rapidly changing climate conditions the world over, GHGs produced by various industry sectors are being investigated, researched and laws put in place to limit the production of GHGs wherever possible.  This includes the agricultural sector where extensive animal husbandry has increased the global carbon footprint and environmental pollution.

The International Panel of Climate Control (2006) has three Tiers that estimates methane (CH4) values, one of the main GHGs, from the use of default values to the use of more complicated models and experimental data to improve the accuracy of reporting.  This study investigated the contribution of manure GHGs emissions to livestock emissions focussing on intensive beef feedlot manure emissions. At present in South Africa, these values are only roughly estimated and are only available on an IPCC Tier 2 level.  Gaseous emissions from livestock waste, specifically beef cattle waste, are affected by a variety of external factors (atmospheric temperature, humidity, soil conditions, ration consumption and manure management practices) as well as internal factors, (ration digestibility, nutrient absorption and gut health).

The objective of the study was to achieve an understanding of the gaseous emissions, specifically methane (CH4) and nitrous oxide (N2O), from beef cattle feedlot pen surfaces from a commercial beef feedlot in South Africa as influenced by diet and season, using the closed chamber method of gas collection over the three prominent seasons experienced in Mpumalanga, South Africa.  The sampling of these various factors would lead to more accurate reporting, conforming to Tier 3 methodology results.

Random pen surface and emissions samples were taken from three pens per each feedlot ration fed. The results indicated significant differences in soil/manure characteristics, but little effect on ultimate CH4 and N2O emissions from the pen surface were found across treatments. Similar results were observed for the rangeland manure analysed and manure emissions from manure management practices at the feedlot.  Ambient temperature had a tendency (p<0.10) to affect CH4 and N2O emissions with higher temperatures resulting in higher emissions but. Overall soil and manure characteristics were affected by diet treatments and seasonal variation.  It must be noted that the lack of significant differences in gas emissions in the present study could have been due to sampling error. The gas emissions observed did show a trend between treatment levels and manure management practices within the feedlot, with the effluent dams and manure piles recording the highest CH4 emissions over each of the measured seasons.  The CH4 emissions varied between seasons within the feedlot, rangeland and manure management practices, but a level of significance was never observed even though manure characteristics observed significant differences.  The N2O emissions observed no set trend between areas measured on the feedlot.  The varying values, and negative values obtained may indicate sample error, or a general uptake of N by soil or microorganisms (Chantigny et al., 2007; Li et al., 2011).

In conclusion, it was found that manure characteristics are affected by season and diet characteristics which tended to have an effect on the rate of CH4 and N2O emissions from the manure, although not significantly.

Popular Article

Feedlot greenhouse gas study analyses emissions from pen surfaces and manure management

By CJL du Toit

Researchers from the University of Pretoria spend time at a commercial beef feedlot in Mpumalanga, South Africa to gain a better understanding of the greenhouse gas emissions originating from feedlots pen surfaces and manure.

Why are GHG emissions important to agriculture?

In agriculture and livestock production systems the three main greenhouse gases (GHG) include methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2).  Greenhouse gases impact the environment through their ability to trap heat which depends on their capacity to absorb and re-emit infrared radiation and the atmospheric life time of the different gasses.  Increasing atmospheric concentrations of GHG caused by fossil fuel combustion, industrial activities, land use change and agricultural activities contributes to changes in global temperatures and rainfall patterns which could impact directly on agricultural and livestock production.

Accurate estimation of GHG from anthropogenic sources is an increasing concern given the current and potential future reporting requirements for GHG emissions.  Research measuring GHG emission fluxes from feedlot surfaces and manure management has been very limited and this was the first research project on the topic under South African conditions.

Livestock manure and GHG emissions

Livestock manure is a source of nutrients and can be used for various purposes including soil amendments to improve fertility and productivity and the generation of green energy.  The main GHG emitted by manure are CH4 and N2O. Methane is produced during anaerobic decomposition of organic matter and N2O is emitted during nitrification and de-nitrification processes. Feedlot manure GHG emissions is influenced by a variety of factors including manure management (pile, anaerobic lagoon, rangeland), manure application (fertilization of rangeland, composting, bio-fermentation), temperature, aeration, moisture and the sources of nutrients in the manure which is in part caused feed inefficiencies. Emission is also influenced by animal factors in the feedlot such as stocking density which will influence the amount of manure deposited, feed intake and digestibility, animal type and age.

What did the researchers do?

Following an extensive review of current literature on GHG emission flux quantification from pasture, cropping and livestock enterprises it was decided to adopt closed static chambers as the measurement methodology. The aim of the study was to determine the effect of feedlot ration and season on the GHG emissions from manure at different sites within in a commercial feedlot operation. Chamber bases were randomly installed at each manure management site (rangeland, pen surface, manure piles and water catchment lagoons) during each season. The seasons were classified as wet and hot (WH), dry and cold (DC) and dry and hot (DH).

Gas samples were drawn from the chambers during mid-day at four time intervals within a 40 min measuring period and analysed using a gas chromatograph to determine average CH4 and N2O fluxes.

What did the researchers learn?

The method employed resulted in large variation within results sets mainly due to difficulty in sealing the chambers bases especially in the pen surfaces which were extremely compacted. The random placement of chambers also caused variation in results as some chambers had a higher manure density and factors such as soil and manure moisture varied between different locations within each pen.  The results yielded an average pen surface manure CH4 emission factor of 449 g/head/year which was 50% lower compared to feedlot manure emission factors previously calculated of 870 g/head/year using IPCC (2006) based models.  The N2O emissions measured from pen surfaces (10.95 g/head/year) were much lower than previously calculated or reported emission factors in literature varying from 54.8 to 2555 g N2O/ head/year.  Within the whole manure management system on the feedlot CH4 emissions from the water catchment dams were the highest followed by manure piles, feedlot pen surfaces and manure deposited on rangeland.  Although no statistical differences were found between the different seasons the wet and hot season produced the highest overall CH4 emissions and the dry and cold season produced the highest N2O emission across all manure management sites.

Managing GHG emissions from manure

The mitigation of GHG emissions from manure management in livestock operations is the topic of many research projects globally. Identified mitigation strategies are already being used by producers but new techniques and fine-tuning of existing options will lead to new and improved alternatives which can be tailored to country or regions specific production systems. The mitigation of GHG emissions from livestock production systems can be complicated as a strategy that reduces one emission may increase the other. Manure emissions can be reduced through two main actions namely input (providing of organic matter e.g. feeds) and manure management.  Overfeeding of nutrients such as nitrogen (N) will result in an increase in the amount of N excreted in manure which will lead to increased N2O emissions. To reduce GHG emission from manure producers will have to use feeding regimes that will maximise feed efficiency and reduce nutrient wastage. The management of on-farm manure can also be tailored to reduce GHG emissions and the effect of production systems on the environment.  The time of manure application to soil and rangeland is important to reduce emissions. Producers should avoid spreading manure when soil is are wet as this will increase CH4 emissions and attempt to reduce the storage time of manure on the farm. The use of technologies such as covered lagoons, digesters, aeration of manure and composting has all been employed to reduce CH4 emissions from manure.

On-going research

There is a need to develop standardised research methodology protocols, for both on-farm and laboratory experiments, which will make it possible to compare mitigation strategies and research results between different studies. Researchers are also attempting to understand the interplay of CH4 and N2O as it seems that the processes that produce these GHG are related.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Linde du Toit on linde.dutoit@up.ac.za

Chilling and electrical stimulation of beef carcasses

Effects of chilling and electrical stimulation on carcass and meat quality attributes of selected breeds of cattle with different carcass weights

Industry Sector: Cattle and Small Stock

Research Focus Area: Animal Products, Quality and Value-adding

Research Institute: University of Pretoria

Researcher: Prof Edward Webb

Title Initials Surname Highest Qualification
Mr Babatunde Agbeniga MSc
Dr P.E. Strydom PhD

Year of completion : 2018

Aims Of The Project

  • To compile a comprehensive literature review on current chilling and electrical stimulation guidelines
  • To compare chilling and electrical stimulation of selected cattle breeds of different carcass weights and to evaluate the effects of different chilling regimes and different stimulation procedures on carcass and meat quality attributes
  • To make recommendations to the meat industry on acceptable ways of chilling and stimulating carcasses in order to obtain the best quality carcasses and meat

Executive Summary

This research focused on acceptable ways of chilling and electrically stimulating beef carcasses in order to obtain the best quality meat, given the current use of growth enhancing molecules (beta-adrenergic agonists) and the current increase in carcasses size to curve the negative impact of escalating maize prices on the economics of intensive feed of beef cattle.

The literature survey suggest that low voltage electrical stimulation (LVES) is safer and more practical in South African abattoirs compared to high voltage electrical stimulation (HVES). The current research indicates that low voltage electrical stimulation has beneficial effects on meat quality of beef carcasses. Furthermore, early post mortem LVES is more beneficial compared to LVES after evisceration in terms of most meat quality attributes. Shorter duration LVES (30 sec.) was more beneficial compared to long duration LVES (60 sec.). Current chilling regimes of larger carcasses demonstrate that the effects of beta-agonist treatment on beef tenderness becomes negligible with increasing carcass size, provided that such carcasses are electrically stimulated early post mortem. Optimum carcass stimulation and chilling regimes were proposed for commercial beef abattoirs in South Africa.

OUTPUTS

Scientific publications (ISI peer reviewed)

  1. Agbeniga, B. & Webb, E.C. (2018). Influence of carcass weight on meat quality of commercial feedlot steers with similar feedlot, slaughter and post-mortem management, Food Research International, 105,793-800. (IF=3,086)
  2. Agbeniga, B. & Webb, E.C. (2018). Effects of timing and duration of low voltage electrical stimulation on selected meat quality characteristics of light and heavy bovine carcasses, Animal Production Science, (Accepted with minor changes).

Scientific conferences

  1.  B. Agbeniga, E.C. Webb, P.E. Strydom & L Frylinck, 2016. Effects of low voltage electrical stimulation and carcass size on meat tenderness and drip loss of beef carcasses treated with Zilmax®, 49th SASAS Congress, Cape Town, (Oral presentation).
  2. B. Agbeniga & E.C. Webb, 2015. Effects of duration of electrical stimulation and carcass weight on carcass pH, temperature profile and shear force of Zilmax treated beef carcasses, 48th SASAS congress, Zululand, (Oral Presentation).

Industry lectures

  1. Webb, E.C. (2016) Growth enhancers, residues and beef quality, Red Meat Abattoir Association Conference, Spier, Western Cape,
  2. Webb, E.C. (2016) Abattoir management and carcass and beef quality, Devon abattoir workshop, Protea Hotel, 22 July 2016.
  3. Webb, E.C. (2015). Factors that affect beef carcass and meat quality, North West RPO Koopmansfontein,  October 2015.
  1. Webb, E.C. (2015).Growth efficiency in feedlot cattle, Cattleman’s conference, South African Feedlot Association, March, Kiewietskroon.

Popular Article

Interactions between early and delayed electrical stimulation and carcass size on pH, temperature decline and instrumental shear force of meat samples from Zilmax treated cattle

Introduction

The time of application and duration of electrical stimulation (ES) on light and heavy carcasses from Zilmax treated animals, poses new challenges in the meat processing industry in South Africa. Owing to the use of Zilmax, larger carcasses are now being processed at abattoirs that were built to accommodate smaller carcasses. This poses new challenges in terms of optimization of conversion of muscle to meat using ES and appropriate chilling regime. In this study, the effects of early or delayed low voltage electrical stimulation (LVES) (110V) applied to light and heavy carcasses of Zilmax treated cattle were evaluated for pH and temperature decline, and the resultant effects on instrumental shear force. One hundred and forty-nine Zilmax treated cattle (mainly steers) were assigned to 10 different treatment groups according to the combination of their carcass weight (≤ 130 or ≥ 145kg side), time of stimulation (early stimulation-3 min post mortem [p.m.] or late stimulation-45 min p.m.), and the duration of stimulation (30 or 60 sec). Analysis revealed significantly (p < 0.05) faster pH decline and the lowest pH in carcasses stimulated before evisceration, at all times of measurement compared to carcasses stimulated late or non-stimulated controls. The time of ES application exerted the greatest influence on the pH profile while duration of stimulation showed minor influence. Heavy carcasses in the early stimulated groups had the lowest rigor- and ultimate pH. Regarding temperature decline, heavy carcasses had the slowest decline (p < 0.05) and the highest carcass temperatures at all times from 45 min to 24 hr p.m. Time of ES application and duration of ES did not affect carcass temperature. In terms of shear force, carcasses stimulated at 3 min p.m. had the lowest (p < 0.05) shear force at 3 and 14 days p.m. compared to carcasses stimulated at 45 min p.m. and controls respectively. Heavy carcass groups, stimulated early, with the lowest rigor and pHu, had the lowest shear force at 3 and 14 days p.m.

Effects of electrical stimulation and chilling on beef quality

Results of our recent study indicates that the time of application of electrical stimulation has an important influence on carcass pH and temperature profile, and in combination with carcass weight, has a large influence on the tenderness of beef. LVES provides a practical way to manipulate glycolysis in order to improve beef tenderness, but it appears that this treatment should be applied early post mortem in ordser to be efficient. Although there has been some suggestions to apply LVES later, the present results show that early post mortem application of LVES produced the lowest shear force, mainly due faster pH decline in combination with high initial carcass temperature.

Previous research suggested that at high muscle temperature combined with low pH, heat shortening may occur, leading to lower beef tenderness. Our results indicate that LVES treatment early post mortem passed through the heat shortening window (above 350C) within 2 hr p.m. when the pH was less than 6. This finding clearly demonstrates that the proteolytic activity was not exhausted by the low pH and elevated initial temperature in the early stimulated carcasses.

Carcass weight also played a part in improving tenderness in the early stimulated carcasses. In addition, Zilmax is known to reduce tenderness in meat but the application of ES could improve tenderness by the early activation of the calpain system. It is important to note that ES-treatment improve but do not completely overcome the negative effects of Zilmax on tenderness. In this study, we found that the combination of early ES and carcass weight significantly lowered the shear force in the heavy carcass groups. Research by Webb and Morris on Zilmax treated cattle also show that heavier carcasses from zilmax treated cattle produced more tender meat.

On the other hand, carcasses stimulated late and the controls had slower pH decline at all times of measurement, which was also reflected in lower tenderness scores at both day 3 and 14 post mortem.

Results on the duration of electrical stimulation indicates that 30 seconds or less (15 seconds) provide most beneficial results, which agrees with a number of other international studies.

Conclusion

It is concluded that the application of low voltage electrical stimulation early p.m (3 min p.m) brought about a significantly (p < 0.05) lower shear force in carcasses from Zilmax treated cattle compared to the ones stimulated late (45 min p.m) and the un-stimulated controls. Heavy carcasses (≥ 145kg) from the early stimulated groups had the lowest shear force values at 3 and 14 days p.m despite passing through the heat shortening window, which was due to lower initial pH and higher initial muscle temperature. More proteolytic activity in the heavy carcass groups was suspected to have contributed to the low shear force values and although, slightly higher (at 5.6 and 5.9 kg) when considering a threshold of 4.9 (Shorthose et al., 1986). It is acceptable, considering the fact that the animals were treated with Zilmax which is known to reduce tenderness.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Prof Edward Webb on edward.webb@up.ac.za