Phenotypic and genetic characterisation of the indigenous Tswana goat population in Botswana

Abstract

The aim of this study was to characterize indigenous Tswana goats in four agro-ecological regions of Botswana i.e. Southern, Central, Northwest and Ghanzi. The following specific objectives were set; description of existing goat production systems in Botswana, phenotypic and genetic characterisation of Tswana goats and investigation of population structure of indigenous and commercial goats using the Goat50K SNP panel. A survey was conducted in four agro-ecological regions to collect data on Tswana goats in smallholder farming systems and phenotypic measurements were recorded for 123 goats that included body weight (BW), body length (BL), heart girth (HG), height at withers (HW) and tail length (TL). Qualitative traits such as coat colour, horns and beard were also recorded. About 80% of the farmers kept goats for financial purposes. Goats in the Northwest region had significantly (P<0.05) higher HG values in all age groups compared to other regions. Goats in the Central (71.83±1.18) and Northwest (69.17±2.04) regions had significantly longer BL compared to the ones in the Southern (64.25±2.50) region at >48 months. For genetic characterisation, hair samples from 48 phenotyped animals of Central region were collected and genotyped with Illumina Goat50K SNP chip. Genomic diversity was high (0.423±0.03) with low inbreeding (FIS) (0.009±0.05). Additional genotypes which included Boer (n=24), Kalahari Red (n = 24) and Swazi (n=48) were included in the analysis to get a broader regional perspective. Genetic diversity, measured as expected heterozygosity was 0.390±0.01, 0.398±0.01 and 0.387±0.02 for Boer, Kalahari Red and Swazi goats, respectively. Inbreeding coefficient ranged from 0.014±0.06 in Boer, 0.012±0.07 in Kalahari Red to 0.011 ± 0.06 in Swazi goats. The populations clustered according to geographical origin. Linkage disequilibrium (LD) for shorter intervals (0-10 kb) ranged from 0.44 to 0.56. Effective population size at 13th generation was approximately 87 for Boer, 93 for Kalahari Red, 180 for Swazi and 266 for Tswana goats. The results indicate potential improvement of Tswana goat through within breed selection and structured crossbreeding that will assist in food security and sustainable utilization.