Sustainable utilization of farm animal genetic resources requires a comprehensive understanding of farmer breeding management and selection criteria. However, site-specific data for indigenous goats in the Ahferom district of Northern Ethiopia was lacking. Therefore, this study aimed to characterize the breeding objectives and selection practices of 147 smallholder goat farmers across midland and lowland agro-ecologies. A pretested semi-structured questionnaire was used to gather data. In addition, focus group discussions (FGDs) were held with eight to ten knowledgeable farmers and key informants. The collected data were analyzed using SPSS statistical software. The goat flock structure (Mean ± Standard Error of the Mean = SEM; 17.35 ± 0.17) was characterized by a high proportion of breeding does. Farmers exhibited a strong market-oriented focus, prioritizing income generation (Index = 0.39) and meat production (0.21) as primary breeding objectives. While most farmers (61.2%) maintained their own breeding bucks, mating remained largely uncontrolled (83.0%). Selection for the next generation was driven by productivity and morphological traits, with litter size (0.29) and body conformation (0.29) identified as the top criteria for does and bucks, respectively. Castration, practiced by over 93% of respondents, was strategically timed (typically at 1-2 years of age) to maximize market value through improved body condition. In the Ahferom district, goat breeding objectives are multi-functional but lean toward market-oriented traits. Hence, breed improvement programs must prioritize marketable body size and rapid growth rates, which are the top ranked selection criteria for bucks while focusing on mothering ability and litter size for does. Furthermore, the significantly (p < 0.05) larger flock sizes, and higher proportion of breeding does in the lowland compared to the midland suggest that improvement strategies should be tailored to the specific management scales and environmental pressures of these distinct agro-ecological zones.

The Tianshan Mountains, which host two native subspecies of western honeybees, represent the easternmost natural distribution limit of Apis mellifera. The managed Xinjiang black honeybee (XJ), introduced a century ago and designated as a Chinese National Animal Genetic Resource, has expanded rapidly under anthropogenic management. However, this expansion simultaneously threatens populations of native subspecies Apis mellifera sinisxinyuan and Apis mellifera pomonella. Herein, we performed the first whole-genome resequencing of the XJ population and analyzed whole-genome data from 19 XJ workers and 172 global A. mellifera samples to clarify the evolutionary history of XJ and evaluate its interactions with native bees. Population structure and phylogenomic analyses showed that XJ clustered within C lineage but formed a divergent clade distinct from other C lineage subspecies, with the closest affinity to Apis mellifera carnica (FST = 0.053). Despite higher inbreeding than other C lineage subspecies, XJ displayed comparatively higher genetic diversity (Θπ = 2.15 × 10-3) and heterozygosity (0.0028) than other C lineage populations (0.0015), although XJ's value falls within the global range of A. mellifera. This genetic pattern can be attributed to substantial introgression (~10%-15%) from the M lineage, specifically from the native A. m. sinisxinyuan. TreeMix and F-branch analysis identified significant gene flow from A. m. sinisxinyuan into the ancestral population of the XJ. Functional enrichment analysis suggested that genes within introgressed regions are involved in cold adaptation and foraging efficiency, and independent transcriptome validation confirmed differential expression of key candidate genes (e.g., LOC552291/MCM4) within these introgressed regions. Overall, our findings indicate that XJ represents an introduced population that has undergone regional adaptation, facilitated by the introgression of potentially adaptive alleles from native taxa. This case underscores the need for conservation strategies balancing management of economically valuable populations with protection of native lineages from genetic swamping and ecological competition.

Genetic variation within livestock populations underpins global food security, resilience, and the long-term sustainability of breeding programs. Despite its fundamental role, harmonized approaches for assessing and monitoring genetic variation across data sources remain limited. This review provides an integrated framework for assessing genetic variation in livestock using demographic, pedigree, and genomic data, developed by FAO experts and international collaborators. Demographic indicators offer essential insight into population size, sex ratio, and reproductive structure, while pedigree data allow detailed evaluation of genetic relatedness, inbreeding, and effective population size (N e ) over time. Genomic information now provides unprecedented accuracy in characterizing allelic variation, population structure with admixture, and the dynamics of inbreeding and drift. Each data source differs in availability, resolution, and interpretive limits; therefore, complementary use of demographic, pedigree, and genomic measures is recommended for effective monitoring and decision-making. This framework outlines the main properties, applications, and constraints of these approaches and provides guidance on selecting appropriate indicators for monitoring genetic variation within and among livestock populations. Its implementation supports the objectives of the Global Plan of Action for Animal Genetic Resources and the Kunming-Montreal Global Biodiversity Framework, contributing to evidence-based management of livestock diversity worldwide.

Freeze-dried (FD) somatic cells serve as a novel method for preserving animal genetic resources; however, the efficiency of cloned mice production from FD somatic cells remains low, owing to severe nuclear damage induced by the freeze-drying. In this study, we aimed to mitigate FD-induced damage by evaluating protectants that have been reported to exert protective effects during freeze-drying of microorganisms, and to identify those most effective for somatic cells. Results showed, that using Tris-EGTA as the basal medium for freeze-drying, together with monosodium glutamate (MSG) as a protective agent, significantly reduced DNA damage in FD somatic cells after injection into oocytes. Subsequent optimization of MSG concentration revealed that the addition of 3% MSG markedly increased the formation rate of premature chromosome condensation from 50.0% to 80.4% compared with the non-MSG condition. Moreover, the rate of normal chromosome segregation at the two-cell stage of cloned embryos increased from 0% to 20.0%. Furthermore, although no blastocysts were obtained in the absence of MSG, the addition of 3% MSG enabled the formation of morphologically good-quality blastocysts, albeit at a low frequency. These findings indicated that the addition of 3% MSG reduces DNA damage in FD somatic cells and improves the developmental competence of somatic cell nuclear transfer embryos, representing the first step toward the practical application of FD somatic cells as genetic resources.

Due to its high efficiency and safety, oocyte vitrification finds broad application in many fields of life sciences, such as clinical assisted reproduction and conservation of animal genetic resources. However, vitrification may cause cellular damage and reduce the quality of oocytes and their cumulus cells (CCs), which could be closely related to disorders in lipid metabolism. At present, the impact of vitrification upon the lipid profile of oocytes and CCs has not been systematically elucidated. In this study, we used porcine germinal vesicle cumulus-oocyte complexes (COCs) as a model to analyze their lipid characteristics after vitrification and in vitro maturation (IVM), utilizing untargeted lipid metabolomics. Our results showed that an overall count of 37 down-regulated and 8 up-regulated differential lipids was identified in the vitrified oocytes. Pathway analysis confirmed the enrichment in glycerophospholipid metabolism and fat digestion and absorption, etc. Combined with transcriptomic analysis, three enriched pathways were revealed, including the AMPK signaling pathway, metabolic pathways, and fatty acid elongation. On the other hand, a total of four down-regulated and eight up-regulated differential lipids were detected in the vitrified CCs. Pathway enrichment implicated autophagy, glycerophospholipid metabolism, etc. A joint analysis of metabolomic and transcriptomic data revealed four enrichment pathways, including cholesterol metabolism, fat digestion and absorption, regulation of lipolysis in adipocytes, and metabolic pathways. Notably, the supplementation of lysophosphatidylcholine during IVM attenuated oxidative stress, enhanced mitochondrial activity, and enhanced the viability and embryonic development of cryopreserved porcine oocytes. The results indicate that vitrification alters lipids in oocytes and CCs, and the supplementation of lipids plays a role in improving the quality of vitrified oocytes.

Objective: This study evaluated the greasy fleece weight (GFW) and shearing live weight at shearing (SLW) of the Kaçeli sheep breed conserved under Türkiye’s National Animal Genetic Resources Conservation Program.Materials and Methods: The animal material for this study consisted of 291 Kaçeli sheep (283 females and 8 males) raised under semi-intensive conditions on the Çeşme Peninsula. The animals ranged in age from 2 to 7 years. Dirty fleece weights were recorded during shearing in May, and live weights at shearing were measured using digital scales. Due to the small sample size and physiological differences in males, ram data were evaluated only descriptively and were excluded from statistical models. Descriptive statistics, general linear models, least squares means, and phenotypic correlation analyses were performed on the ewe data using SAS software. Farm, age, and live weight were included as fixed effects in the models, and between-group differences were determined using the Duncan Multiple Range Test.Results: Mean GFW was 1.70 kg in rams and 1.26 kg in ewes, while mean SLW was 57.61 kg and 41.40 kg, respectively. Farm effects were significant; Farm 2 showed the highest SLW (45.38 kg). Each 1 kg increase in SLW resulted in a 0.020 kg rise in GFW. Age negatively affected GFW (–0.046) but positively influenced SLW (1.112).Conclusion: Kaçeli sheep display moderate productivity, broad phenotypic diversity, and strong adaptability, providing key data for sustainable breeding and conservation strategies.

Wild relatives of domestic animals are crucial reservoirs of genetic diversity, yet pervasive hybridization with domestic animals poses significant conservation challenges. Here, we developed a deep learning-based pipeline, consisting of a multi-layer perceptron for SNP panel selection and a Deep & Cross Network for model training, to discern wild relatives from their closely related domestic animals using genomic SNP data. Leveraging the 1960 genomes from 164 red jungle fowl (RJF; Gallus gallus) and 1796 domestic chicken samples, we applied this pipeline to yield the RJF identification model based on a 285-SNP panel. We employed this model to characterize domestic chickens, RJF, and hybrids in the independent genomic datasets from contemporary samples and historical specimens, respectively. The accuracy was 97.8% for historical samples with missing genotypes. The benchmarking multiple hybrid detection tools indicated that the RJF identification model was effective and practical. The further application to the genomic data from wild boar (Sus scrofa), domestic pigs, and their hybrids validated the pipeline. Our method has potential in not only monitoring genetic diversity in wild relatives of domestic animals but also supporting animal genetic resource conservation and management.

Local farm animal genetic resources play a central role in sustaining food security, enhancing production efficiency, and supporting the resilience of agricultural systems. As climate change intensifies and production environments become increasingly variable, characterizing the genetic diversity embedded in local breeds has become essential for informed management, conservation, and breeding strategies. This Research Topic brings together four original research articles that collectively advance our understanding of genomic diversity, adaptive traits, and population structure in cattle, sheep, and pigs across diverse production landscapes. By integrating genomic analyses with production and environmental contexts, these studies highlight the adaptive potential of local breeds and provide actionable insights for their sustainable use and conservation.In the first article, Milia et al. investigate shared genomic regions among local cattle breeds from Sardinia. By applying high-resolution genomic tools, the authors identify conserved haplotypes and signatures of selection that provide new insights into historical connections and adaptive potential within insular bovine populations. Their work highlights the value of regional genetic resources for long-term breeding and conservation planning.The contribution by Fetene et al. presents a qualitative and quantitative characterization of the Surma cattle population in the Bench Maji Zone of Southwest Ethiopia. Through an integrated approach combining phenotypic measurements and field-based assessments, the authors document the unique morphological and adaptive traits of this indigenous breed. Their findings highlight the vital role of community-based conservation and, and at the same time, reinforce the need to protect pastoral production systems that sustain these valuable genetic resources.In the third article, Punuru et al. analyze genetic diversity in semi-arid sheep populations in Andhra Pradesh India using microsatellite markers. The study provides robust estimates of genetic variability, including within-and between-population variability of Andhra Pradesh local sheep populations and identifies management factors shaping current structures. High diversity was observed alongside admixture and endogamy, with distinct differentiation among populations. These results carry practical implications for breeding programs seeking to enhance productivity while retaining locally adapted traits crucial for dryland environments.Finally, Škorput et al. examine the effect of African swine fever on genetic diversity within the Black Slavonian pig. By evaluating population parameters before and after disease outbreaks, the authors demonstrate the vulnerability of small local breeds to epidemic events and emphasize the need for proactive genetic monitoring and conservation frameworks.Collectively, the studies in this special issue underscore the dynamic interactions between genetics, management, environment, and resilience in livestock systems. They demonstrate that characterizing local animal genetic diversity is not only a scientific endeavor but also a cornerstone of sustainable agriculture, climate change adaptation, and cultural heritage preservation. We extend our sincere thanks to all authors and reviewers for their valuable contributions and hope this Research Topic will inspire further collaborative work aimed at safeguarding the genetic resources that underpin global livestock production.EN: Writing -original draft, Writing -review & editing. LHD and RR: Writing -review & editing.

Background: This investigation aimed to portray the existing management practices, phenotypic variability, performance traits and distribution of the native goat (Surguji) population of Northern hills of Chhattisgarh. Methods: A comprehensive survey involving a sample size of 636 goats across 50 villages of Surajpur, Surguja and Balrampur districts was designed for exploring the morphological traits and performance potential of Surguji goats. All parameters were recorded following standard breed descriptor format prescribed by the National Bureau of Animal Genetic Resources (NBAGR), Karnal, Haryana. Result: Surguji goats were medium-sized, light brown and exhibit early puberty and sexual maturity, with favorable meat production characteristics. The average birth weights for male and female goats were 2.64±0.02 and 2.13±0.02 kg and adult body weights averaged 33.10±0.54 and 28.60±0.09 kg, respectively. The study reveals that the males were significantly heavier and taller than female goats. The average ages at first estrus, first mating, first kidding, service period and kidding interval were recorded as 208.15±1.21, 253.87±1.53, 441.99±1.88, 126.87±5.48 and 276.28±0.15 days, respectively. Milk production was reported to be very low, although multiple births were common. The findings indicate the presence of a unique goat population characterized by distinct morphometric, productive and reproductive traits.

The large Japanese field mouse, Apodemus speciosus, is a rodent species endemic to Japan and is widely distributed throughout the country. It has been extensively used as a model organism in studies of geographic isolation and as an environmental bioindicator. However, there have been no reports on the establishment of pluripotent stem cells from this species that could be applied to developmental engineering. In this study, we attempted to generate induced pluripotent stem cells (iPSCs) from A. speciosus and successfully obtained cells that formed dome-shaped colonies and expressed pluripotency markers. These cells were capable of forming embryoid bodies that expressed markers of the three germ layers, and in vivo analysis using immunodeficient mice confirmed their ability to form teratomas. A. speciosus iPSCs established in this study not only contribute to the conservation of Japan's valuable animal genetic resources, but also provide a novel platform for investigating various biological processes that remain unexplored in this wild species.

The indigenous cattle of Tripura is an unique animal genetic resources, well adapted to the humid subtropical climate. An Extensive study was conducted across all eight districts of Tripura to explore the morphology, reproductive, managemental, and productive traits, through field surveys, questionnaires, and interviews with farmers about housing management, breeding, feeding, disease, production etc. For the phenotypic characterisation and performance evaluation of this indigenous cattle, a total of 278 animals (23 males and 255 females) were studied. Study revealed that, this indigenous cattle of Tripura are small-sized, compact animals with a robust, cylindrical body and an average body weight of 154.49±1.86 kg. Mean body length, height at withers, and heart girth were 99.42±0.50 cm, 99.44±0.50 cm, and 128.84±0.57 cm, respectively. Prime qualitative traits included straight forehead (90.28%), medium hump (73.02%), a medium to small dewlap, and laterally elongated ears. Coat colour with considerable variation, with light red (50.7%) most common, followed by black, dark red, grey, white, and fawn. Muzzle and hoof were mostly black. Bowl-shaped udder with cylindrical teats. The average daily milk yield was 1.32±0.03 kg with a lactation length of 153.24±1.54 days, milk fat content of 4.98±0.04% and SNF of 8.57±0.02%. The age at first calving was 43.56±0.21 months, the calving interval of 454.81±4.68 days, and the lifespan of 15-18 years with 5-9 calvings during the lifetime. These cattle are mainly reared under extensive grazing systems with natural breeding by local bulls. The study highlights that the indigenous cattle of Tripura are with valuable adaptive traits, superior milk quality, and are resilient to low-input farming systems. These unique characteristics and traits invite a need for systematic conservation, genetic improvement, and formal breed recognition.

The study aimed to evaluate the phenotypic diversity of indigenous goats reared in three agroecological zones of southeastern Ethiopia based on their morphometric traits. Multi-stage purposive and random sampling methods were applied to select the study areas and the goats. A total of 601 (463 female and 138 male) goats were randomly sampled, measured and described using 16 morphometric traits. Data collected were analyzed using univariate and multivariate statistical procedures in SAS version 9.4. Univariate analysis revealed significant variations of all morphometric traits across the agroecological zones. The goats in the lowland agroecological zone were larger (p &lt; 0.05) than those reared in other agroecological zones. Goats reared in the highland agroecological zone were smaller and lighter in size, while those from the midland agroecological zone showed intermediate body size and weight. Multivariate analysis (i.e. canonical discriminant and cluster analysis) showed that the goats in the three agroecological zones were different in terms of their morphology, with the largest Mahalanobis distance (42.3%) being observed between lowland and highland goat populations. Discriminant analysis correctly assigned 86% of goats to their source populations. These results indicate the existence of morphological diversity among goat populations in the three agroecological zones of southeastern Ethiopia and suggest the need to develop conservation and breeding strategies aimed at retaining the observed diversity at the phenotypic level. Further studies using molecular tools are needed to elucidate the observed diversity at the phenotypic level and to design appropriate strategies for the sustainable management of these animal genetic resources.

Nepal is rich in animal genetic resources (AnGR) both in terms of diversity and numbers. Animal genetic resources play a key role in livestock development in the country mainly through their contribution to income generation and livelihood enhancement. They have also non-economic values (socio and cultural values) or bequest value, which doesn’t seem to be valued. The diversity both species and breeds levels are enormous in the country. A total of 25 indigenous breeds from seven livestock species have been characterized so far. There are several transboundary breeds (regional and international) in the country. Despite of these several breeds, particularly indigenous breeds are declining making system non-sustainable. The major threats for animal genetic resources are genetic erosion, indiscriminate crossbreeding, low productivity, small holding size, lack of specific policies, changing production systems, lack of valuation of local breeds, increasing competition for natural resources and environmental degradation. These factors are contributing to genetic erosion of indigenous breeds in the country. Several breeds have population declined and few are about to be extinct if careful measures are not taken. Strategic actions should be undertaken in order to check genetic erosion and improve their contribution. Effective management of AnGR will address these constraints precisely. Management for AnGR includes its understanding (characterization), using (utilization), maintaining (conservation), accessing and benefit sharing.

Cryopreservation technology has become a primary method for preserving animal genetic resources in the biomedical field. It achieves long-term storage by placing gametes or embryos in an ultra-low-temperature environment, enabling them to retain biological activity after thawing. However, the cytotoxicity issues associated with traditional cryoprotectants limit their application, making the development of non-toxic and highly effective novel cryoprotectants a current research priority. This review systematically reviews the development history and principles of cryopreservation technology, and summarizes the classification and mechanisms of action of cryoprotectants, with a particular focus on five types of novel cryoprotectants featuring bioinspired structural characteristics. Their ice-suppression performance and mechanisms of action are analyzed. These protectants possess structures similar to those of natural antifreeze substances and exhibit low toxicity, thereby demonstrating higher cryopreservation efficiency, and are thus referred to as novel bioinspired cryoprotectants. Furthermore, this review examines the potential applications of the aforementioned protectants in the cryopreservation of animal gametes (sperm, oocytes, and embryos), offering new insights into expanding the use of bioinspired cryoprotectants in the preservation of animal genetic resources.

Phylogenetic analysis and diversity of the Colombian creole donkey from sequences of the mitochondrial DNA D-loop region.

Bulgaria is a country rich in genetic resources, with more than 120 native, locally adapted, and exotic livestock and poultry breeds and lines. The documentation and monitoring of these resources are essential for their management, conservation, and sustainable use. The objective of this work is to analyse the development, current state, and trends in the monitoring and documentation of animal genetic resources in Bulgaria, as well as the presentation of the data at the national and international levels. Data from the periodicals “Farm Animal Breeds in the Republic of Bulgaria” and the world information system DAD-IS were used for the analysis and compared with other countries in Europe. The results indicate that in Bulgaria there is a well-organized system for collecting and publishing information about livestock breeds, controlled by breeding organizations. It is one of the countries with the most consistent reporting of population data to DAD-IS, providing, on average, data about 87% of its breeds annually in 2019–2023. A trend of increase compared to the values in 2010–2015 (65%) was also observed, which indicates an improvement in the organization of data presentation at the international level. A weakness in reporting data about the state of ex situ in vitro collections was identified: Bulgaria reported data to DAD-IS only in 2017. However, the data about the current state of the national gene bank are regularly published online at the national level. Regarding the completeness of data about genetic resources from Bulgaria in DAD-IS, the country is among the top three in Europe, surpassed only by Austria and Iceland.

Access and Benefit-Sharing (ABS) was formalized through the Convention on Biological Diversity (CBD), adopted at the 1992 UN Conference on Environment and Development, providing an institutional framework that contributes to biodiversity conservation by allowing each country to exercise sovereignty over its biological resources and equitably share the benefits arising from their utilization. Subsequently, the Nagoya Protocol strengthened the legal binding nature of access to genetic resources; however, discussions on ABS in the field of animal genetic resources (AnGR) remain relatively insufficient compared to those on plants and microorganisms. This study therefore compares and analyzes the current ABS frameworks for animal genetic resources across major countries, highlighting the effectiveness of these systems and drawing policy implications. In conclusion, while countries have established diverse ABS frameworks tailored to their legal and institutional contexts, international cooperation mechanisms specifically focused on animal genetic resources remain limited. Accordingly, the establishment of a global governance framework is needed in the future, focusing on harmonization of national systems, clarification of the inclusion of digital information, and strengthening the practical enforcement of benefit-sharing.

Background: The growing demand for animal products has driven changes in the livestock sector. As a result, a new poultry farming system has recently emerged in Burkina Faso’s urban and suburban areas with the production of local chicken breeds and crossbreds in permanent confinement. Aim: This study aims to characterize the production system and genetic resource management using a survey. Methods: Snowball sampling was employed using 11 independent entry points in different Ouagadougou suburban areas. A total of 120 producers were sampled and interviewed. Results: The results showed that the average age of farmers was 38 ± 12 years, with a fairly high level of education. Chicken farming was essentially a secondary activity. The main objective was commercial. Various food resources were used, including industrial feed, household waste, grain, and insects. Health management revealed that antibiotics were used as a preventive measure. Crossbred chicks were produced with no precise crossbreeding scheme, and crossbred cockerels were often used or sold as breeding stock, even in rural areas. Conclusions: Given its characteristics, this production system occupies an intermediate position between free-range systems and the intensive production of commercial strains. However, this ad hoc approach to breeding may contribute to genetic erosion. Moreover, the preventive use of antibiotics raises concerns about the presence of residues in consumer products. Strengthening the management of animal genetic resources and improving poultry health practices would help safeguard both local genetic diversity and public health.

Preservation of animal genetic resources is a key component of food security and economic stability. Genetic diversity provides the foundation for breeding work, allows the production systems to adapt to climate change, and reduces risks associated with epidemics and productivity decline. To assess economic efficiency, it is necessary to conduct specific economic calculations for regions or breeds, taking into account costs, risks, time, market conditions, and climatic factors. The study was carried out at the experimental base of the State Poultry Research Station of the Institute of Animal Science of the National Academy of Agrarian Sciences of Ukraine using genetic resources of chickens of different productivity types (egg – Birky Colored; dual-purpose – Poltava Clay; meat-and-egg – Hercules (Plymouth Rock) White) from the collection of the national poultry gene pool of Ukrainian selection. The article presents the results of scientific research aimed at a systematic analysis of economic efficiency and the identification of ways to improve it in maintaining poultry gene pool populations of various productivity directions. The research established the level of economic efficiency of maintaining gene pool flocks of chickens of different productivity directions and identified the main ways to improve their profitability. The obtained indicators serve as an analytical basis for further calculations aimed at improving technologies for the maintenance and conservation of breeding stock. The profitability level of hatching egg production for 42 weeks of life ranged from -14.08 to 19.75 % (egg-type chickens), -14.28 to 3.5 % (dual-purpose), and -32.56 to 2.6 % (meat-and-egg). For the production and sale of day-old chicks, the profitability indicators were -7.03 to 29.57 % (egg-type), -13.50 to 4.4 % (dual-purpose), and -36.35 to -3.15 % (meat-and-egg). Extending the keeping period of birds from 42 to 52 weeks led to an increase in total egg production and profitability indicators. The profitability level of hatching egg production for 52 weeks of life was 30.10 % (egg-type), 36.83 % (dual-purpose), and 4.66 % (meat-and-egg). For day-old chick production and sales, the profitability levels were 40.77 %, 48.89 %, and -1.23 %, respectively. Keywords: chickens, economic evaluation, genetic resources, productivity, poultry farming, production.

Domestic cattle in Africa can be categorized as either taurine (Bos taurus) or indicine (Bos indicus) based on their domestication histories from the extinct aurochs (Bos primigenius). Close to 150 breeds of indigenous cattle are estimated to exist in Africa and have a complex mixture of B. taurus and B. indicus ancestries. Native cattle in Uganda fall into three broad categories: the Sanga, East African Shorthorn Zebu, and Zenga. There is limited information about the genetics of Ugandan indigenous cattle, despite their representation of nearly 80% of the national herd. In the present study, we describe the genetic diversity and population structure of five native breeds using whole genome sequences of 95 animals. For a comparative context, we included published whole genome sequences of 97 animals in the analysis. Our findings indicate a clear distinction between Zebu, Sanga, and Zenga breeds, with elevated inbreeding and lower genetic diversity levels among the Ugandan breeds. We also observed an introgression of European genetic resources into Ugandan native cattle breeds. Notably, our results suggest existence of two subpopulations within the Nganda breed, a finding that has implications on the conservation efforts of native animal genetic resources. The findings of this study show that indigenous cattle genetic resources in the country are threatened by admixture with imported genetic material and underscore the need for targeted efforts to characterize and conserve them before they are lost to crossbreeding and breed substitution.