Slaughter conditions to optimise chevon meat quality

Determination of slaughter conditions to optimise chevon visual and eating quality

Industry Sector: Cattle and Small Stock

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

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Dr L Frylinck PhD

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

Year of completion : 2018

Aims of the project

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

Executive Summary

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

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

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

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

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

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

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

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

Popular Article

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

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

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

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

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

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

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

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

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

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

Genomic markers in beef tenderness

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

Industry Sector: Cattle and Small Stock

Research focus area: Livestock production with global competitiveness: Breeding, physiology and management

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Dr L Frylinck PhD

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

Year of completion : 2018

Aims of the project

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

Executive Summary

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

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

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

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

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

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

Popular Article

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

Basson, A

Inleiding

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

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

Die Proef

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

Vleis se Kwaliteitseienskappe

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

Genetika en Fisiologie

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

Resultate

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

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

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

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

Bespreking

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

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

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

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

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

Marker detection in beef cattle II

Marker detection in beef cattle Phase II

Industry Sector: Cattle and Small Stock

Research focus area: Livestock production with global competitiveness: Breeding, physiology and management

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Dr A Maiwashe PhD

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

Year of completion : 2018

Aims of the project

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

Executive Summary

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

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

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

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

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

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

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

Popular Article

Marker detection in beef cattle

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

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

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

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

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

Karoo Predator Project

Karoo Predator Project Management Survey

Industry Sector: Cattle and Small Stock

Research focus area: Predation management

Research Institute: University of Cape Town

Researcher: Beatrice Conradie

Title Initials Surname Highest Qualification
Robertson N Nattrass D Phil
Prof J Piesse PhD

Year of completion : 2018

Aims of the project

  • Conduct an extra wave of the panel survey
  • Study the productivity of the sheep performance system
  • Analyse the effectiveness of predator control
  • Work towards integrating the science and the management data

Executive Summary

The Karoo Predator Project was established in November 2011. Farm management data were collected in four waves (Nov 2012, Sept 2014, Oct 2015, Oct 2016). Analysis of this rich dataset is question-driven and is designed to learn as much as possible about the performance of the farming system. This work has been supported by two RMRDSA contracts (signed 12 November 2014 and 30 June 2016, Pretoria). This report covers all work conducted between January 2016 and July 2018. My main collaborators in this period were profs Nicoli Nattrass on human-wildlife conflict and Jenifer Piesse on farm productivity and farmer attitudes. Students and other colleagues were involved in specific papers.

Survey design and analytical approach

Wave 4 of the Karoo Management Survey was collected in November 2016 on the 2015 production season. This wave of the survey produced 55 useable responses which increased the number of observations in the panel dataset to 255. The three-wave dataset consisting of n = 200 observations was released for analysis in early 2016, and has been used since then to:

  • calculate a new estimate for predation losses for the Karoo
  • model culling effectiveness
  • estimate a stochastic frontier with inefficiency model which identifies opportunities for commercialisation
  • investigate the effect of grazing conditions on farm performance
  • model the structure of farmers’ risk perceptions
  • investigate the effect of information searching behaviour on farm performance

This list adds two outcomes to the original list of three analytical aims. Paper 3 is still under review at the South African Journal of Agricultural Extension, but was enthusiastically welcomed at the South African Society for Agricultural Extension’s June conference in East London and has since been shared with various producer and government stakeholder groups. Paper 4 is in the final review stage for special edition on the Karoo of the African Journal of Range and Forage Science.

The four-wave panel, released at the beginning of 2018, is currently being analysed by two honours students who are studying:

  • the stability of Karoo farmers’ risk perceptions, and
  • the effect of the 2016 drought on farm productivity

All papers in this series broadly share the same analytical strategy namely the quantitative analysis of questionnaire survey data. Methods depend on the question at hand and include descriptive statistics, principal component analysis, k-means clustering, OLS modelling, data envelopment analysis, and error components and technical efficiency effects stochastic frontier analysis.

A new estimate of predation losses for the Karoo

This analysis updates Van Niekerk’s estimate for the Karoo, which for the purpose of the study was defined as the Central Karoo, Cacadu, Pixley Ka Seme and Namakwa district municipalities.

According to Van Niekerk (2010) small stock farmers in the Karoo loses 13 thousand adult sheep, 393 thousand weaners and 517 thousand newborn lambs to predators every year. Since the latter figure is largely an impression, this category of potential losses was not considered in the Karoo Management Survey. Its estimates for predation losses in the Karoo is therefore much lower at 6700 adult sheep and 278 thousand weaner lambs. These figures represent a cost of approximately R278 thousand per year in current prices. When the same calculation is applied to both datasets, the predation figures for the Central Karoo converge on 5% (4.85% in 2008 and 4.7% for the period 2012-2014). This suggests that farmers were providing consistent estimates irrespective of the interview period or the timing of the survey.

A model of culling effectiveness

Models were specified to investigate the effect on livestock losses of culling predators. Farmers cull predators in response to livestock losses, and those who depend more on farming tend to cull more. Predator control however is probably counterproductive as culling is associated with greater subsequent livestock losses. This finding is robust to the inclusion of a set of socio-economic variables and farm characteristics. It is also consistent with ecological models which hypothesises that culling can create vacancies for dispersing juveniles to move into resulting in greater livestock losses later. The results of paired t-tests conducted across waves 1 and 3 of the panel revealed a great degree of churn in the use and perceived effectiveness of lethal and non-lethal methods which means that nobody has come up with a lasting solution yet. Given jackals’ ability to adapt to new control methods, a lasting solution probably does not exist even in principle. Much higher rates of poison use were reported in Wave 3, which is a concern because poison use is illegal, although it might simply reflect higher levels of disclosure rather than a change in practices. A model of the likelihood of using poison shows that poison is used by younger farmers and by people who experience large losses.  Lambing in pens close to the homestead did not matter. Another specification showed that farmers who believe that minor carnivores such as African wildcats, black eagles and crows were a problem too, were more likely to resort to poison, than farmers who were willing to accommodate this wildlife. This variable however lost statistical significance when socioeconomic controls were added to the model.

The key success factors in Karoo agriculture

To investigate the question of effective commercialisation, production data from commercial operations were used to benchmark farming in extensive grazing areas. The inputs in the technical efficiency effects model were stock sheep, labour, feed and animal remedies and fuel. The functional form was Cobb Douglas and the inefficiency model contained management experience, a dummy variable for a Grootfontein diploma and a dummy variable to indicate fulltime or parttime farming. The farm characteristics considered were  size, grazing conditions, a dummy variable to indicate flexibility and breed type.

The exercise revealed that every fifth commercial farmer in the sample is less than 50% efficient and therefore is as much in need of extension as any smallholder might be. Experience is an important determinant of performance and could be developed in the smallholder sector through appropriate vocational training. A commercial farmer needs at least eleven years of managerial experience to move from the bottom to the middle productivity cohort and a Grootfontein diploma adds eight percentage points to mean efficiency compared to any other configuration of education. Introducing a fiber component (wool, mohair) increases productivity by 13 percentage points. Sheep farming is amenable to smallholder production, because it can be done successfully on a part-time basis. The grazing index was significant but carried the incorrect sign. If all six farm and farmer characteristics identified in the model are set at the optimal levels a farm’s predicted level of productivity rises by 50%, which if incorporated in extension programs will substantially enhance the Black Farmers’ Commercialisation Programme’s chances of success.

The drought

The effect of grazing conditions on productivity was pursued further in stochastic frontier error components model. Results show that during the period 2012-2014, which was a good year followed by two normal seasons, the best farmers were able to maintain productivity at around 93%, while the bottom third producers suffered serious productivity declines. Several bottom-third producers dropped out of wool and mutton production even before the drought started, while many more are expected to have failed since due to the drought.

Risk perceptions

Waves 1 and 4 collected Likert scale data on farmers’ risk perceptions. Principal component analysis uncovered the structure of farmers’ risk perceptions. In round 1 the top threats were predators and rising input costs and the main components of farmers risk perceptions were institutional, market-related, rural safety and security and the environment. The environmental risk component combined drought and predators. OLS models explained individual risk scores with profitability, share of income from farming and key demographic variables. Profitability and income diversification lowers risk perceptions. More experience and education were generally risk mitigating too. Farm size and the amount of time spent the veld explained environmental risk perceptions.

A second round of risk  data, collected during a politically more turbulent and drier period, revealed stable risk perceptions. Four new sources of risk were added in round 2, including weather weirding (a technical term to describe perceived departures from typical conditions), politics, fracking and uranium mining and prospecting. On the longer list, farmers bundled together market risk with regulatory and political risk, which show that risk perceptions are rapidly updated as new threats emerge. Predators were dropped from environmental risk which now focusses on drought / climate change.

Productivity and information searching behaviour

Wave 1 productivity scores (Conradie and Piesse, 2015, Agrekon) were correlated to farmers information searching behaviour on the topics of rangeland management, animal husbandry and predator management. For information on rangeland management farmers still turn to the retired FSD extension agent who is a fellow farmer. For animal husbandry information they rely mainly on breeders and buyers and the representatives of input suppliers and for predator management Niel Viljoen in the preferred source. Farmers do not think that the government has any experience in this domain. A preference for private sources of information correspond to higher levels of productivity than the use of public sources.

POPULAR ARTICLE

To follow soon

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Beatrice Conradie on beatrice.conradie@uct.ac.za

Dairy ranching for beef and milk

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

Industry Sector: Cattle and Small Stock

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

Research Institute: Agricultural Research Council – Animal Production Institute

Researcher: Dr. Susanna Maria Grobler PhD

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

Year of completion : 2018

Aims of the project

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

Executive Summary

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

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

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

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

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

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

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

POPULAR ARTICLE

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

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

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

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

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

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

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

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

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

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

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

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 : 2018

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

Does short duration grazing work in grasslands?

Does short duration grazing improve livestock production, veld condition and climate resilience compared to other grazing systems in a mesic grassland of South Africa?

Industry Sector: Cattle and Small Stock

Research focus area: Sustainable natural resource utilization

Research Institute: Universtity of Cape Town

Researcher: Dr Heidi Hawkins

Research Team

Title Initials Surname Highest Qualification
Prof S Vetter PhD
A/Prof MD Cramer PhD
Prof V Muchenje PhD
Dr C Mapiye PhD
Mr AS Venter MSc
Ms N Mgwali BSc Hons

Year of Completion : 2018

Aims of the project

  • Overall we wish to test the alleged mechanisms by which short duration grazing (or Holistic Planned Grazing, HPG) “works” explicitly by looking at the underlying mechanisms at the fine scale and overall effects at the camp/farm scale and how these vary and interact with rainfall, temperature, time and specific camps. We wish to apply this understanding to inform efforts being undertaken by government and NGOs to generate sustainable and more commercial red meat production from communal rangelands and land redistribution farms in one of South Africa’s biodiversity ‘hot spots’.
  • At the scale of an experimental farm and experimental plots we test claims that high animal densities in HPG reduces selectivity during defoliation of key plant species leading to conservation of species composition (biodiversity), forage quantity and quality throughout the year
  • At the scale of the farm, plots and pot experiments we determine how grazing intensity (recovery periods /defoliation frequency x defoliation intensity) affects plant recovery.
  • At the scale of the farm and plot we test claims that trampling (from intense hoof action during HPG) results in increased incorporation of nutrients (litter, dung, urine) and water, resulting in increased soil organic matter, nutrients including carbon, microbial activity, soil water infiltration, and reduced compaction and erosion.
  • At the farm scale, we test claims that the increased forage quantity and quality HPG increases animal gain ha-1, meat quality and profit of marketable animals; and at the scale of the individual animal, that HPG results in improved average daily gain per animal, including sufficient nutrition for pregnancy, lactation and re-conception.
  • At the farm and animal scale, we test whether high animal densities alter animal behavior (walking, resting, grazing) and energy expenditure.
  • Also on the individual animal scale, we test whether HPG results in a reduced parasite load (specifically ticks) because of, e.g. rapid movement of animals between camps, and whether the stress of movement compromises disease resistance.

Executive Summary

It has been claimed that Holistic Management (HM) and specifically, Holistic Planned Grazing (HPG, hereafter holistic grazing), can reduce desertification and reverse climate change by using livestock as a tool. At the same time, high animal densities and stocking rates associated with holistic grazing are claimed to result in improved plant and animal production but with little evidence or suggested mechanisms for these changes. The project addressed these gaps in knowledge via a three-year trial and corral studies, fence-line contrasts of existing and long-term practitioners of holistic grazing in the grassland biome, and remote sensing over sub-Saharan Africa.

We found nuanced differences in forage utilization, plant selectivity by animals, litter production, as well as small differences in animal behaviour and more marked differences in forage quality and animal parasites between grazing approaches (continuous, season-long, four camp and holistic planned grazing) in the trial. Some of these differences depended on season, but in all cases the scale of these differences were not enough to affect overall plant or animal production. Thus, the season-long and four-camp approaches were more profitable than the holistic approach due to capital outlay ((fences ands water points for multiple camps, or herders to create virtual camps), with the break-even point for holistic grazing being two years after that for other approaches. Provisional results from a national survey of long-term working farms supported results from the three-year trial. The use of a corrals is associated with holistic grazing in communal livestock systems, and our work showed that if the starting condition of the rangeland was poor with bare ground cover above 12% then basal cover increased under corraling, i.e. at very high animal densities of more than 400 livestock units per hectare, but otherwise increased bare ground so that corraling as a tool may be useful but should be applied with caution. In a remote sensing study, we found that woody plant encroachment has increased by 8% over the last three decades over sub-Saharan Africa and that while this is largely driven by climate, fire and herbivory are important drivers so that judicious use of fire and livestock (possibly at high densities) could help reverse this trend, with implications for the global carbon balance and productivity.

Overall, if animal gain is the priority of a land owner, the additional labour and/or infrastructure associated with holistic grazing is not justified. However, holistic grazing may be useful for rangeland restoration or specific goals.

Useful applications of holistic grazing based on our data may be:

  1. Reduction of under-utilized plant standing biomass and/or creation of a litter layer;
  2. Reduction of external and internal parasite loads (from an already low infestation to slightly lower infestation in our data so the practical usefulness would have to be tested at high infestation rates);
  3. Increased forage quality in some seasons (from normal quality to slightly increased quality in our data);
  4. Possibly, to reduce woody plant encroachment (and runaway fires), especially if browsers are included.

Popular Article

Does holistic grazing improve livestock production, veld condition and climate resilience compared to other grazing systems?

by Heidi-Jayne Hawkins

Director of Research at Conservation South Africa and Honorary Research Associate at University of Cape Town; contacts hhawkins@conservation.org and heidi-jane.hawkins@uct.ac.za

Rangelands, a source of biodiversity and agricultural products, are under threat globally. It has been claimed by the Savory Institute that Holistic Management (HM) and specifically, Holistic Planned Grazing, can reduce desertification and reverse climate change by using livestock as a tool. At the same time, high animal densities and stocking rates associated with holistic grazing are claimed to result in improved plant and animal production but with little evidence or suggested mechanisms for these changes. A recent review of the literature found that holistic grazing has no impact on plant and animal production (Hawkins 2017). In general, any management approach that is adaptive can be expected to sustainably manage rangeland resources by considering both ecological processes and livelihoods. Holistic Management or the Holistic Management Framework (Savory and Butterfield, 2016) is such a framework. While the adaptive approach of HM is not contentious, the livestock management part of this framework has been the subject of debate since the 1980s. Holistic Planned Grazing (HPG; hereafter holistic grazing) describes an intensive, rotational, time-controlled approach much like short duration-, cell-, multi-paddock- and mob-grazing. In South Africa, it is commonly called high-density, short-duration stocking.

During holistic grazing, livestock are kept at high densities using fences or herders with the intention of mimicking free-moving herds of herbivores that are migrating or bunched by predators; and grazing rather than fire is generally favoured as a way of recycling soil nutrients. Our recent article (Venter et al 2017) discusses the great numbers, densities and diversity of herbivores that occurred in the past before mass extinctions and hunting associated with humans spreading over the earth, and it is indeed reasonable to think that higher densities or animals would be ecologically appropriate and that the current use of fire to manage rangelands could in part be replaced by herbivores including livestock. However, the claims made by Savory go beyond this and need testing. Considering the renewed debate and existing threats to our rangelands including grassland and savanna, we examined the evidence for claims and tested various possible mechanisms that could underly these claims ((increased production, nutrient cycling, plant utilization and reduced plant selectivity).

The project addressed these gaps in knowledge via a three-year trial and corral studies, fence-line contrasts of existing and long-term practitioners of holistic grazing in the grassland biome, and remote sensing over sub-Saharan Africa. The research was a collaboration between Conservation South Africa and academics including five researchers and five students from the University of Cape Town, Stellenbosch University and the University of Fort Hare.

The controlled study was conducted on sections of a private farm (30.351767°S, 29.043433°E near Cedarville Flats and 30.394363°S, 29.020521°E on slopes near Goedhoop), called Merino Walk within the Matatiele Local Municipality, Eastern Cape in the grassland biome. Each flats and slopes section was divided into holistic grazing, conventional four-camp rotation, and continuous season-long grazing treatments with the same overall HM management and stocking rate but different animal densities. A national survey of working holistic farms and their neighbours allowed us to broaden the scope of the work from the scale of a local trial to the national scale. Also, the survey allowed us to assess holistic farming over longer time periods than the three years farm trial, as well gain insights into real farms. The questionnaire can be found at https://www.surveymonkey.com/r/grazing_research_survey .

We found nuanced differences in forage utilization, plant selectivity by animals, litter production, as well as small differences in animal behaviour and more marked differences in forage quality and animal parasites between grazing approaches (continuous, season-long, four camp and holistic planned grazing) in the trial. Some of these differences depended on season, but in all cases the scale of these differences were not enough to affect overall plant or animal production and in winter animal production in the rotational treatments was relatively low. Provisional results from a national survey of long-term working farms supported results from the three-year trial.

The season-long and four-camp approaches were more profitable than the holistic approach due to capital outlay (fences ands water points for multiple camps, or herders to create virtual camps), with the break-even point for holistic grazing being two years after that for other approaches.

Looking closer at animal behaviour, there was no evidence that holistic grazing increases dung trampling, the number of steps taken or selectivity at the plant or patch scales. An interesting effect of holistic grazing was a reduction in tick infestation that is thought to be associated with the rapid movements of animals between the mobile camps, so that ticks do not have time to complete their life-cycles. Out of the three grazing treatments, tick counts were higher in the continuous herd compared to the holistic grazing and four-camp herd in spring and summer. In general, internal parasites were very low with faecal egg counts being highest in the hot-rainy season. Both tick and faecal egg counts were not at levels of concern for animal health regardless of treatment effects.

The use of a corrals is associated with holistic grazing in communal livestock systems, and our work showed that if the starting condition of the rangeland was poor with bare ground cover above 12% then basal cover increased under corraling, i.e. at very high animal densities of more than 400 livestock units per hectare, but otherwise increased bare ground increased, so corraling should be applied with caution.

In the remote sensing study, we found that woody plant encroachment has increased by 8% over the last three decades over sub-Saharan Africa and that while this is largely driven by climate, fire and herbivory are important drivers so that judicious use of fire and livestock (especially browsers, possibly at high densities) could help reverse this trend.

Implications

From our results in a mesic grassland:

  • Holistic grazing may be useful as a tool for specific purposes such as increasing the litter layer and reducing tick loads but does not increase production;
  • High-density grazing practices are less profitable than conventional season-long grazing or the four-camp approach;
  • Corrals at animal densities over 400 LSU ha-1 may be a useful disturbance regime for restoration of bare ground and increasing phosphorus concentrations for cropping but only on already disturbed ground;
  • Browser/grazer mix and fire may be useful tools managed to reduce woody plant (bush) encroachment (and runaway fires).

Information sources

Hawkins H-J. 2017. African Journal of Range and Forage Science 34: 65-75.

Savory A, Butterfield J. 2016. Holistic Management. A commonsense revolution to restore our environment (3rd edn). USA: Island Press. ISBN 9781610917445 (e-book).

Venter, ZS., H-J Hawkins, MD Cramer 2017.  Ecosphere 8 (10), http://dx.doi.org/10.1002/ecs2.1946

Venter ZS, Cramer MD, Hawkins H-J 2018. Nature Communications 9, 2272 http://dx.doi.org/10.1038/s41467-018-04616-8

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Heidi on heidi-jane.hawkins@uct.ac.za

Landscape genomics in South Africa

Genomic technologies for the improvement of South African beef cattle

Industry Sector: Cattle and Small Stock

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

Research Institute: Agriculture Research Institute – OVI

Researcher: Dr. Pranisha Omduth Soma

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

Year of completion : 2018

Aims Of The Project

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

Executive Summary

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

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

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

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

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

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

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

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

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

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

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

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

Popular Article

Genomic technology for South African Beef Cattle

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

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

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

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

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

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

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

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

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

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

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

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

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