Genomics for the Improvement of Productivity and Robustness of South African Goat Breeds

Abstract

South Africa is one of the major goat-producing countries with over 6 million goats, 63% of which are farmed under smallholder communal farming systems where poor nutrition, disease infestation, and harsh climatic conditions are common. The Boer, Kalahari Red, and Savanna breeds were developed in South Africa and have turned out to be regionally and internationally relevant. Adaptation and tolerance to local conditions are crucial for survival of these goat genetic resources in suboptimal conditions. The full genetic potential of veld goat populations is not yet fully unraveled. Complete mtDNA sequencing and diversity analysis revealed multiple maternal lineages in South African goat populations that were shared amongst the breeds and populations with absence of population sub-structuring. Median joining network analysis using different mtDNA genes suggests that South African populations have multiple maternal lineages that are shared with other global populations. Caprine SNP50K panel data analysis highlighted elevated levels of genetic diversity in South African indigenous goats compared to industrial breeds as well as the utility of the genome-wide SNP marker panels in population genetic studies. Landscape genomic analysis suggests a strong role of environmental factors in shaping the genetic diversity of South African indigenous goats. Selected loci responsible for the adaption of goat populations to local production systems may be targeted in breed improvement programs particularly under marginalized communal production systems. Successful sequencing and analysis of the Tankwa and other South African goat genomes could screen for potentially numerous genomic variants such as copy number variants. Community-based breeding programs would be the appropriate tool for breed improvement allowing sharing of production capital, pooling of resources and services and enabling joint processes of decision-making. Genomics could complement breed improvement efforts by providing pedigree estimates and can be useful in monitoring and control of inbreeding and genetic gain.