利用微卫星标记鉴定德州驴亲子关系

试验旨在建立一套适用于德州驴亲子关系的鉴定体系。选取13个微卫星基因座作为标记,采集了53头德州驴血液样本,其中子代驴驹16头,候选父本13头,候选母本24头,用酚-仿法抽提血液基因组进行PCR扩增和基因扫描,并利用Peak Scanner Software v1.0软件读取基因型分型结果。对微卫星基因座的遗传多样性进行分析,利用似然法（Cervus 3.0软件）和排除法对个体间的亲子关系进行了鉴定。结果显示,13个微卫星基因座的平均等位基因数、平均观测杂合度（Ho）、平均期望杂合度（He）和平均多态信息含量（PIC）分别为6.846、0.689、0.671和0.625。期望杂合度与观测杂合度之差在0.002~0.088之间,差值较小。13个微卫星基因座的累计排除概率（EP）达到0.990以上。微卫星基因座具有高度多态性和较高的排除概率,适用于遗传分析和个体鉴定。利用Cervus 3.0软件基于似然法分析得到了16头子代驴驹的最似亲本,结合排除法对这16头驴驹及其最似亲本进行基因型比对,最终在53头德州驴中确定了11个亲子对。本试验建立了以13个微卫星位点作为核心标记,将似然法和排除法相结合作为主要分析方法的德州驴亲子关系鉴定体系,为育种工作提供参考资料。     

Extension of the concept of kinship, relationship, and inbreeding to account for linked epistatic complexes

Although epistatic effects are well defined and, in principle, can be exploited in quantitative-genetic selection theory, they often are ignored or even treated as nuisance parameters in practical applications. Traditionally, epistasis is considered as an interaction between genes at unspecified loci. Inspired by the observation that functional genes are often organised in physical clusters, we developed a model to combine additive effects and additive × additive interactions in linked gene clusters of defined length. Malécot's kinship concept is extended to identity by descent probabilities for chromosome segments of a given length in Morgan units, called epistatic kinship. Using the analogy of Malécot's kinship and Wright's relationship and inbreeding coefficients, epistatic relationship coefficients and epistatic inbreeding coefficients are defined. Simple rules are given to set up the epistatic numerator relationship matrix and its inverse directly from a pedigree list. The well-known single locus parameters and algorithms to set up the additive numerator relationship matrix and its inverse are a special case of the suggested methodology for a chromosome segment length of null Morgan. A proof of concept of the suggested method is given with a small simulation study. Assuming additive, linked epistatic and residual variance components, 100 replicated data sets for 1000 individuals are generated. From these data, residual maximum likelihood estimates of the variance components and of the chromosome segment size are obtained. Potential applications of the methodology are discussed. Given that a substantial variance component is attributed to this effect, the expected genetic gain can be increased on the short term if selection is on additive and epistatic effects, the latter comprising additive × additive interaction effect of loci in linkage disequilibrium. This extra benefit, however, will diminish through crossing over in subsequent generations. Despite some practical problems yet to be solved, the suggested model and algorithms open new perspectives to use a higher proportion of genetic variability in selection and breeding.     

Epistatic kinship a new measure of genetic diversity for short-term phylogenetic structures – theoretical investigations

The epistatic kinship describes the probability that chromosomal segments of length x in Morgan are identical by descent. It is an extension from the single locus consideration of the kinship coefficient to chromosomal segments. The parameter reflects the number of meioses separating individuals or populations. Hence it is suggested as a measure to quantify the genetic distance of subpopulations that have been separated only few generations ago. Algorithms for the epistatic kinship and the extension of the rules to set up the rectangular relationship matrix are presented. The properties of the epistatic kinship based on pedigree information were investigated theoretically. Pedigree data are often missing for small livestock populations. Therefore, an approach to estimate epistatic kinship based on molecular marker data are suggested. For the epistatic kinship based on marker information haplotypes are relevant. An easy and fast method that derives haplotypes and the respective frequencies without pedigree information was derived based on sampled full‐sib pairs. Different parameters of the sampling scheme were tested in a simulation study. The power of the method decreases with increasing segment length and with increasing number of segments genotyped. Further, it is shown that the efficiency of the approach is influenced by the number of animals genotyped and the polymorphism of the markers. It is discussed that the suggested method has a considerable potential to allow a phylogenetic differentiation between close populations, where small sample size can be balanced by the number, the length, and the degree of polymorphism of the chromosome segments considered.     

Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole‐genome genotyping assay

Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers. The allelic frequencies for each SNP were estimated using additional individuals by PCR‐RFLP (restriction fragment length polymorphism). A total of 87 SNP markers added in conjunction with previously developed 27 SNPs were evaluated to assess the utility of the test. The estimated identity power was 2.01 × 10^?34. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.99999997 and 0.99998010, respectively. This developed SNP panel was quite powerful and could successfully exclude false sires with a probability of >0.9999 even if the dam's genotype information was not obtained. The SNP system would contribute to management of the beef industry in Japan.     

Studies on the Taxonomy of the South African Tectocepheidae Grandjean 1953 (Oribatei,Acari)

Mousebirds (Coliiformes) exhibit well-developed communal roosting behaviour as well as a pronounced capacity for facultative hypothermic responses. We recorded body temperature (T_b)) in speckled mousebirds (Colius striatus) under semi-natural conditions in outdoor aviaries, and examined interactions between behavioural and metabolic thermoregulation by experimentally manipulating food availability and communal roosting behaviour. When food was available ad libitum, mousebirds roosting in a cluster maintained approximately constant rest-phase T_b, with 32°C < T_b < 42°C. By contrast, rest-phase T_b in single mousebirds decreased at 0.5°C/hr and minimum rest-phase T_b was significantly lower than when clustering. When food availability was restricted, the mousebirds exhibited facultative hypothermic responses that were less pronounced in clustering groups (minimum rest-phase T_b = 33.3°C, circadian amplitude of T_b = 9.5°C) compared to single birds (minimum rest-phase T_b = 30.7°C, circadian amplitude of T_b = 11.8°C). When clustering, rest-phase T_b was highly synchronized among individuals. Our data reveal that communal roosting has profound consequences for rest-phase thermoregulation in C. striatus, and provide further insights into the potential role of physiological constraints in the evolution of avian sociality.     

Analysis of genetic variability in the Czech Dachshund population using microsatellite markers

The primary goal of this study was to analyse genetic variation within and among six Dachshund varieties in the Czech Republic using 10 microsatellites from StockMarks^® Paternity Polymerase Chain Reaction (PCR) Typing kit. A total of 632 Dachshunds were sampled – 99 Standard Smooth-haired, 72 Standard Long-haired, 272 Standard Wire-haired, 42 Miniature Smooth-haired, 73 Miniature Long-haired and 74 Miniature Wire-haired. Average observed heterozygosity and polymorphic information content ranged in particular Dachshund varieties between 0.58–0.70 and 0.57–0.64, respectively. Subsequent analysis of the population structure ( F -statistics; Nei's genetic identity) showed that Standard Dachshunds shared allele frequencies most closely with their miniature equivalents, and smooth coat type is closer to Wire-haired coat type than to the Long-haired one. Analysis of molecular variance revealed that 11.81% of the total variance occured among varieties. The value of combined exclusion probability (0.9955) validated usefulness of this panel of microsatellites for parentage verification in all analysed populations. We carried out 234 parentage verifications with 1.28% cases where parentage did not match.     

Estimation of total genetic effects for survival time in crossbred laying hens showing cannibalism,using pedigree or genomic information

Mortality of laying hens due to cannibalism is a major problem in the egg‐laying industry. Survival depends on two genetic effects: the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its group mates (IGE). For hens housed in sire‐family groups, DGE and IGE cannot be estimated using pedigree information, but the combined effect of DGE and IGE is estimated in the total breeding value (TBV). Genomic information provides information on actual genetic relationships between individuals and might be a tool to improve TBV accuracy. We investigated whether genomic information of the sire increased TBV accuracy compared with pedigree information, and we estimated genetic parameters for survival time. A sire model with pedigree information (BLUP) and a sire model with genomic information (ssGBLUP) were used. We used survival time records of 7290 crossbred offspring with intact beaks from four crosses. Cross‐validation was used to compare the models. Using ssGBLUP did not improve TBV accuracy compared with BLUP which is probably due to the limited number of sires available per cross (~50). Genetic parameter estimates were similar for BLUP and ssGBLUP. For both BLUP and ssGBLUP, total heritable variance (T²), expressed as a proportion of phenotypic variance, ranged from 0.03 ± 0.04 to 0.25 ± 0.09. Further research is needed on breeding value estimation for socially affected traits measured on individuals kept in single‐family groups.     

STR技术在种用东北细毛羊遗传管理中的应用

以10个STR基因座作为遗传标记系统，分析东北细毛羊种群的遗传多样性和亲缘关系。在遗传多样性分析中，群体的平均等位基因数为8．2，平均杂合度为0．794，平均多态信息含量为0．768，遗传多样水平较丰富。在亲缘关系鉴定和确认中，双亲鉴定时，10个微卫星基因座的累积非父排除概率为0．9999，平均父权相对机会(RCP)为99．999％；单亲鉴定时，累积非父排除概率为0．9962，平均RCP为99．993％。根据所选的STR基因座，可建立一套适用于种用东北细毛羊遗传资源分析和亲缘关系鉴定的方法体系，为我国东北细毛羊品种资源的保护和经济性状的筛选提供科学指导。同时，也可为解决东北细毛羊归属纠纷提供一个科学的鉴定方法。     

Observation of intra‐group and extra‐group copulation and reproductive characters in free ranging groups of western black crested gibbon (Nomascus concolor jingdongensis)

Black crested gibbons (Nomascus concolor) are 1 of only 3 gibbon species that have been observed in long‐term polygynous groups, but their mating behavior and reproductive characters have never been reported. Based on population monitoring over 7 years and direct observation for 26 months of the study groups in Wuliang Mountain, central Yunnan, we describe for the first time the copulation behavior and breeding pattern of free‐ranging western black crested gibbons. The gestation period of black crested gibbons is estimated to be between 6 and 7 months. The average breeding interval is 3.5 years, with infant independence at approximately 2.5 years. We observed 2 intra‐group copulations and 5 extra‐group copulations. Copulations were initiated when a female gave a ‘solicitation’ gesture. When a male made any mating attempt, the female might refuse it. These results demonstrate direct female mate choice. Both male and female gibbons dispersed from their natal groups and sometimes replaced paired adults in other groups. We observed no evidence of infanticide during inter‐group conflicts or after replacement of adults. Together with extra‐group copulations, these phenomena indicate a flexible social organization and complex mating system. We also observed a male‐biased sex ratio among offspring. More genetic work is necessary to describe the effects of inter‐group copulation and the genetic diversity of this population.     

Widespread infection with hemotropic mycoplasmas in bats in Spain,including a hemoplasma closely related to “Candidatus Mycoplasma hemohominis”

Molecular analyses of blood samples revealed infection with hemoplasmas in 97% of 31 cave bats captured in three caves in North-Eastern Spain. The characterization of 1250 bp of the 16S rRNA gene in 29 of the positive bats identified two different groups of sequences. Twenty-two Schreibers’ bats (Miniopterus schreibersii) and one long-eared bat (Myotis capaccinii) shared one group, composed of seven closely related sequences. These sequences showed an identity of about 97% with “Candidatus Mycoplasma hemohominis” and the phylogenetic branch including bat and human sequences showed a 100% bootstrap value, supporting a close phylogenetic relationship between these hemoplasmas. The second group, representing a potentially novel species, was composed of a single sequence shared by six Schreibers’ bats that had 91% identity with the recently reported hemoplasma from little brown bats in North America. Large bat aggregations in roosting caves probably benefits intra and inter-species transmission explaining the high observed prevalence.     

Accuracy of pastoralists' memory-based kinship assignment of Ankole cattle: a microsatellite DNA analysis

This study aimed to estimate the level of relatedness within Ankole cattle herds using autosomal microsatellite markers and to assess the accuracy of relationship assignment based on farmers' memory. Eight cattle populations (four from each of two counties in Mbarara district in Uganda) were studied. Cattle in each population shared varying degrees of relatedness (first-, second- and third-degree relatives and unrelated individuals). Only memory-based kinship assignments which farmers knew with some confidence were tested in this experiment. DNA isolated from the blood of a subsample of 304 animals was analysed using 19 microsatellite markers. Average within population relatedness coefficients ranged from 0.010 ± 0.005 (Nshaara) to 0.067 ± 0.004 (Tayebwa). An exclusion probability of 99.9% was observed for both sire-offspring and dam-offspring relationships using the entire panel of 19 markers. Confidence from likelihood tests performed on 292 dyads showed that first-degree relatives were more easily correctly assigned by farmers than second-degree ones (p < 0.01), which were also easier to assign than third-degree relatives (p < 0.01). Accuracy of kinship assignment by the farmers was 91.9% ± 5.0 for dam-offspring dyads, 85.5% ± 3.4 for sire-offspring dyads, 75.6% ± 12.3 for half-sib and 60.0% ± 5.0 for grand dam-grand offspring dyads. Herd size, number of dyads assigned and length of time spent by the herder with their cattle population did not correlate with error in memorizing relationships. However, herd size strongly correlated with number of dyads assigned by the herder (r = 0.967, p < 0.001). Overall, we conclude that memorized records of pastoralists can be used to trace relationships and for pedigree reconstruction within Ankole cattle populations, but with the awareness that herd size constrains the number of kinship assignments remembered by the farmer.     

Application of DNA markers in parentage verification of Boran cattle in Kenya

Boran cattle provide livelihood to thousands of households in the arid and semiarid lands of Kenya. Due to their superior adaptive and productive traits in comparison to other breeds of cattle, they have also become a popular choice for breeders in Eastern and Southern Africa. Continued genetic improvement of the breed is important, and therefore accurate performance and pedigree records are required. One hundred seventy-eight pedigree records and blood samples of four Boran stud herds were evaluated for accuracy of parentage allocation using 11 microsatellite markers recommended by ISAG for parentage verification. The panel of the 11 microsatellite markers was found to be highly polymorphic (PIC of 0.6901) with a combined probability of exclusion of 0.9997. The dam misidentification was low ranging between 0% and 5% for the herds tested. The estimated rate of mispaternity however ranged between 4.3% and 80% among the four stud herds, and more than 50% of the offspring of some herds were misidentified. The high rate of mispaternity will have a negative impact on the response to selection. The use of DNA markers for parentage assignment will improve the accuracy of the pedigree records of Boran stud cattle in Kenya and contribute to more accurate selection of superior animals.     

Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes

We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross‐breed. Elite nucleus herds had access to high‐quality feed, and production herds were fed low‐quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (r_g = 0.2), medium (r_g = 0.5) and high (r_g = 0.8). In our alternative breeding schemes, different proportion of production animals were recorded for feed efficiency and genotyped with high‐density panel of genetic markers. Genomic breeding value of the selection candidates for feed efficiency was estimated based on three different approaches. In one approach, genomic breeding value was estimated including nucleus animals in the reference population. In the second approach, the reference population was containing a mixture of nucleus and production animals. In the third approach, the reference population was only consisting of production herds. Using a mixture reference population, we generated 40–115% more genetic gain in the production environment as compared to only using nucleus reference population that were fed high‐quality feed sources when the production animals were offspring of the nucleus animals. When the production animals were grand offspring of the nucleus animals, 43–104% more genetic gain was generated. Similarly, a higher genetic gain generated in the production environment when mixed reference population was used as compared to only using production animals. This was up to 19 and 14% when the production animals were offspring and grand offspring of nucleus animals, respectively. Therefore, in genomic selection pig breeding programmes, feed efficiency traits could be improved by properly designing the reference population.     

Space use at night and social relationship between roosting partners in a large flock of laying hens

1. Laying hens in two aviary flocks of 1250 females and 12 males were investigated to determine if hens used the same roosting site more often than expected by chance and whether hens that roost next to each other for two consecutive nights (close groups) had fewer agonistic interactions than hens roosting far away from each other (distant groups) when put into a new environment in groups of 4 birds.

2. Hens showed a significant preference for using the same roosting site on consecutive nights. There was no difference between close groups and distant groups in agonistic interactions. However, in close but not distant groups, a low or high level of interaction on day 1 predicted a low or high level on day 2 that might reflect established relationships in the close groups.

3. It was concluded that hens prefer the same roosting site in the short term but further research is needed to investigate whether hens roosting next to each other recognise roosting partners or not.     

Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap

Breeding circles allow genetic management in closed populations without pedigrees. In a breeding circle, breeding is split over sub‐populations. Each sub‐population receives breeding males from a single sub‐population and supplies breeding males to one other sub‐population. Donor‐recipient combinations of sub‐populations remain the same over time. Here, we derive inbreeding levels both mathematically and by computer simulation and compare them to actual inbreeding rates derived from DNA information in a real sheep population. In Veluws Heideschaap, a breeding circle has been in operation for over 30 years. Mathematically, starting with inbreeding levels and kinships set to zero, inbreeding rates per generation (ΔF) initially were 0.29%–0.47% within flocks but later converged to 0.18% in all flocks. When, more realistically, inbreeding levels at the start were high and kinship between flocks low, inbreeding levels immediately dropped to the kinship levels between flocks and rates more gradually converged to 0.18%. In computer simulations with overlapping generations, inbreeding levels and rates followed the same pattern, but converged to a lower ΔF of 0.12%. ΔF was determined in the real population with a 12 K SNP chip in recent generations. ΔF in the real population was 0.29%, based on markers to 0.41% per generation based on heterozygosity levels. This is two to three times the theoretically derived values. These increased rates in the real population are probably due to selection and/or the presence of dominant rams siring a disproportionate number of offspring. When these were simulated, ΔF agreed better: 0.35% for selection, 0.38% for dominant rams and 0.67% for both together. The realized inbreeding rates are a warning that in a real population inbreeding rates in a breeding circle can be higher than theoretically expected due to selection and dominant rams. Without a breeding circle, however, inbreeding rates would have been even higher.     

Lineage diversification and niche evolution in the Reeves’ Butterfly Lizard Leiolepis reevesii (Agamidae)

We used mitochondrial cytochrome b and ND4 genes and 9 microsatellite loci to determine genetic diversity, population structure, evolutionary history, and migration patterns within the Reeves’ butterfly lizard Leiolepis reevesii (Agamidae). Considering molecular-based phylogeographical lineages, we then performed niche equivalency and similarity tests between divergent lineages. Phylogenetic analyses based on mitochondrial DNA (mtDNA) data revealed 2 lineages (A and B) diverging ≈0.84 million years ago and, respectively, restricted to the northern and southern portions of the Wuzhishan and Yinggeling mountain ranges. Lineage B contains individuals from southern Hainan; Lineage A includes individuals from all other localities and can be further divided into 3 clusters according to microsatellite data. The null hypothesis that the 2 lineages shared identical niches was rejected in all niche equivalency tests, indicating niche shifts during genetic divergence. Similarity tests provided evidence of niche conservatism, suggesting that the 2 lineages share more characteristics of their niche spaces than randomly expected. The niche similarity and equivalency tests indicated a complex niche pattern in which both lineages share a main portion of their ecological spaces. The climatic niche of Lineage B represented a marginal and specialized fraction of the entire ecological space of the climatic niche of Lineage A, with warmer conditions. Isolation caused by orogenesis and subsequent niche divergence, together with local adaptation, may have led to genetic differentiation and further lineage sorting in L. reevesii.     

Genetic Analysis of Dobrava–Belgrade Virus from Western Serbia – A Newly Detected Focus in the Balkan Peninsula

Dobrava–Belgrade virus (DOBV) is a hantavirus species that causes the most severe form of haemorrhagic fever with renal syndrome (HFRS) in Europe. DOBV has been detected in three Apodemus rodents: A. flavicollis, A. agrarius and A. ponticus. These emerging viruses appear throughout the Balkan Peninsula including Serbia as its central part. In this study, we examined the seroprevalence, molecular epidemiology and phylogenetics of DOBV from A. flavicollis captured at six Serbian localities. Furthermore, we applied microsatellite typing of host animal genome to analyse the role of host kinship in DOBV animal transmission. The overall IgG seropositivity rate over 3 years (2008–2010) was 11.9% (22/185). All seropositive samples were subjected to RT‐PCR and DNA sequencing for S and L genome segments (pos. 291–1079 nt and 2999–3316 nt, respectively). DOBV was genetically detected in three samples from mountain Tara in western Serbia, a newly detected DOBV focus in the Balkans. No sequence data from human cases from Serbia are available for the studied period. However, collected DOBV isolates in this work phylogenetically clustered together with isolates from Serbian human cases dating from 2002, with 1.9% nucleotide divergence. We determined the level of kinship between seropositive and seronegative animal groups and found no significant difference, suggesting that horizontal virus transmission in the studied population was the same within and among the hatches. Our findings are the first genetic detection of DOBV in rodents in Serbia. We confirm wide and continuous hantavirus presence in the examined parts of the Balkans, underlying the necessity of continual monitoring of hantavirus circulation in A. flavicollis.     

Genetic diversity and matrilineal genetic origin of fat-rumped sheep in Ethiopia

Ethiopia is home to a diverse gene pool of indigenous sheep populations. Therefore, a better understanding of genetic variation holds the key to future utilization through conservation. Three of these breeds, Afar, Blackhead Somali, and Hararghe Highland, are found in eastern Ethiopia where they contribute significantly to the livelihood of most pastoralist, agro-pastoralist, and smallholder farmers. These indigenous sheep are recognized on the basis of morphotype and their genetic distinction remains unknown. Here, to assess genetic variation, and matrilineal genetic origin and relationship of fat-rumed sheep found in eastern Ethiopia, 300 individuals from the three breeds were genotyped for 22 microsatellite markers and sequenced for the mitochondrial DNA displacement loop (mtDNA d-loop) region. The overall H_O and H_E were 0.57 and 0.75, respectively. Differentiation statistics revealed that a high proportion (97%) of the total genetic variation was explained by differences between individuals within populations. Genotype assignment independent of the population of origin showed K?=?2 to be the optimum number of genetic backgrounds present in the dataset. This result was further confirmed by mtDNA D-loop sequences comparison in which the matrilineal genetic origin of eastern Ethiopia sheep is from two haplotype groups (types A and B) among the five haplotypes globally observed. Taken together, our findings suggest that the sheep populations from three breeds originated from two ancestral genetic backgrounds that may have diverged prior to their introduction to Ethiopia. However, to obtain a complete picture of the evolutionary dynamics of Ethiopian indigenous sheep, more samples and populations from within and outside of the country will need to be analyzed.

     

Genetic evaluation using parentage information from genetic markers

Genetic evaluation relies on pedigree information to account for the trait information on individuals and their relatives. Recording pedigrees may place unfavorable restrictions on the management of breeding populations, such as the use of single-sire mating groups and the observation of parturition. The use of DNA marker information is an alternative method to identify parents, but it is difficult to assign the parents unambiguously for all progeny in extensively farmed livestock without the use of very many markers. We present methods that use DNA information on parentage within a genetic evaluation system that allow for genotyping errors and for the parentage information to be incomplete, with probabilities assigned to possible parent pairs (i.e., fractional parentage assignment). Two of these methods use a computing strategy that circumvents the high memory requirements associated with the application of previous methods designed for use with fractional parentage assignment. This strategy has an additional advantage of allowing the same statistical models to be used in the evaluation as with recorded pedigrees. The use of DNA marker-based parentage for genetic evaluation is associated with lower genetic gain (at the same survival levels) than by using the true pedigree. This decrease in gain depends on a number of factors, including trait heritability and the DNA markers used. The methods we have described show how DNA marker information could be used to replace traditional pedigree recording.     

Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms

Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (F_it) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (F_is) amounted to 6.1%. The breeds were moderately differentiated (F_st = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the F_st value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub‐clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub‐clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds.