Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker

Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (N_e), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current N_e of Gauteng was the lowest at 371 animals, while the historical N_e across populations suggests that the ancestor N_e has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (F_ROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high N_e and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.

Relationship between population genomic structure and growth profiles of South African goats under different production systems

Goats play a major role in poor marginalized communities of South Africa for food security and socio-economic purposes. Majority of the goats are raised in villages with poor infrastructure and resources, therefore facing challenges that affect growth performance which leads to low mature weights. Investigating growth profiles will shed light on growth performances and will aid in goat improvement and selection. This study investigated the growth profiles and genomic structure of SA indigenous breeds raised in different production systems to unravel the genetic potential of indigenous goat populations. Live weights and morphological body measurements were collected from a total of 83 kids representing the commercial meat-producing SA Boer (n = 14); the indigenous veld goats (IVG) of NC Skilder (n = 14), Mbuzi (n = 13), and Xhosa lob (n = 14) raised under intensive systems; and nondescript village goat populations (n = 14) raised in intensive and others (n = 14) raised in extensive production systems. The remaining 72 of 83 phenotyped goats were genotyped using the Illumina Caprine SNP50K BeadChip. The SA Boer had a higher weight (28.96 ± 0.30 kg) gain as compared to other populations. The Mbuzi population was the smallest (14.83 ± 0.33 kg), while the village goats raised in Pella Village were relatively smaller (17.55 ± 0.37 kg) than those raised on the research farm (19.55 ± 0.36 kg). The study concluded that both genetics and management systems can lead to improved growth performance in goat production. The outputs of this study can be used to identify suitable breeds and potential genotypes for optimal growth and establish optimal goat management systems suitable for communal farmers for improved productivity.