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

Crossbreeding Afrikaner, Bonsmara and Nguni cows

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

Industry Sector: Cattle and Small Stock

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

Research Institute: Agriculture Research Institute – Animal Production Institute

Researcher: Dr. M Scholtz

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

Year of completion : 2018

Aims Of The Project

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

Executive Summary

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

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

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

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

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

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

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

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

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

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

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

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

Popular Article

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

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

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

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

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

atheunissen@ncpg.gov.za (Corresponding author)

 Background and deliberations

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

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

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

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

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

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

Weight

Kg

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

Calf

Heifer (>12 months) Cow &

Calf

Heifer (>12 months) Cow &

Calf

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

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

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

  Sire Breed
 

Dam breed

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

(0.0)

144.2

(1.1%)

145.7

(2.1%)

151.2

(6.0%)

143.7

(0.7%)

B 142.0

(-0.4%)

C 124.9

(-12.4%)

H 149.3

(4.6%)

S 139.3

(-2.3%)

BA 148.9

(4.4%)

147.1

(3.1%)

155.6

(9.1%)

162.0

(13.6%)

160.1

(12.3%)

CA 152.3

(6.7%)

155.5

(9.0%)

154.5

(8.3%)

157.1

(10.1%)

158.4

(11.0%)

HA 155.7

(9.2%)

170.1

(19.2%)

175.1

(22.7%)

161.2

(13.0%)

176.8

(23.9%)

SA 155.9

(9.3%)

156.6

(9.8%)

161.1

(12.9%)

163.8

(14.8%)

162.1

(13.6%)

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

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

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

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

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

where Y = cow efficiency.

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

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

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

Conclusions

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

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

Acknowledgement

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

References

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

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

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

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

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

Landscape genomics in South Africa

Genomic technologies for the improvement of South African beef cattle

Industry Sector: Cattle and Small Stock

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

Research Institute: Agriculture Research Institute – OVI

Researcher: Dr. Pranisha Omduth Soma

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

Year of completion : 2018

Aims Of The Project

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

Executive Summary

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

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

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

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

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

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

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

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

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

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

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

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

Popular Article

Genomic technology for South African Beef Cattle

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

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

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

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

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

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

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

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

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

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

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

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