Most livestock production systems in low—and middle-income countries rely on crossbred cattle derived from exotic and indigenous genetics to harness the local adaptation traits of Indigenous breeds and the high milk yield potential of exotic dairy breeds. Most smallholder dairy systems in Africa are characterised by using poorly defined multi-generation genotypes of exotic and local breeds and managing fewer than ten dairy cows.

Despite the overall low productivity compared to intensive systems, these smallholder farms are responsible for up to about 85% of the total milk produced within the region. In particular, Rwanda benefits from national and non-governmental initiatives to promote farmer income and dairy productivity among smallholder households. Rwanda’s dairy sector largely depends on smallholder farmers using crossbred cattle, including local and exotic breeds.

A recent study by Oluyinka Opoola et al. evaluated the genetic makeup of 2,229 crossbred animals in Rwanda's dairy-producing regions. The results revealed a highly admixed cattle population with well-established, novel and lesser-known genes under selection. The breed composition in Rwanda was Holstein-Friesian (42%), Jersey Island (18%), non-Island Jersey (12%) and other/indigenous breeds [Ankole, N’dama, Gir, etc.] (28%). Crossbreeding patterns were similar across provinces, with slight regional variations due to climate and feed availability. The study also revealed a high average heterozygosity, which indicates good genetic diversity and low inbreeding levels, suggesting a healthy genetic structure.

This observed diversity offers the opportunity to decipher the presence and/or lack of genetic variations to inform short- and long-term breed improvement programmes for adaptation traits, disease resistance, heat tolerance, productivity and profitability of smallholder dairy systems in Rwanda.

While the study provides insights into the sustainable application of genomics for livestock adaptability to climate change and the availability of animal-based sourced foods, it also emphasises the need to monitor and maintain the diversity of locally adapted Indigenous cattle breeds in Rwanda, East Africa, and the tropics to prevent biodiversity losses.

This study was funded by Jersey Overseas Aid. Among the researchers of the study are Mizeck G. G. Chagunda, Raphael Mrode, and Appolinaire Djikeng, members of the African Animal Breeding Network (AABNet) - a pan-African initiative established to enhance livestock genetic improvement across the continent. Through its core pillars of (1) multi-country genetic evaluation, (2) professional development, (3) advocacy, awareness, and business development, and (4) collaboration, networking, and partnerships, AABNet seeks to drive the development and dissemination of improved livestock genetics and broader genetic improvement solutions in Africa.

The study is documented on Springer Nature’s BioMed Central (BMC) Genomic Data open access publisher and can be accessed here: https://bmcgenomdata.biomedcentral.com/articles/10.1186/s12863-025-01323-4.