Genomics for the advancement of livestock production: A South African perspective

Abstract

Most of the growth of human populations worldwide will be in developing countries, including South Africa. Natural resources are under immense pressure and animal scientists are faced with the challenges for increased efficiency and long-term sustainability of livestock production. Since the completion of the Human Genome Project, animal genomes have been mapped with genomics, enabling new opportunities for application in farm animal species. The use of microsatellite markers has made significant contributions to the insight in genetic characterisation of indigenous and local developed breeds in most farm species in South Africa and Africa. The single nucleotide polymorphic (SNP) marker discovery and development of commercial SNP arrays made genomic selection possible and genomic enhanced breeding values (GEBVs) are used widely in the First World. In South Africa, genomic programmes for beef and dairy cattle were established in 2015 and 2016, with the focus on building training populations for genomic selection. The SA Bonsmara breed was the first to receive GEBV. The availability of hard-to-measure phenotypes is limited, and these are the traits that hold the most potential for genomic selection and answering to the challenges of methane (CH 4) emissions and higher efficiency. Genome editing, which involves zinc-finger nucleases (ZFNs), transcription-activators such as endonucleases (TALEN) and RNA-programmable genome editor (CRISPR/CAS9), includes the most recent technology for application in precision genetics. Welfare and ethical concerns will be an important consideration in the acceptability of genome editing to consumers. Applications that benefit the animals are more acceptable to the public. The use of genome editing to produce polled cattle is one of the first applications with a direct welfare impact as it nullifies the need for painful dehorning. In this paper, genomic technology is reviewed with the focus on the most recent research trends and commercial application of genomics towards the genetic improvement of livestock with specific reference to South Africa.

Strategies for Sustainable Use of Indigenous Cattle Genetic Resources in Southern Africa

“…The genetic diversity among South African indigenous cattle breeds has been assessed using DNA markers (i.e., microsatellites and single nucleotide polymorphism) [24]. Makina et al [20] reported that the average genetic distance was lowest among indigenous (i.e., Afrikaner, Nguni, and Drakensberger) and locally developed (i.e., Bonsmara) breeds, and greatest between indigenous and exotic cattle breeds (i.e., Angus and Holstein).…”

Domestic Free-Range Pig Genetic Resources in Southern Africa: Progress and Prospects

“…The well-established adaptations to prevailing environmental and management conditions exhibited by domestic free-range animal populations represent valuable genetic resources for improving breeds and the efficiency of animal production. Domestic free-range populations may add potential characteristic genetic variation, which could be valuable to producers in supplying new diversity for the improvement of commercial lines [16]. However, domestic free-range pigs were long regarded as unsuitable for intensive commercial breeding because of their slow growth and inadequate meat production [17].…”

“…Other issues include overarching constraints that are external to the production system, which include conflicts, globalization, population growth, changing consumer tastes, religious taboos, developments in science and technology, and climate change. These will obviously impact conservation and use of AnGR in some way [16].…”

“…Goals for smallholders include aesthetic (color and patterning), behavioral aspects (temperament, mothering ability, foraging behavior, herdability, and any other aspects that minimize labor on livestock), adaptability, and the ability to survive on low management levels [28]. Rege et al [16] highlight the need 'to improve, produce, deliver and sustain genotypes appropriate for the objectives of the target poor livestock keeper/producer'. This will obviously incorporate indigenous knowledge in the breeding programs.…”

“…This will obviously incorporate indigenous knowledge in the breeding programs. Several possible schemes have been proposed, including sire rotation or loan schemes, nucleus-based programs run by the public sector and linked to community-level multipliers, and other community-based programs where selection is done at the community level [16]. There is an opportunity to use recent advances in technology, especially assisted reproductive technologies and genomics, to quicken the process without a loss of diversity [5,29].…”