Summer season induced rhythmic alterations in metabolic activities to adapt to heat stress in three indigenous (Osmanabadi,Malabari and Salem Black) goat breeds

A study was conducted to assess the adaptive capability of three indigenous goat breeds to heat stress. Thirty six 10 months to one-year-old female goats of Osmanabadi, Malabari and Salem Black breeds were randomly divided into six groups, OC (n = 6; Osmanabadi control), OHS (n = 6; Osmanabadi heat stress), MC (n = 6; Malabari control), MHS (n = 6; Malabari heat stress), SBC (n = 6; Salem Black control) and SBHS (n = 6; Salem Black heat stress). Among the metabolic activity controlling hormones, the breed factor significantly (P < 0.05) influenced only plasma triiodothyronine (T3). However, heat stress significantly (P < 0.05) decreased thyroid stimulating hormone (TSH) in both MHS and SHS groups while significantly (P < 0.05) decreased the plasma T3 in MHS. The rumen metabolites such as acetate, propionate, butyrate and total volatile fatty acids (TVFAs) showed significant (P < 0.05) variation for both breed and treatment effect. The Salem Black breed did not show any significant variation for most of the rumen metabolites as compared to both Osmanabadi and Malabari breeds for the heat stress treatment. The study indicated the importance of the metabolic alterations in indigenous goat breeds to cope to the seasonal rhythms. The results indicated that on comparative basis, Salem Black breed adapted better to the heat stress challenges.     

Genetic Structuring of Nine Indian Domestic Goat Breeds Based on SNPs Identified in IGF-1 Gene

The caprine Insulin like Growth Factor1 (IGF1) gene was analyzed for identification of single nucleotide polymorphisms (SNPs) and genetic structuring of Indian goat breeds. A panel of 80 samples belonging to nine Indian goat breeds (Capra hircus) including three large sized breeds (Jamunapari, Beetal and Jakhrana); three medium sized breeds (Sirohi, Barbari, and Osmanabadi) and three small sized breeds (Black Bengal, Changthangi, and Gaddi) were screened for SNP identification and diversity analysis. The comparative gene sequence analysis of all the nine goat breeds studied revealed a total of 18 SNPs in IGF1 gene. All the nucleotide changes were found to be synonymous. The mean observed heterozygosity was found to be maximum (0.074) in Sirohi, Beetal, Osmanabadi, and Gaddi breeds of goat, whereas it is found to be minimum (0.019) in Black Bengal breed of goat. The rest of the breeds were intermediate in terms of heterozygosity. The same has been confirmed by allele frequency distribution across the studied loci. Barbari and Gaddi were found to be more differentiated (0.0123), Changthangi and Jamunapari were least differentiated (0.00110) based on Nei's genetic distance.     

Microsatellite Analysis of Genetic Population Structure of Zebu Cattle (Bos indicus) Breeds from North-Western Region of India

The present study aims to understand the existing genetic diversity and structure of six native cattle breeds (Rathi, Tharparkar, Nagori, Mewati, Gir, and Kankrej) adapted to the north-western arid and semi-arid region of India based on microsatellite loci. Various diversity estimates, mean number of alleles (12.84); effective number of alleles (5.02); gene diversity (0.769), and observed heterozygosity (0.667) reflected the existence of substantial within-breed diversity in all the investigated cattle breeds. Mean estimates of F-statistics: F_IT = 0.144 ± 0.023, F_IS = 0.071 ± 0.021, and F_ST = 0.078 ± 0.014 were significantly different from zero (P < 0.05). The interbreed relationships indicated moderate level of breed differentiation between the six cattle breeds with least differentiation between Kankrej-Mewati pair. The phylogeny structuring further supported close grouping of Kankrej and Mewati breeds. Correspondence analysis plotted Rathi, Tharparkar, and Gir individuals into three separate areas of multivariate space; whereas, Kankrej, Mewati, and Nagori cattle showed low breed specific clustering. This reflected the existence of discrete genetic structure for Tharparkar, Rathi, and Gir, the prominent dairy breeds of the region; whereas, admixture was observed for Kankrej, Mewati, and Nagori individuals.     

Microsatellite analysis of genetic population structure of zebu cattle (Bos indicus) breeds from north-western region of India

The present study aims to understand the existing genetic diversity and structure of six native cattle breeds (Rathi, Tharparkar, Nagori, Mewati, Gir, and Kankrej) adapted to the north-western arid and semi-arid region of India based on microsatellite loci. Various diversity estimates, mean number of alleles (12.84); effective number of alleles (5.02); gene diversity (0.769), and observed heterozygosity (0.667) reflected the existence of substantial within-breed diversity in all the investigated cattle breeds. Mean estimates of F-statistics: F(IT) = 0.144 ± 0.023, F(IS) = 0.071 ± 0.021, and F(ST) = 0.078 ± 0.014 were significantly different from zero (P < 0.05). The interbreed relationships indicated moderate level of breed differentiation between the six cattle breeds with least differentiation between Kankrej-Mewati pair. The phylogeny structuring further supported close grouping of Kankrej and Mewati breeds. Correspondence analysis plotted Rathi, Tharparkar, and Gir individuals into three separate areas of multivariate space; whereas, Kankrej, Mewati, and Nagori cattle showed low breed specific clustering. This reflected the existence of discrete genetic structure for Tharparkar, Rathi, and Gir, the prominent dairy breeds of the region; whereas, admixture was observed for Kankrej, Mewati, and Nagori individuals.     

DNA variants of the MHC show location-specific convergence between sheep, goat and cattle

Interspecific convergent evolution in sheep, goat and cattle was analysed with the help of orthologous microsatellite markers. Six of the loci are located in the major histocompatibility complex (MHC) region and three on different chromosomes. Samples from at least 60 animals per autochthonous breed of the three species were collected in central and southeast Anatolia (Turkey) as well as Baden-Württemberg (Germany). Allelic diversity, heterozygosity, population differentiation and genetic distances were calculated. The loci were polymorphic in all species and breeds. Apart from MSDRB, the loci linked to the MHC were similarly polymorphic as compared to the other loci. Allele numbers in the Turkish sheep and in the cattle breeds were higher than in the other breeds. The predominant occurrence of distinct allele lengths per locus differed depending on the species. For the three geographic locations, the genetic distances between species based on the MHC loci were significantly closer in comparison with distances based on quasi-neutral loci. This indicates convergent evolution of the MHC loci between sheep, goat and cattle caused by effects of location and demonstrates an approach for quantifying influences of adaptation on genetic variability.     

Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses

Assignment tests have been utilized to investigate population classification, measure genetic diversity and to solve forensic questions. Using microsatellite data from 26 loci genotyped in eight horse breeds we examined how population differentiation, number of scored loci, number of scored animals per breed and loci variability affected individual assignment precision applying log likelihood methods. We found that both genetic differentiation and number of scored loci were highly important for recognizing the breed of origin. When comparing two and two breeds, a proportion of 95% of the most differentiated breeds (0.200 < or = FST < or = 0.259) could be identified scoring only three loci, while the corresponding number was six for the least differentiated breeds (0.080 < or = FST < or = 0.139). An identical proportion of simulated breed crosses, differentiated from their parental breeds by FST estimates in the range 0.050-0.069, was identified when scoring 12 loci. This level of source identification was not obtained for the less differentiated breed crosses. The current data further suggested that population sample size and locus variability were not critical for the assignment precision as long as moderately large sample sizes (> or = 20 animals per population) and fairly variable loci were used.     

Analysis of 22 heterologous microsatellite markers for genetic variability in Indian goats

The genetic variability of 22 heterologous microsatellite markers was analyzed in two Indian goat breeds, namely Bengal and Chegu. The heterozygosity, polymorphism information content (PIC), and probability of identity of two individuals were calculated for all microsatellite loci in both the breeds. The observed number of alleles varied between 4 and 13 at the studied microsatellite loci. The evaluated microsatellite loci exhibited high mean heterozygosity of 0.69 +/- 0.11 and 0.66 +/- 0.07 in Bengal and Chegu goats, respectively. The mean PIC values of the studied loci in these breeds were 0.79 +/- 0.08 and 0.78 +/- 0.05, respectively. The probability of identity of two random individuals from different breeds, taking into account, all the 22 microsatellite loci was as low as 5.523 x 10(-40). On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying genetic diversity and for identification of individuals in Indian goat breeds.     

Comparison of microsatellite and blood protein diversity in sheep: inconsistencies in fragmented breeds

Finnsheep, Romanov, Oxford Down and three local breeds from Finland or northwestern Russia were assessed at 15 microsatellite and 7 protein loci. A novel albumin allele was identified. Diversity patterns were mostly concordant between marker types, but discrepancies appeared for the local Viena and Vepsia sheep, both demonstrating frequent linkage disequilibria for both marker types and excess of homozygotes for microsatellites, and in the case of Vepsia also for proteins as signs of breed fragmentation. On the basis of microsatellite data, the neighbour-joining tree and two-dimensional map constructed from DA distances suggested that difference in longitude of breed origin would relate to breed relationship, whereas on the basis of protein data latitude would have this quality. These different impressions resulted because genetic distances involving Vepsia sheep were relatively low for protein variation compared with microsatellites. Microsatellite variation correlated positively with protein variation, but for the local Viena sheep protein variation was comparatively low. Populations had significant differences in allelic richness, but not in genetic diversity. Analysis implied that at least 30 polymorphic loci were needed to detect a difference in diversity between populations using a paired t-test, if the true mean diversity difference was 0.2. In the total sample, proteins demonstrated larger theta-values, but this was reversed for Finnsheep, for which model-based clustering of microsatellite genotypes revealed a structure associated with coat colour. Imported and rare sheep exhibited lowered allelic variability and increased frequency of pairwise disequilibria between unlinked markers. Our results emphasize that more loci are required for studying fragmented breeds.     

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene

Background

The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones.

Results

The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The D_A measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution.

Conclusion

Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information.     

河南地方山羊品种的遗传多样性

采用18个微卫星位点对河南省5个地方山羊品种（牛腿山羊、槐山羊、河南奶山羊、太行黑山羊和伏牛白山羊）的遗传多样性进行了评价.结果表明：18个微卫星位点在5个山羊品种均为高度多态;5个山羊品种的多态信息含量、群体杂合度、有效等位基因数值较高,说明其遗传多样性和各品种内的遗传变异比较丰富;聚类分析显示,牛腿山羊与太行黑山羊的关系较近,与河南奶山羊的关系较远.群体遗传分化系数和群体遗传距离表明,河南省地方山羊的变异主要存在于品种内,品种间的变异相对较小.结合5个山羊品种的实际生态地理分布,提出了避免近交,并有选择地进行品种间杂交的保种模式.     

Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet)

Southwest China contains about one third Chinese indigenous goat breeds representing special economic and ecological characteristics. Mitochondrial DNA (mtDNA) D-loop sequences of 312 individuals (including 109 new individuals, 203 individuals retrieved from GenBank) from 18 Chinese domestic goat breeds were used to investigate breed genetic diversity, origin and phylogeography. All goat breeds in this study proved to be extremely diverse, average haplotype diversity and nucleotide diversity being 0.9829 ± 0.0027 and 0.03615 ± 0.03257, respectively. The 312 sequences gave 148 different haplotypes. Phylogenetic analyses revealed that there were two mtDNA haplogroups identified in domestic goats in Southwest China, in which haplogroup A was predominant. Mismatch analysis showed haplogroup A had experienced population expansion events, whereas haplogroup B did not. Amova analysis showed there was no significant geographical structuring. Almost 86.23% of genetic variation was included in the within-breed variance component and only 3.5% was observed among the four geographic provinces. The results of this study contribute to the knowledge of the genetic structure and origin of domestic goats in Southwest China.     

Assessing genetic diversity in Italian goat populations using AFLP® markers

Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variation in a sample of seven goat (Capra hircus) populations. A total of 210 individuals (30 per population) were analysed using seven selected AFLP primer combinations that produced 219 clear polymorphisms. Four autochthonous goat breeds (Bionda dell'Adamello, Frisa, Orobica and Verzaschese), two primary populations, one from the Lombardy Alps (Val di Livo) and the other from Sardinia island (Sarda) and a reference cosmopolitan breed (Saanen) were included in the analysis. The expected heterozygosity (Het) did not differ significantly among breeds (range 0.21-0.24). No breed specific markers were identified. The variability at AFLP loci was largely maintained within breeds, as indicated by the coefficient of genetic differentiation (Gst) value (0.11). Dice similarities calculated between pairs of individuals belonging to the same or to different breeds largely overlapped. Bootstrapping on markers indicated that the coefficient of variation (CV) of the genetic indexes tested decreases only marginally by adding markers over 100 AFLPs. Cluster analysis based on standard genetic distance between breeds indicates that Sarda is the most distant population, while Bionda, Frisa, Verzaschese and Val di Livo seem to be highly related populations. Interestingly, Saanen is closer than Orobica to the other four goat populations of the Lombardy Alps. Principal co-ordinates analysis based on Dice similarities confirms these observations. Genetic diversity of the goat populations investigated confirms what is expected on the basis of their geographical location. Results from Orobica are not correlated with geographical distances and may reflect undocumented migrations and gene flows and identify an original genetic resource.     

Polymorphism of BMP4 gene in Indian goat breeds differing in prolificacy

Bone morphogenetic proteins (BMPs) are members of the TGF-β (transforming growth factor-beta) superfamily, of which BMP4 is the most important due to its crucial role in follicular growth and differentiation, cumulus expansion and ovulation. Reproduction is a crucial trait in goat breeding and based on the important role of BMP4 gene in reproduction it was considered as a possible candidate gene for the prolificacy of goats. The objective of the present study was to detect polymorphism in intronic, exonic and 3′ un-translated regions of BMP4 gene in Indian goats. Nine different goat breeds (Barbari, Beetal, Black Bengal, Malabari, Jakhrana (Twinning > 40%), Osmanabadi, Sangamneri (Twinning 20–30%), Sirohi and Ganjam (Twinning < 10%)) differing in prolificacy and geographic distribution were employed for polymorphism scanning. Cattle sequence (AC_000167.1) was used to design primers for the amplification of a targeted region followed by direct DNA sequencing to identify the genetic variations. Single nucleotide polymorphisms (SNPs) were not detected in exon 3, the intronic region and the 3′ flanking region. A SNP (G1534A) was identified in exon 2. It was a non-synonymous mutation resulting in an arginine to lysine change in a corresponding protein sequence. G to A transition at the 1534 locus revealed two genotypes GG and GA in the nine investigated goat breeds. The GG genotype was predominant with a genotype frequency of 0.98. The GA genotype was present in the Black Bengal as well as Jakhrana breed with a genotype frequency of 0.02. A microsatellite was identified in the 3′ flanking region, only 20 nucleotides downstream from the termination site of the coding region, as a short sequence with more than nineteen continuous and repeated CA dinucleotides. Since the gene is highly evolutionarily conserved, identification of a non-synonymous SNP (G1534A) in the coding region gains further importance. To our knowledge, this is the first report of a mutation in the coding region of the caprine BMP4 gene. But whether the reproduction trait of goat is associated with the BMP4 polymorphism, needs to be further defined by association studies in more populations so as to delineate an effect on it.     

Geographical partitioning of goat diversity in Europe and the Middle East

Thirty microsatellite markers were analysed in 1426 goats from 45 traditional or rare breeds in 15 European and Middle Eastern countries. In all populations inbreeding was indicated by heterozygosity deficiency (mean FIS = 0.10). Genetic differentiation between breeds was moderate with a mean FST value of 0.07, but for most (c. 71%) northern and central European breeds, individuals could be assigned to their breeds with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed at least four discrete clusters: eastern Mediterranean (Middle East), central Mediterranean, western Mediterranean and central/northern Europe. About 41% of the genetic variability among the breeds could be explained by their geographical origin. A decrease in genetic diversity from the south-east to the north-west was accompanied by an increase in the level of differentiation at the breed level. These observations support the hypothesis that domestic livestock migrated from the Middle East towards western and northern Europe and indicate that breed formation was more systematic in north-central Europe than in the Middle East. We propose that breed differentiation and molecular diversity are independent criteria for conservation.     

Genetic Structure of Chinese Indigenous Goats and the Special Geographical Structure in the Southwest China as a Geographic Barrier Driving the Fragmentation of a Large Population

Background

China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers.

Methodology/Principal Findings

Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (H_S of 0.644) and high population diversity at the species level (H_T value of 0.737) were estimated. Significant moderate population differentiation was detected (F_ST value of 0.129). Significant excess homozygosity (F_IS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China.

Conclusions/Significance

Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats.     

Genetic variation and relationships among eight Indian riverine buffalo breeds

Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy-Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of F(ST) index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of F(ST) values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800-2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.     

Genetic relationships of five Indian horse breeds using microsatellite markers

The genetic relationships of five Indian horse breeds, namely Marwari, Spiti, Bhutia, Manipuri and Zanskari were studied using microsatellite markers. The DNA samples of 189 horses of these breeds were amplified by polymerase chain reaction using 25 microsatellite loci. The total number of alleles varied from five to 10 with a mean heterozygosity of 0.58 ± 0.05. Spiti and Zansakari were the most closely related breeds, whereas, Marwari and Manipuri were most distant apart with Nei's D_A genetic distance of 0.071 and 0.186, respectively. In a Nei's D_A genetic distances based neighbour joining dendrogram of these breeds and a Thoroughbred horse outgroup, the four pony breeds of Spiti, Bhutia, Manipuri and Zanskari clustered together and then with the Marwari breed. All the Indian breeds clustered independently from Thoroughbreds. The genetic relationships of Indian horse breeds to each other correspond to their geographical/environmental distribution.     

Combination of multiple microsatellite data sets to investigate genetic diversity and admixture of domestic cattle

Microsatellite markers are commonly used for population genetic analyses of livestock. However, up to now, combinations of microsatellite data sets or comparison of population genetic parameters from different studies and breeds has proven difficult. Often different genotyping methods have been employed, preventing standardization of microsatellite allele calling. In other cases different sets of markers have been genotyped, providing differing estimates of population genetic parameters. Here, we address these issues and illustrate a general two-step regression approach in cattle using three different sets of microsatellite data, to combine population genetics estimates of diversity and admixture. This regression-based method is independent of the loci genotyped but requires common breeds in the data sets. We show that combining microsatellite data sets can provide new insights on the origin and geographical distribution of genetic diversity and admixture in cattle, which will facilitate global management of this livestock species.     

Evaluation of Genetic Differentiation in Bos indicus Cattle Breeds from Marathwada Region of India Using Microsatellite Polymorphism

Elucidation of genetic variability and genetic relationship among breeds has direct relevance with the issues of sustainable use of domestic animal genetic resources. In the present study, genetic polymorphism was evaluated using 22 microsatellite loci in unrelated samples of Red Kandhari and Deoni cattle breeds inhabiting the same geographical area of Marathwada region in Maharashtra state (western India). This work was mainly aimed at assessing the current genetic diversity to understand whether the two zebu populations in question are genetically differentiated. A total of 164 alleles were detected with an average of 5.82 and 5.86 alleles per locus (MNA) in Red Kandhari and Deoni breeds, respectively. The estimated mean observed (Ho) and expected (He) heterozygosity were 0.47 and 0.64 in Red Kandhari vs. 0.57 and 0.69 in Deoni cattle, respectively, demonstrating considerable level of genetic variation in both the populations. Mean estimates of F statistics were: F (FIT) = 0.315±0.035, f(FIS) = 0.231±0.031, θ(FST) = 0.110±0.022, with both the breeds exhibiting significant deficit of heterozygotes (FIS = 0.179 in Deoni; 0.278 in Red Kandhari). The multilocus FST values implied that 11.0% of the total genetic variation corresponds to breed and were statistically greater than zero for the two populations, suggesting population division. The evaluation of exact test also indicated that allele frequencies across all the loci differed significantly (P < 0.001) between two zebu breeds, further supporting population differentiation. Different genetic distance measures showed considerable levels of distances between the two cattle breeds (0.318 = Nei's standard DS; 0.250 = Nei's DA; 0.416 = Cavalli-Sforza and Edwards's DC; 0.164 = Reynold's, and 2.64 = Delta mu square (dμ)2. Bayesian statistical approach to assign each individual to the population also supported considerable differentiation between the two cattle breeds, possibly reflecting the limited gene flow between the two Marthwada cattle populations. The existence of cohesive breeding structure of both the breeds was further substantiated by allele-sharing distance measures (DAS) among individual animals. The results of this study thus revealed that the two Bos indicus breeds sharing the common breeding tracts are genetically differentiated enough as separate breeds.     

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Uganda 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 (H_O) and expected (H_E) 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.