**5.3 The application of genomics in South African beef and dairy cattle production sectors to narrow the gap between the developed and developing sectors**

In South Africa, the beef and dairy cattle industry had been developed based on the well-developed sector versus the developing sector. The developed sector was made up of the commercial cattle farmers and feedlot companies while the developing sector consisted of the smallholder farmers [33].

#### *A Global Overview of the Intensification of Beef and Dairy Cattle Production Systems DOI: http://dx.doi.org/10.5772/intechopen.106062*

Van Marle-Koster and Visser [33] reported that the South African government funded genomic programs were established in the beef and dairy cattle industries in 2015 and 2016. The aim was to set up technological advancement towards moving forward into the application of genomic selection (GS) and a technology driven commercial livestock sector. Blasco and Toro [37] outlined that the phenotyping of some important reproductive and productive traits such as fertility in dairy cows and carcass quality traits in beef cattle for use in genomic selection applications could be of great benefit since these had posed major challenges in the past. The aim of the previous researchers [33] was to bridge the gap in disseminating genetic materials and information to both the farmers in the developed sector and the smallholder farmers in the developing sector in the beef and dairy cattle industry. These could have gone a long way to help lead to an advancement in the application of genomics for sustainable long-term genetic advancement and progress.

South Africa had more than 30 registered beef breeds such as the locally developed Bonsmara composite breed, Nguni, Tuli, Brangus and Simbra breeds [38]. These researchers [38] mentioned that it was only from the locally developed SA Bonsmara breed that the recording of a number of traits such as fertility, growth rate and feed efficiency measuring traits were made. Van Marle-Koster *et al*. [38] stated that for most commonly-measured traits of economic importance, there had been the application of modern selection tools such as the use of estimated breeding value (EBV) by livestock producers. Also under beef production, intensive feedlot testing program results were made available for use in some beef breeds, with data generated for growth rate, feed efficiency and carcass quality measurement traits [38]. In South Africa, the most common exotic dairy cattle breeds were the Holstein and Jersey cattle breeds with average herd sizes of about 400 cow herds and automatic milking system and recording were most commonly used especially in the large dairy herds. Van Marle-Koster and Visser [33] explained that for the emerging and smallholder sectors, genetic tools such as EBVs could not be provided due to small number of animals, incomplete recordings for small number of traits, low percentage recordings and insufficient contemporary groups of animals of similar age groups.

#### **5.4 The application of genomics in beef and dairy cattle breeding in South Africa**

Several applications of genomics had become available for beef and dairy cattle farmers [33] in South Africa. Single nucleotide polymorphisms (SNP) arrays of genomics of cattle were widely used in routine genotyping for genomic selection in beef and dairy cattle. These provided added advantage information for using these genotypes for the detection and prediction of carriers of genetic defects [39]. Also the provision of beef and dairy cattle genotypic information could provide the potential for the identification of beneficial genes such as the celtic variant of the polled gene for homozygous polled animals [40].

Some research workers [33] reported that a number of test facilities were available in South Africa for carrying out diagnostic test in ruminants in South African laboratory as shown in **Table 1**. This information however could be useful for the developed commercial industry farmers in particular.

The application of DNA technology could thus serve as a tool for livestock breeders for detecting and removing or culling defective animals from their herds. These could also be used for solving some basic problems while carrying out genetic improvement in the breeding herds [33].


#### **Table 1.**

*Diagnostic tests available for ruminants in South African laboratory.*

The DNA-based percentage verification was however costly and was mainly employed or used in the developed livestock sector. The genomic technology application programs were started in 2015 for beef genomic program (BGP) and in 2016 for the dairy genomic program (DGP) (http://www.livestockgenomics.co.za). These were designed to be funded through the commercial livestock farm industries. Also in the South African livestock sector, DNA marker technology was employed for use under the indigenous farm animal resources conservation [33]. The DNA marker technology was found useful during livestock genetic diversity selection which involved crossbreeding, inbreeding and population structure ecotypes [33].
