Breeding objectives and trait prioritization in indigenous goat systems: insights from South African smallholders

Defining farmer-driven breeding objectives is essential for designing community-based breeding programs (CBBPs) that improve productivity and sustainability of indigenous goats. This study investigated herd structures, management practices, and trait preferences of 240 smallholder households keeping Xhosa goats across three agro-ecological zones (Savanna, Nama Karoo, and Grassland) in Eastern Cape Province, South Africa. Structured questionnaires were administered, and data analyzed using descriptive statistics, chi-square tests, ranking indices, and K-means cluster analysis. Results showed that goat ownership was predominantly male-headed (68%), with average herd sizes of 21.4 ± 5.7 goats. Breeding does comprised 54% of herds, while buck ownership was low (27%), raising concerns of inbreeding. The main reasons for keeping goats differed significantly across zones (χ² = 18.42, p = 0.016), with cultural uses ranked highest in Savanna, while meat and investment dominated in Nama Karoo and Grassland. Culling was primarily due to poor reproduction (31%), old age (26%), and disease (22%). Cluster analysis identified three typologies of goat keepers, traditional (41%), semi-modern (35%), and commercial-oriented (24%), that differed significantly in herd size (p < 0.01), mating control (p < 0.05), and trait prioritization. Trait ranking revealed that farmers prioritized fertility (Index = 0.241; Rank 1), maternal ability (0.192; Rank 2), and twinning ability (0.175; Rank 3) for does, while overall health (0.181; Rank 1), testes size (0.150; Rank 2), and reproductive soundness (0.156; Rank 1 in Ngqwara) were most important for bucks. Aesthetic traits such as coat colour (0.091–0.114) and horns (0.118) were consistently ranked lowest. This study demonstrates that farmers in communal systems emphasize reproductive, maternal, and adaptive traits over appearance or record-based criteria when selecting breeding stock. Aligning CBBPs with these farmer-defined priorities, while progressively integrating pedigree and performance data, is crucial for sustainable genetic improvement and resilience of indigenous goat populations in South Africa.