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Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda’s indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda’s goat genetic resources.

In Uganda, beef production is mainly based on local cattle breeds like the Short Horn Zebu (SHZ) which graze unimproved natural pastures. Sole grazing on natural pastures cannot meet the annual nutrient requirements of SHZ due to seasonal variability in quantity and quality of the pastures resulting in delayed attainment of market slaughter weight. In order to meet the nutrient requirements of SHZ and hence to shorten the time to attain market weight, we evaluated the effect of providing ad libitum supplements of varying crude protein (CP) levels (90, 110 and 130 g CP kg−1 dry matter (DM)) on the performance and carcass characteristics of grazing SHZ bulls. Ninety-six SHZ (6 ± 2 months old) were allocated to one of four treatment diets including the control T1 (sole grazing), T2, T3 and T4 grazing plus a supplement containing 90, 110 and 130 g CP kg−1 DM, respectively. Crude protein of natural pastures ranged between 103.9 to 158.4 g kg−1DM. Dry matter intake (DMI) varied with month (P0.05) with level of CP in supplement. However, CP intake of animals increased with level of CP of the supplement offered. Final live weight and average daily weight gain (ADG) increased (P