Immunogenetic and population genetic analyses of Iberian cattle

Blood samples were collected from more than 100 animals in each of 2 Spanish cattle breeds (Retinto and De Lidia), 2 Portuguese breeds (Alentejana and Mertolenga), and American Longhorn cattle. All samples for the 4 Iberian breeds were tested for 20 polymorphic systems; American Longhorn were tested for 19 of the 20. For each breed an average inbreeding coefficient was estimated by a comparison of the observed and expected heterozygosity at 7 or 8 codominant systems tested. All breeds had positive values but only 3 breeds had estimates of inbreeding that were statistically significantly different from 0: De Lidia with = 0.17, Retinto with = 0.08 and Mertolenga with f = 0.05. The De Lidia breed especially may be suffering from inbreeding depression since this high value is greater than expected if all of the animals were progeny of half-sib matings. Genetic distances were calculated from the gene frequency data on these 5 breeds plus 9 other European breeds. Analyses of these distances show a closely related group of the 4 Iberian breeds and American Longhorn, confirming the close relationships among the Iberian breeds and the Iberian, probably Portuguese, origin of American Longhorn cattle.     

Genetic diversity and patterns of population structure in Creole goats from the Americas

Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in‐depth analysis of the within‐ and between‐breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora‐type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well‐differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P < 0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas.     

Genetic diversity in the Churra tensina and Churra lebrijana endangered Spanish sheep breeds and relationship with other Churra group breeds and Spanish mouflon

The aim of the present study was to estimate the genetic intra-breed variability of Churra tensina and Churra lebrijana endangered breeds and to establish genetic relationships with Churra, Latxa and Merino breeds, as well as Spanish mouflon, by using 28 microsatellite markers, to provide useful information for their conservation. Allele frequencies and heterozygosity revealed high genetic variation in the two endangered breeds despite their small population size. Estimates of inbreeding coefficient (F_IS) were significant for all breeds studied, except for Churra lebrijana breed. The highest inbreeding coefficient (F_IS = 0.143) was found in the Spanish mouflon. Genetic differentiation tests (F_ST = 0.121) and assignment of individuals to populations indicated the existence of defined breed populations, and low genetic flow between these breeds. The highest pairwise Reynolds distance (D_R) values were observed between Mouflon and the domestic sheep breeds. Considering only domestic sheep breeds, the Churra lebrijana breed showed the highest pairwise D_R values_. The lowest values were found between Latxa and the other domestic sheep, except for Churra lebrijana. Results of pairwise D_R values, as well as phylogenetic tree and bottleneck analysis showed an important genetic isolation of the Churra lebrijana breed from the other Churra types, and genetic signatures of a demographic bottleneck. Finally, structure analysis of populations detected a population subdivision in the Latxa sheep breed. In conclusion, this study presents valuable insight into the existing genetic variability of two Spanish endangered breeds, as well as the first study in Spanish mouflon based on microsatellite analysis. The high degree of variability demonstrated in Churra tensina and Churra lebrijana implies that these populations are rich reservoirs of genetic diversity.     

Ancestral matrilineages and mitochondrial DNA diversity of the Lidia cattle breed

To clarify the genetic ancestry and the mitochondrial DNA (mtDNA) diversity of the Lidia cattle breed, a 521-bp D-loop fragment was sequenced in 527 animals belonging to 70 herds distributed across 29 lineages. The mtDNA diversity recorded was similar to that seen for Middle Eastern breeds and greater than that recorded for the majority of European breeds. Haplotype T3 was the most common (81%), followed by the African T1 haplotype (17%); very low frequencies were recorded for haplotypes T and T2. The results agree with there being two major ancestral lines for the Lidia breed, European and African, similar to that seen for other Mediterranean breeds. A wide range of variation in haplotype frequencies was seen between the examined lineages. Haplotype T3 was present in all those analysed; in five it was the only one present, and in only one lineage (Miura) was its frequency lower than that of T1. T1*, a haplotype reported in Criollo breeds and to date in only a single European breed (the Retinta breed from Spain), was found in a single animal belonging to the Concha y Sierra lineage. Network analysis of the Lidia breed revealed the presence of two major haplotypes: T3 and T1. The Lidia breed appears to be more closely related to prehistoric Iberian and Italian than to British aurochs.     

Genetic structure,relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Background

Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies.

Methods

A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results.

Results

Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity.

Conclusions

Native pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.     

Unfolding of population structure in Baltic sheep breeds using microsatellite analysis

Studies of domestic animals are performed on breeds, but a breed does not necessarily equate to a genetically defined population. The division of sheep from three native and four modern Baltic sheep breeds was studied using 21 microsatellite loci and applying a Bayesian clustering method. A traditional breed-wise approach was compared to that relying on the pattern of molecular diversity. In this study, a breed was found to be inconsistent with a distinct genetic population for three reasons: (i) a lack of differentiation between modern Baltic breeds, since the majority of the studied sheep formed a single population; (ii) the presence of individuals of foreign ancestry within the breed; and (iii) an undefined local Saaremaa sheep was referred to as a breed, but was shown to consist of separate populations. In the breed-wise approach, only the clearly distinct Ruhnu sheep demonstrated low within-breed variation, although the newly identified Saaremaa populations also have low variability. Providing adequate management recommendations for the Saaremaa sheep is not possible without further studies, but the potential harmful effects of inbreeding in the Ruhnu sheep could be reduced through the use of two genetically related Saaremaa populations. In other breeds, excessive crossing appears to be a larger concern than inbreeding. Assigning individuals into populations based on the pattern of genetic diversity offers potentially unbiased means of elucidating the genetic population structure of species. Combining these genetic populations with phenotypic and aetiological data will enable formulation of the most informed recommendations for gene resource management.     

Genetic relationships between Spanish Assaf (Assaf.E) and Spanish native dairy sheep breeds

At present, the Assaf is the main dairy sheep in Spain. The Spanish Assaf (Assaf.E) was formed by male-mediated absorption of native Spanish sheep. Here we assess the genetic relationships among the Assaf.E and major native Spanish dairy breeds using microsatellites to contribute to the knowledge of the formation and within-population genetic variability of the breed. Blood samples from 44 unrelated Assaf.E individuals from 23 different Assaf.E flocks spread throughout 6 different Spanish provinces were obtained and genotyped using 14 microsatellites. Up to 312 additional samples belonging to the Awassi and Milchschaf sheep breeds and to six native Spanish dairy sheep breeds (Castellana, Churra, Latxa, Manchega, and Rubia de El Molar) as well as samples from Merino individuals to be used as the outgroup were also analysed observed (H_o) and expected (H_e) heterozygosity, rarefacted number of alleles per locus and distances based on molecular coancestry information were computed. Probabilities of assignment of the Assaf.E individuals to native Spanish dairy sheep breeds and cryptic genetic structure in the whole dataset were also assessed. It can be concluded that the Assaf.E breed has low genetic variability and high genetic distance with respect native Spanish dairy sheep breeds. From our results, the formation of the Assaf.E breed basically occurred via the absorption of individuals belonging to the Entrefino type, particularly to the Castellana and Manchega populations. Furthermore, Churra individuals may have participated in the formation of the Assaf.E breed at an early moment of the introduction of the breed into Spain.     

Genetic relationships between Spanish Assaf (Assaf.E) and Spanish native dairy sheep breeds

At present, the Assaf is the main dairy sheep in Spain. The Spanish Assaf (Assaf.E) was formed by male-mediated absorption of native Spanish sheep. Here we assess the genetic relationships among the Assaf.E and major native Spanish dairy breeds using microsatellites to contribute to the knowledge of the formation and within-population genetic variability of the breed. Blood samples from 44 unrelated Assaf.E individuals from 23 different Assaf.E flocks spread throughout 6 different Spanish provinces were obtained and genotyped using 14 microsatellites. Up to 312 additional samples belonging to the Awassi and Milchschaf sheep breeds and to six native Spanish dairy sheep breeds (Castellana, Churra, Latxa, Manchega, and Rubia de El Molar) as well as samples from Merino individuals to be used as the outgroup were also analysed observed (H_o) and expected (H_e) heterozygosity, rarefacted number of alleles per locus and distances based on molecular coancestry information were computed. Probabilities of assignment of the Assaf.E individuals to native Spanish dairy sheep breeds and cryptic genetic structure in the whole dataset were also assessed. It can be concluded that the Assaf.E breed has low genetic variability and high genetic distance with respect native Spanish dairy sheep breeds. From our results, the formation of the Assaf.E breed basically occurred via the absorption of individuals belonging to the Entrefino type, particularly to the Castellana and Manchega populations. Furthermore, Churra individuals may have participated in the formation of the Assaf.E breed at an early moment of the introduction of the breed into Spain.     

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H_E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.     

Reconstructing the population history of Nicaragua by means of mtDNA,Y‐chromosome STRs,and autosomal STR markers

Before the arrival of the Spaniards in Nicaragua, diverse Native American groups inhabited the territory. In colonial times, Native Nicaraguan populations interacted with Europeans and slaves from Africa. To ascertain the extent of this genetic admixture and provide genetic evidence about the origin of the Nicaraguan ancestors, we analyzed the mitochondrial control region (HVSI and HVSII), 17 Y chromosome STRs, and 15 autosomal STRs in 165 Mestizo individuals from Nicaragua. To carry out interpopulation comparisons, HVSI sequences from 29 American populations were compiled from the literature. The results reveal a close relationship between Oto‐manguean, Uto‐Aztecan, Mayan groups from Mexico, and a Chibchan group to Nicaraguan lineages. The Native American contribution to present‐day Nicaraguan Mestizos accounts for most of the maternal lineages, whereas the majority of Nicaraguan Y chromosome haplogroups can be traced back to a West Eurasian origin. Pairwise Fst distances based on Y‐STRs between Nicaragua and European, African and Native American populations show that Nicaragua is much closer to Europeans than the other populations. Additionally, admixture proportions based on autosomal STRs indicate a predominantly Spanish contribution. Our study reveals that the Nicaraguan Mestizo population harbors a high proportion of European male and Native American female substrate. Finally, the amount of African ancestry is also interesting, probably because of the contribution of Spanish conquerors with NorthAfrican genetic traces or that of West African slaves. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites

Genotype data from 30 microsatellites were used to assess genetic diversity and relationships among 10 native Portuguese cattle breeds, American Charolais and the Brazilian Caracú. Hardy–Weinberg equilibrium was observed for all loci/population combinations except for five loci in Brava de Lide and one locus in Alentejana that exhibited heterozygote deficiency. Estimates of average observed and expected heterozygosities, total number of alleles (TNA) per breed and mean number of alleles (MNA) per locus/population were obtained. A total of 390 alleles were detected. TNA among Iberian cattle ranged from 170 to 237 and MNA ranged from 5.67 to 8.07. The highest observed heterozygosities were found in the Caracú, Maronesa, Garvonesa and Arouquesa and the lowest in Brava de Lide and Mirandesa. Estimation of population subdivision using Wright's F_ST index showed that the average proportion of genetic variation explained by breed differences was 9%. Neighbour‐joining phylogenetic trees based on D_A distances showed that the genetic relationships of present‐day Portuguese native breeds are consistent with historical origins in the Brown Concave (Arouquesa, Mirandesa, Marinhoa) and Red Convex (Mertolenga, Alentejana, Garvonesa, Minhota) evolutionary groups. The Iberian Black Orthoide group, represented by Brava de Lide and Maronesa, and the Barrosã breed appeared to be more closely related to the Brown Concave group but may represent a separate lineage. The Caracú breed was not found to be closely associated with any of the native Portuguese breeds.     

Genetic characterization and breed assignment in five Italian sheep breeds using microsatellite markers

The knowledge of the genetic relationship and admixture among neighbouring populations is crucial for conservation efforts. The aim of this study was to analyse the genetic diversity of five Italian sheep breeds (Appenninica, Garfagnina Bianca, Massese, Pomarancina and Zerasca) using a panel of 24 microsatellite markers. Blood samples from 226 individuals belonging to the aforementioned populations were obtained and genotyped. All the investigated breeds showed a significant heterozygote deficiency caused by the high level of inbreeding indicated also by the high level of F_IS (0.146). Genetic differentiation between breeds was moderate (F_ST = 0.05) but significant and the individuals could be assigned to their breeds with an high success rate even if the inter-individual distances showed that few animals clustered separately from the other individuals of the same breed, especially for Pomarancina breed. The genetic distances reflect the historical knowledge of these breeds and some patterns of ancestral and recent gene flow between neighbour populations arise. The clustering analysis detects the presence of six clusters. Massese and Zerasca breeds were grouped together as well as Appenninica and Pomarancina with the latter forming two distinct clusters equally represented. The formation of this last breed is occurred with the absorption of individuals of the Appenninica breed and the gene flow probably continued in these recent years allowing the presence of a population substructure for Pomarancina breed. Such substructure supports the high level of heterozygote deficiency found for this breed despite the relatively high population size. The five populations analysed presented some genetic similarities but a clear uniqueness of the populations has been showed for almost all of them. Special attention to monitor genetic variability and to organize mating plans should be given especially for the three endangered breeds.     

Population admixture,biological invasions and the balance between local adaptation and inbreeding depression

When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important role in biological invasions. In contrast, populations in their native range often remain differentiated and frequently suffer from inbreeding depression owing to isolation. While the advantages of admixture are evident for introduced populations that experienced recent bottlenecks or that face novel selection pressures, it is less obvious why native range populations do not similarly benefit from admixture. Here we argue that a temporary loss of local adaptation in recent invaders fundamentally alters the fitness consequences of admixture. In native populations, selection against dilution of the locally adapted gene pool inhibits unconstrained admixture and reinforces population isolation, with some level of inbreeding depression as an expected consequence. We show that admixture is selected against despite significant inbreeding depression because the benefits of local adaptation are greater than the cost of inbreeding. In contrast, introduced populations that have not yet established a pattern of local adaptation can freely reap the benefits of admixture. There can be strong selection for admixture because it instantly lifts the inbreeding depression that had built up in isolated parental populations. Recent work in Silene suggests that reduced inbreeding depression associated with post-introduction admixture may contribute to enhanced fitness of invasive populations. We hypothesize that in locally adapted populations, the benefits of local adaptation are balanced against an inbreeding cost that could develop in part owing to the isolating effect of local adaptation itself. The inbreeding cost can be revealed in admixing populations during recent invasions.     

Genetic diversity and relationships of endangered Spanish cattle breeds

Information on the genetic structure and variability of autochthonous livestock breeds is essential for effective conservation programs. Here we present a molecular characterization on the basis of 30 microsatellite markers of 5 Spanish endangered cattle breeds Betizu (BET), Mallorquina (MAL), Menorquina, Monchina (MON), and Serrana de Teruel (ST) and of 2 fighting bull populations, Casta Navarra (CN) and Casta Vistahermosa. The feral and critically endangered BET is divided into 2 subpopulations, one of which has exceptionally low diversity values. A low number of alleles was also observed in the island population MAL. Although the small population size and genetic drift have caused a considerable divergence between the breeds, phylogenetic analysis is in accordance with historical and geographical data. The 2 northern Spanish feral breeds BET and MON cluster together. The local fighting breed CN is relatively close to the more inbred Casta Vistahermosa, which is the progenitor of most other fighting bulls in Spain. Comparison with nonendangered breeds suggests admixture of Alpine and/or Pyrenean mountain cattle in the ST, which may contribute to the high level of linkage disequilibrium in this population.     

Pedigree analysis of eight Spanish beef cattle breeds

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña – Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163).     

Variation in the gene frequencies of three generations of humans from Monterrey, Nuevo León, Mexico

Allele frequencies for the ABO, Rh, MNSs, Duffy, Kidd, Lutheran, P and Lewis blood group systems in 207 persons whose 4 grandparents were born in the Monterrey Metropolitan area (MMA), grouped into 3 generations, were ascertained along with other related population from the MMA, Mestizos from Saltillo, Coahuila and Tlaxcala, and from the populations thought to have contributed to their genetic constitution (native Mexican Indians and Spanish). Genetic admixture and distance estimates were calculated. Gene frequencies of the three generations from MMA are intermediate to those of the ancestral populations, indicating that they are Mestizo but with a genetic structure different from Mestizos of Saltillo and Tlaxcala. Both genetic admixture and distance estimates indicate that the oldest generation exhibits the greatest Spanish influence which decreases in the youngest generation and in the other MMA populations as a result of the immigration from the central states of Mexico.     

Inferring the population structure of the Maghreb sheep breeds using a medium‐density SNP chip

North Africa has a great diversity of indigenous sheep breeds whose origin is linked to its environmental characteristics and to certain historical events that took place in the region. To date, few genome‐wide studies have been conducted to investigate the population structure of North African indigenous sheep. The objective of the present study was to provide a detailed assessment of the genetic structure and admixture patterns of six Maghreb sheep populations using the Illumina 50K Ovine BeadChip and comparisons with 22 global populations of sheep and mouflon. Regardless of the method of analysis used, patterns of multiple hybridization events were observed within all North African populations, leading to a heterogeneous genetic architecture that varies according to the breed. The Barbarine population showed the lowest genetic heterogeneity and major southwest Asian ancestry, providing additional support to the Asian origin of the North African fat‐tailed sheep. All other breeds presented substantial Merino introgression ranging from 15% for D'man to 31% for Black Thibar. We highlighted several signals of ancestral introgression between North African and southern European sheep. In addition, we identified two opposite gradients of ancestry, southwest Asian and central European, occurring between North Africa and central Europe. Our results provide further evidence of the weak global population structure of sheep resulting from high levels of gene flow among breeds occurring worldwide. At the regional level, signs of recent admixture among North African populations, resulting in a change of the original genomic architecture of minority breeds, were also detected.     

Genetic structure of Eurasian cattle (Bos taurus) based on microsatellites: clarification for their breed classification1

We pool three previously published data sets and present population genetic analyses of microsatellite variation in 48 Bos taurus cattle breeds from a wide range of geographical origins in Eurasia, mostly its northern territory. Bayesian model‐based clustering reveals six distinct clusters: besides a single‐population cluster of the Yakutian Cattle from Far Eastern Siberia and a cluster of breeds characteristic of an early origin, the other four major clusters largely correspond to previously defined morphological subgroups of Red Lowland, Lowland Black‐Pied, Longhorned Dairy and North European Polled cattle breeds. The results highlighted past expansion events of the productive breeds such as Danish Red, Angeln, Holstein‐Friesian and Ayrshire in northern and Eastern Europe. Based on genetic assignment of the breeds and the availability of breed information, we provide a preliminary classification of the five breeds that were to date undefined. Furthermore, in the analysis of molecular variance, despite some correspondence between geographical proximity and genetic similarity, the breed classification appears to be a better predictor of genetic structure in the cattle populations (the among‐group variance component: breed classification, 2.47%, P < 0.001; geographical division, 0.77%, P < 0.001).     

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.     

Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers

Twenty-seven domesticated yellow cattle breeds of China and three introduced cattle breeds were analysed by means of 30 microsatellite markers to determine the level of genetic variation within and among populations as well as the population structure. In all, 480 microsatellite alleles were observed across the 30 breeds with the mean number of alleles per locus of 9.093 for native breeds and 6.885 for the three introduced breeds. Mean F -statistics (0.08) for Chinese native cattle breeds implied that 92% of the total genetic variation was from genetic differentiation within each breed and 8% of the genetic variation existed among breeds. A phylogenetic tree was constructed based on Nei's genetic distances, and three clusters were obtained. According to the tree, the three introduced breeds were distinct from the 27 native breeds. The indigenous cattle breeds were divided into two clusters, one cluster including five humpless breeds and the other cluster containing 22 humped breeds. This study identifies multiple origins of yellow cattle of China from Bos taurus and Bos indicus . Furthermore, population structure analysis implies that there are possibly five independent original domestications for yellow cattle in China. Four of five origins were four different Bos indicus types, mainly in areas of the Chang Jiang, the Zhu Jiang River basin, the Yellow River and the Huai River basin. The other origin was for Bos taurus type of Mongolian descent, mainly located in Northwestern China, the Mongolian plateau and Northeastern China or north of the Great Wall.