Addressing production challenges in goat production systems of South Africa: The genomics approach

• Characteristics and challenges to goat production in South Africa are discussed.
• Conventional genetic evaluations and organized breeding produced successful breeds.
• Untapped genetic variation is found in feral and non-descript village goat populations.
• Genomics can unravel the uncharacterized diversity for use in breed improvement.

Functional traits have become increasingly important for efficient breeding schemes in the goat industry due to rising costs of production relative to product prices and consumers demanding healthy and nutritious food in addition to abiding to animal welfare standards. The challenges facing South African and other developing countries’ goat industries is in the implementation of cost-effective production systems for high quality meat and milk which is safe to the consumer from communal farming regions riddled by many production challenges. Genetic improvement for economically important traits such as growth, reproduction, health and product quality is currently based on convectional estimated breeding values. These methods have been practiced for several decades for breeds benefiting from efficient breeding schemes. South Africa is one of the few countries in the world that have successfully developed high producing commercialised goat breeds some of which have been adopted in other regions. Genetic progress using conventional genetic evaluations is however lengthy and based on a few traits. Molecular and genomic tools are increasingly being used for the detection and mapping of genes of economic importance in goats. Attention is turning to the simultaneous identification of genes for production and functional traits using whole genome sequence and genome-wide SNP data. South Africa has a rich genetic pool of feral, commercial, and indigenous non-descript goat populations to select from. Preliminary studies using the Illumina Goat SNP60K bead chip have revealed high genetic diversity and uniqueness of the South African goat breeds. The unique genomes of the different breeds and populations are a potential source of genetic variation, which could be useful for genetic improvement programs. Next generation sequencing and genotyping technologies present opportunities for genomic breeding schemes in the near future. This paper reviews current challenges faced by the goat industry in South Africa and worldwide. The feasibility of using second-generation genomic tools to improve traits of economic importance in the goat industry is discussed.