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1.
In this study, we genotyped 117 autosomal single nucleotide polymorphisms using a DigiTag2 assay to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations, including nine cattle breeds and seven native cattle. Phylogenetic and principal component analyses showed that Bos taurus and Bos indicus populations were clearly distinguished, whereas Japanese Shorthorn and Japanese Polled clustered with European populations. Furthermore, STRUCTURE analysis demonstrated the distinct separation between Bos taurus and Bos indicus (K=2), and between European and Asian populations (K=3). In addition, Japanese Holstein exhibited an admixture pattern with Asian and European cattle (K=3‐5). Mongolian (K=13‐16) and Japanese Black (K=14‐16) populations exhibited admixture patterns with different ancestries. Bos indicus populations exhibited a uniform genetic structure at K=2‐11, thereby suggesting that there are close genetic relationships among Bos indicus populations. However, the Bhutan and Bangladesh populations formed a cluster distinct from the other Bos indicus populations at K=12‐16. In conclusion, our study could sufficiently explain the genetic construction of Asian cattle populations, including: (i) the close genetic relationships among Bos indicus populations; (ii) the genetic influences of European breeds on Japanese breeds; (iii) the genetic admixture in Japanese Holstein, Mongolian and Japanese Black cattle; and (iv) the genetic subpopulations in Southeast Asia.  相似文献   

2.
Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (FST). The exact test for Hardy‐Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds.  相似文献   

3.
In Iberia there are 51 officially recognized cattle breeds of which 15 are found in Portugal and 38 in Spain. We present here a comprehensive analysis of the genetic diversity and structure of Iberian cattle. Forty of these breeds were genotyped with 19 highly polymorphic microsatellite markers. Asturiana de los Valles displayed the greatest allelic diversity and Mallorquina the least. Unbiased heterozygosity values ranged from 0.596 to 0.787. The network based on Reynolds distances was star-shaped with few pairs of interrelated breeds and a clear cluster of 4 breeds (Alistana/Arouquesa/Marinhoa/Mirandesa). The analysis of the genetic structure of Iberian cattle indicated that the most probable number of population clusters included in the study would be 36. Distance results were supported by the STRUCTURE software indicating a relatively recent origin or possible crossbreeding or both between pairs or small groups of breeds. Five clusters included 2 different breeds (Betizu/Pirenaica, Morucha/Avile?a, Parda de Monta?a/Bruna de los Pirineos, Barros?/Cachena, and Toro de Lidia/Brava de Lide), 3 breeds (Berrenda en Negro, Negra Andaluza, and Mertolenga) were divided in 2 independent clusters each, and 2 breeds were considered admixed (Asturiana de los Valles and Berrenda en Colorado). Individual assignation to breeds was not possible in the 2 admixed breeds and the pair Parda de Monta?a/Bruna de los Pirineos. The relationship between Iberian cattle reflects their geographical origin rather than their morphotypes. Exceptions to this geographic clustering are most probably a consequence of crossbreeding with foreign breeds. The relative genetic isolation within their geographical origin, the consequent genetic drift, the adaptation to specific environment and production systems, and the influence of African and European cattle have contributed to the current genetic status of Iberian cattle, which are grouped according to their geographical origin. The greater degree of admixture observed in some breeds should be taken into account before using molecular markers for genetic assignment of individuals to breeds.  相似文献   

4.
Abstract

Comparisons of seven different individual assignment methods based on likelihood and distances were carried out with four different sets of data, which varied both in number of populations and genetic divergence. Based on 27 microsatellites genotyped in eight cattle breeds (Icelandic and seven Norwegian), 28 hybrid populations were simulated. Factors affecting individual assignment success, such as number and divergence of populations, sample size and number of loci, were assessed from actual and simulated data. The Bayesian, frequency and Nei-minimum methods performed more or less similarly. Individual assignment success depended mainly on population number and divergence (FST). Higher success was observed at high level of divergence among populations and at low number of source populations considered. With eight pure breeds and 27 loci considered the assignment success rate ranged from 55 to 70%. Generally, assignment success increased with increasing number of loci and/or sample size.  相似文献   

5.
ABSTRACT

Breed assignment was performed for pigs putatively belonging to Pied Danish Pigs, an endangered Danish conservation breed. DNA array data were available for the candidates who had insufficient pedigree information. So were data for a reference population of animals from Danish conservation breeds as well as data from a range of Northern European pig breeds, and wild boar. Breed proportions were estimated using the program ADMIXTURE. Half the candidates were found to have at least 95% of their ancestry from Pied Danish Pigs. Several candidates showed varying degrees of admixture with other breeds, most notably Gloucester Old Spot. The same was observed for several of the Pied Danish Pig reference animals. The analyzes identified suitable breeding candidates and prevented unwanted recent admixture from spreading in the breeding population.  相似文献   

6.
The gene pool of indigenous Faroe Islands Cattle is strongly affected by crossing with Norwegian Red. In this study, the genetic structure in 191 animals representing five North European cattle breeds (Faroe Islands, Icelandic, Blacksided Troender, Western Fjord and Norwegian Red) and the genetic admixture in the contemporary Faroe Islands Cattle at the population and individual level were evaluated using 20 polymorphic microsatellite loci. Only 6.7% of the total genetic variation could be attributed to the differences amongst the breeds. The factorial correspondence analysis based on all allele frequencies could hardly reveal a divergence between Faroe Islands Cattle and Norwegian Red. In addition, a Neighbor‐Net tree constructed to examine the allocation of individuals of Faroe Islands Cattle and Norwegian Red provided a detailed interrelationship network for all the 72 animals. An estimation of the population admixture proportion showed a strong genetic contribution by Norwegian Red (47.3%) in the contemporary Faroe Islands Cattle. On the other hand, individual admixture analysis demonstrated that only seven of the individual Faroe Islands Cattle analysed, which also showed more traditional colour patterns, could be assigned to the Faroe Islands Cattle cluster, probably representing the breed's remaining purebred animals. Strategies for preserving the original native genes in Faroe Islands Cattle should be considered in order to prevent the breed from becoming extinct and to strengthen the breed's capability in future breeding programmes.  相似文献   

7.
Genetic variability and relationships among five cattle breeds (Holstein, Pinzgau, Limousin, Slovak Spotted and Charolais) bred in the Slovak Republic were investigated separately using 11 microsatellite markers and 61 blood group systems. Allele frequency, heterozygosity (Ho, HE) and PIC values were investigated. F-statistics were computed separately. For microsatellite markers FIS, FIT, FST and for blood groups HS, HT, GST parameters were calculated. Microsatellite and blood group comparison showed similar results by F-statistics but some differences were marked using the other methods. Both methods were able to detect close relation between Slovak Pinzgau and Slovak Spotted cattle breeds. Their relation was confirmed by genetic distance, principal component analysis (PCA) and coefficient of admixture (mY). Important divergences between different markers used in the study were observed by the characterisation of Limousin and Charolais breeds.  相似文献   

8.
From a genetic point of view, the selection of breeds and animals within breeds for conservation in a national gene pool can be based on a maximum diversity strategy. This implies that priority is given to conservation of breeds and animals that diverge most and overlap of conserved diversity is minimized. This study investigated the genetic diversity in the Dutch Red and White Friesian (DFR) cattle breed and its contribution to the total genetic diversity in the pool of the Dutch dairy breeds. All Dutch cattle breeds are clearly distinct, except for Dutch Friesian breed (DF) and DFR and have their own specific genetic identity. DFR has a small but unique contribution to the total genetic diversity of Dutch cattle breeds and is closely related to the Dutch Friesian breed. Seven different lines are distinguished within the DFR breed and all contribute to the diversity of the DFR breed. Two lines show the largest contributions to the genetic diversity in DFR. One of these lines comprises unique diversity both within the breed and across all cattle breeds. The other line comprises unique diversity for the DFR but overlaps with the Holstein Friesian breed. There seems to be no necessity to conserve the other five lines separately, because their level of differentiation is very low. This study illustrates that, when taking conservation decisions for a breed, it is worthwhile to take into account the population structure of the breed itself and the relationships with other breeds.  相似文献   

9.
Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure.  相似文献   

10.
In 2002, it was discovered that several Cika cattle in the mountain areas of Slovenia had escaped the official policy of cross‐breeding. Here, we report a genetic characterization to assess their status as autochthonous breed. We compared genotypes for 14 microsatellite markers in 150 Cika cattle individuals with data from 16 Central European cattle breeds. We show that Cika cattle are genetically as diverse as other Eastern Alpine breeds, are more diverse than Austrian Simmental but less than the Balkan Busha cattle. STRUCTURE analysis showed Pinzgauer admixture in several individuals but also indicated a unique genetic identity for Cika. This analysis also allowed a selection of the most genetically pure Cika individuals as assessed by the panel of microsatellites. These original Cika cattle form an Eastern Alpine breed cluster together with Pinzgauer and Pustertaler cattle. Cika cattle should be considered as an authentic and valuable genetic resource, which offers clear opportunities for sustainable agriculture and landscape conservation in marginal and mountain areas.  相似文献   

11.
The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.  相似文献   

12.
Although many research papers have studied diversity and differentiation within livestock species, genetic relationships among neighboring populations remain poorly understood. Here we apply recent methodologies to analyze the polymorphism of 14 microsatellites in 238 unrelated individuals belonging to six sheep breeds from Northern Spain to ascertain their historical relationships and the relative genetic contributions existing between populations. Individual genotypes were analyzed to assess the existence of an underlying genetic structure. Long-term and recent migration rates were estimated to identify patterns of relative genetic contribution among breeds. The complete data set showed a strong population structure derived from both different ancestral origins and some geographical patterns of recent gene flow. Two of the analyzed breeds (Black-faced Latxa and Churra) had a marked genetic background, supporting the hypothesis that, regardless of their phenotypical similarities, they have different ancestral origins. Some of the more presumably related breeds had negative long-term admixture coefficients, showing that they diverged only recently. In addition, we show how methodologies for estimation of long-term gene flow and recent patterns of migration are complementary, providing information about migration rates on different timescales.  相似文献   

13.
Genetic variability and relationships among six native French cattle breeds (Abondance, Tarentaise, Villard de Lans, Montbéliarde, Limousin, and Charolais) and one foreign breed (Holstein) were investigated using 23 microsatellite markers. These breeds were also compared with four Swiss breeds genotyped in a previously published study. Interestingly, the French alpine breeds have smaller population sizes but showed higher genetic variability than the larger Holstein breed. Neighbor-joining trees and PCA (principal components analysis) showed that alpine breeds tend to cluster together. Abondance and Tarentaise breeds were closely related, whereas the Holstein was highly differentiated from all breeds analyzed. Two different assignment tests for determining the breed of origin of individuals were compared: "direct" and "exclusion-simulation" approaches. The exclusion-simulation significance test correctly assigns fewer individuals than the direct approach but provides a confidence level (e.g., P < 0.01) for each individual being assigned. Accurate assignment with high statistical confidence is required for animal traceability. Unfortunately, the accuracy of assignment greatly decreases as the threshold level of confidence of assignment increases (e.g., from P < 0.05 to P < 0.001). Assignment accuracy also greatly declines as the level of population differentiation decreases below the level often found between related breeds (e.g., F(ST) < 0.1).  相似文献   

14.
Genetic diversity among some cattle breeds in the Alpine area   总被引：2，自引：0，他引：2  
Seven autochthonous Italian cattle breeds bred in the alpine area (Aosta Black Pied, Aosta Red Pied, Aosta Chestnut, Oropa Red Pied, Grey Alpine, Rendena and Burlina) were investigated in order to characterise their genetic structure and to study their phylogenetic origin. Two cattle breeds from Germany (Original German Brown and Holstein) and four from Switzerland (Simmental, Herens, Evolene and Brown Swiss) were included in the study in order to determine the genetic diversity existing among Italian local breeds, similar breeds bred on the other side of the Alps and in the well known Holstein.
Seventeen microsatellites, of the internationally accepted panel for the study of cattle biodiversity, were used for the analysis.
Microsatellites were highly polymorphic with a mean number of 5,5 alleles (ranging from 2 to 12 per locus). For each locus, allelic frequencies, heterozygosity (H) and the Polymorphism Information Content (PIC) were computed. The genetic equilibrium according to Hardy–Weinberg was calculated for each population and for each locus. Allele frequencies were used to estimate genetic distances and to draw a phylogenetic tree. The two closest breeds were Aosta Red Pied and Aosta Black Pied, while the two genetically most different were Holstein and Aosta Chestnut. Aosta valley breeds, Evolene and Herens constituted a tight cluster in the phylogenetic consensus tree. Principal component analysis showed a similar pattern for all the alpine breeds, while Holstein and Original German Brown were far away. The genetic differences among breeds were in accordance with their geographical and historical origins.  相似文献   

15.
Abstract

The Icelandic cattle breed is believed to have been brought to Iceland from Norway around 1100 years ago. Since then it is thought to have been almost completely isolated and to have gone through large fluctuations in population size. Here molecular markers were used to assess the breed's genetic diversity and the current within-population genetic structure using a randomly selected unbiased sample from the population as verified by calculations of the coefficient of relationship (R). Measures of genetic diversity suggest that there is considerable diversity within the breed despite long-term isolation and the effective population size is high considering the isolation and the breeding system used in recent years. No evidence of recent bottlenecks was found and analysis of population structure suggests that the population is uniform in structure.  相似文献   

16.
ABSTRACT

Genetic diversity in livestock animals has become recognized as important genetic resource for future sustainable livestock production. Especially native breeds, adapted to their local environment, are of considerable interest. Here, we report a genome-wide characterization of two native Danish sheep breeds, the Danish Landrace sheep and the Danish White-Headed Marsh sheep. We investigated the genetic diversity both at national and European breed level using a European-derived reference panel. The native Danish breeds are genetically distinct from other Nordic breeds. Their closest relatives are Border Leicester, Galway, and Texel. Apart from gene flow between native Danish breeds, Texel admixture was most dominant. For Danish Landrace sheep, a population split into two genetically distinct sub-populations was detected. Compared to other livestock species, genomic inbreeding was moderate. However, among European-derived sheep the native Danish breeds were among the 10 most inbred investigated, illustrating the need for sustainable management strategies to preserve genetic diversity.  相似文献   

17.
Recovering native uniqueness has major importance for breeds with historic introgression. The aim of the study was to estimate population genetic parameters for two local red cattle breeds from Northern Germany and to study possibilities to reverse introgression. Genealogical information consisted of 90,783 individuals for German Angler and 187,255 individuals for Red Dual-Purpose cattle breed, with additional information on sex, born, breed, status, and conventional breeding values. It is concluded that the native genetic contribution could be included as an additional trait in the total merit index in order to recover a part of the native genetic background. Native contributions should be estimated in the long term from marker data in order to account for Mendelian sampling. The maintenance of a sufficient genetic diversity of native alleles can be achieved by an advanced OCS with appropriate constraints.  相似文献   

18.
Growth- and breed-related changes of marbling characteristics in cattle   总被引：1，自引：0，他引：1  
The objective of this study was to investigate the growth- and breed-related changes of marbling characteristics in cattle. Four cattle breeds with different growth impetus and muscularity were reared and slaughtered under experimental conditions. German Angus, as a typical beef cattle; Galloway, as a smaller, environmentally resistant beef cattle; Holstein-Friesian, as a dairy-type cattle; and double-muscled Belgian Blue, as an extreme type for muscle growth, were used. These 4 breeds were expected to have differences in muscle development and i.m. fat deposition. Between 5 and 15 bulls of each breed were slaughtered at 2, 4, 6, 12, or 24 mo of age. Marbling characteristics were determined and classified in LM and semitendinosus muscle by computerized image analysis. Among breeds, differences appeared in the quantity, structure, and distribution of the marbling flecks in both muscles. The deposition of fat in the double-muscled Belgian Blue bulls remained substantially inferior to that of the other breeds, up to the age of 24 mo. Marbling in German Angus bulls particularly showed larger (P < 0.05) marbling fleck areas. Galloway cattle had the greatest (P < 0.05) number and the most regular (P < 0.05) distribution of the marbling flecks in young animals. Furthermore, for marbling characteristics in Holstein-Friesian animals, a great number and slightly finer structure were observed compared with the other breeds investigated. Postnatal growth-related changes of marbling in LM were characterized by as much as a 40-fold increase in the number of marbling flecks from 2 to 24 mo of age but also by up to a 4-fold enlargement in the area of the marbling flecks. The structure of marbling flecks was determined by 2 development trends. On the one hand, the marbling flecks became larger (P < 0.05), and the structure became coarser, which was reflected by an increasing (P < 0.01) proportion of long marbling flecks as well as an increasing (P < 0.01) maximum skeleton line length. On the other hand, continually new small, round marbling flecks appeared. This caused a decrease (P < 0.01) in the proportion of the 3 largest marbling fleck areas. The distribution of the marbling flecks became more regular (P < 0.05) with increasing proportion and number of marbling flecks. The results suggest that hyperplasia of adipocytes plays an important role in marbling during growth of muscle in cattle.  相似文献   

19.
Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well‐documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree‐based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario.  相似文献   

20.
Genetic diversity in Swiss cattle breeds   总被引：1，自引：0，他引：1  
Introduction First attempts at establishing the genetic relationships among cattle populations relied on archeological evidence (Epstein 1971; Epstein and Mason 1984) and protein polymorphisms (Baker and Manwell 1980, 1991). Loftus et al. (1994) examined mitochondrial DNA to determine the divergence time between Bos taurus and Bos indicus. Today most studies on genetic diversity are based on microsatellite analysis (Litt and Luty 1989; Tautz 1989; Weber and May 1989). Microsatellites were used in, e.g. man (Bowcock et al. 1994), canids (Roy et al. 1994; Fredholm and Winter ø ; 1995) and sheep (Buchanan et al. 1994). Recent studies in cattle are also microsatellite based (e.g. Machugh et al. 1994; Ciampolini et al. 1995; Moazami -Goudarzi et al. 1997) and aim at facilitating the development of management programs for endangered breeds (FAO 1981). Our microsatellite-based investigation on the genetic diversity between and within Swiss cattle breeds included Original Swiss Brown, purebred Simmental, Holstein, Hérens and Evolènard. Previous studies in Swiss breeds made use of blood group systems (Reuse 1969), serum transferrin and hemoglobin (Krummen 1964), amylase (Buser 1970) and carboanhydrases (Kä ;stli et al. 1980). The Hérens breed is endemic to the canton of Wallis. The Evolènard, which are very few in numbers and restricted to a single valley in the canton of Wallis, are phenotypically very similar to the Hérens with the exception of the coat colour. In the Aosta valley (Italy) which borders the canton of Wallis these two breeds find their counterparts. The phenotype of the Aosta Chestnut fits the Hérens and the Aosta Black Pied fits the Evolènard. The Holstein breed replaced the Fribourg breed which was a colour variant of the purebred Simmental breed (Engeler et al. 1961) and is now extinct. The Original Swiss Brown and the purebred Simmental are endemic to Switzerland.  相似文献   

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