Abstract
SummaryUganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.
Highlights
According to archaeo-zoological evidence, goats were among the first ungulates to be domesticated, about 10 000 years ago near the fertile crescent that spans from Eastern Anatolia to the Zagros Mountains in Northern Iran (Zeder & Hesse 2000; Naderi et al 2008)
After quality control procedures on the 53 347 single nucleotide polymorphism (SNP) included in the SNP chip, 7242 SNPs were excluded (Table 1), which resulted in 46 105 loci available for downstream analysis
The highest number of SNPs that showed a minor allele frequency (MAF) of less than 0.05 was found in Small East African (n = 7818), whereas Sebei showed the lowest number of SNPs excluded (n = 6826)
Summary
According to archaeo-zoological evidence, goats were among the first ungulates to be domesticated, about 10 000 years ago near the fertile crescent that spans from Eastern Anatolia to the Zagros Mountains in Northern Iran (Zeder & Hesse 2000; Naderi et al 2008). Raised in diverse production systems (Mason & Maule 1960; Nsubuga 1996; MAAIF & UBOS 2009). Besides these three indigenous breeds, several indistinct ecotypes of Ugandan indigenous goat breeds exist, including Karamojong and Sebei. Boer goats are widely used as a source of breeding stock to cross with the indigenous goats (Onzima et al 2014). The existence of the various breeds presents an enormous source of diversity in the current goat populations that needs to be characterized, conserved and utilized in a sustainable manner under the existing production systems. Genetic diversity in populations is important, as it provides the basis for natural as well as artificial selection (Qanbari & Simianer 2014)
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