Genetic diversity in the Afrikaner cattle breed
English: This study was a first attempt to use microsatellite markers to determine the genetic diversity in an indigenous cattle breed, namely the Afrikaner. It was also the first study to combine genetic markers and pedigree analysis to estimate the genetic variability within an indigenous cattle breed. The objectives of the study were to estimate genetic diversity and inbreeding levels within the breed and to utilize the results to preserve and ultimately improve the genetic resources offered by the breed. A total of 1214 stud animals (representing 28 herds) and 166 commercial animals (nine herds) from different geographical areas within and adjoining South Africa were included in this study. Animals were genotyped at the two major animal molecular laboratories in South Africa, with both using the same standardized 11 marker microsatellite set. Estimates of genetic diversity did not support the hypothesis of significant loss of genetic diversity in the Afrikaner breed. Heterozygosity estimates ranged from 0.737-0.456 within individual populations, with an overall heterozygosity estimate of 0.568 for the Afrikaner breed. Assignment methods (based on STRUCTURE software) revealed a real structure consisting of four genetic populations (K=4). No consistent pattern of significant differentiation between stud- and commercial herds could be identified. Pedigree information, based on a total of 244714 recorded animals from 1940 to 2011, were analysed to determine the mean level of inbreeding (F), effective population size (Ne), generation interval, effective number of founders (fe), effective number of ancestors (fa) and average relatedness (AR). The average inbreeding coefficient calculated was 1.83% and the effective population size computed using the increase in the individual rate of inbreeding was estimated at 167.54. A total of 84138 animals (34.4%) were inbred to some degree. The effective numbers of founders and ancestors were 288 and 226 respectively, with an average relatedness of 0.44% and with results confirming a total of six complete generations. The average generation interval for the whole population was calculated as 6.554 ± 3.883 years. It is concluded that a moderate to high degree of variation is still present within the Afrikaner cattle breed, despite the recent decline in numbers of this indigenous breed. Levels of inbreeding appear to be at acceptable and at manageable levels. The current study provided results than can be utilized by farmers and breeders’ society to conserve the Afrikaner and develop the breed to its full potential.
Afrikaans: Hierdie studie verteenwoordig ‘n eerste poging om die genetiese diversiteit in ŉ inheemse beesras, naamlik die Afrikaner, met mikrosatelliet merkers te bepaal. Dit is ook die eerste studie wat beide genetiese merkers en stamboomdata gekombineer het om die genetiese diversiteit van ŉ inheemse beesras te bepaal. Die doelstellings vir die studie was om die genetiese diversiteit en vlakke van inteling van die ras te bepaal en sodoende die resultate te gebruik om die ras te bewaar en uiteindelik die genetiese hulpbronne wat die ras bied te benut. In totaal is 1214 stoet diere (verteenwoordigend van 28 kuddes) en 166 kommersiële diere (nege kuddes) vanaf verskillende geografiese areas van binne en aangrensend aan Suid Afrika in die studie ingesluit. Stoetdiere is gegenotipeer by twee van die vernaamste diere molekulêre laboratoriums in Suid Afrika, wat albei dieselfde gestandardiseerde 11 mikrosatelliet merkerstel gebruik het. Beramings van die genetiese diversiteit het nie die hipotese ondersteun wat voorspel het dat daar beduidende verliese aan genetiese diversiteit in die Afrikaner ras was nie. Heterosigositeit waardes het gewissel tussen 0.737-0.456 binne individuele kuddes, met ‘n algehele heterosigositeit waarde van 0.568 vir die Afrikaner ras. Toewysings metodes (gebasseer op STRUCTURE sagteware) het ŉ werklike struktuur wat bestaan uit vier genetiese bevolkings (K=4) getoon. Geen konstante patroon van beduidende differensiasie tussen stoet- en kommersiële kuddes kon geïdentifiseer word nie. Stamboom inligting, gebaseer op ŉ totaal van 244714 aangetekende diere vanaf 1940 tot 2011, is geanaliseer om die gemiddelde vlak van inteling (F), effektiewe bevolkingsgrootte (Ne), generasie interval, effektiewe aantal stigters (fe), effektiewe aantal voorouers (fa) en die gemiddelde verwantskap (AR) te bepaal. Die berekende gemiddelde inteelkoëffisiënt was 1.83% en die effektiewe bevolkingsgrootte bereken deur gebruik te maak van die verhoging in die individuele tempo van inteling was 167.54. ŉ Totaal van 84138 diere (34.4%) was tot ŉ mate ingeteel. Die effektiewe aantal stigters en voorouers was 288 en 226 onderskeidelik, met ŉ gemiddelde verwantskap van 0.44%. Die resultate het ŉ totaal van ses volledige generasies bevestig. Die gemiddelde generasie interval vir die hele bevolking was bepaal as 6.554 ± 3.883 jaar. Dit is vasgestel dat ŉ matigde tot hoë vlak van genetiese variasie steeds teenwoordig is in die Afrikaner beesras, ten spyte van die onlangse verlaging in die aantal diere van dié inheemse ras. Die vlakke van inteling is ook op aanvaarbare en hanteerbare vlakke. Die huidige studie het resultate gelewer wat deur telers en telersgenootskap benut kan word om die Afrikaner te bewaar en die ras te ontwikkel tot sy volle potensiaal.