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1.
The Japanese Brown is the second most common domestic beef breed in Japan. However, nowadays this breed is facing reduction in numbers because of pressure from a profitable domestic breed. This breed is uniformly characterized by its brown coat colour, but is comprised of two isolated sub‐breeds, Kumamoto and Kouchi, each possessing a different gene pool. Pedigree analyses were carried out for the two sub‐breeds using the pedigree records of animals born from 1970 to 2000. The effective population size has been found to be consistently reducing during the last three decades in both sub‐breeds. The current effective sizes were estimated to be 25.5 and 6.0 for the Kumamoto and Kouchi sub‐breeds, respectively. The estimate of the effective number of founders (Nef) in the Kumamoto sub‐breed decreased from 152.1 to 74.4; that of non‐founders (Nenf), from 41.7 to 5.3; and that of founder genome equivalents (Nge), from 32.7 to 4.9. The corresponding changes in the Kouchi sub‐breed were from 108.2 to 79.4, 16.2 to 4.1, and 14.1 to 3.9. Increasing differences between the two genetic diversity indices in the sub‐breeds indicate that the greater part of the reduction of genetic diversity can be attributed to genetic drift that accumulated in the non‐founder generations. A comparison with published estimates for several cattle breeds suggests the extremely limited genetic diversity of Japanese Brown. In addition to the avoidance of further reduction of genetic diversity, it will be important to counteract the process of breed decline by establishing a production system to efficiently utilize the unique characteristics of this breed and by developing links between the breed and products with market value.  相似文献   

2.
Gene dropping simulation was applied to Japanese Black cattle population in Hyogo prefecture, to examine the survivals of alleles originated from founder animals. In the analysis, unique alleles were assigned to founders, and the genotypes of all descendants along the actual pedigree were generated through Monte Carlo simulation following Mendelian segregation rules. By replicating this process 10 000 times, the distribution of frequencies of alleles from each founder was estimated. From the distribution, several quantities useful for the management of genetic diversity, such as the probability of allele extinction and the probability of alleles surviving at a critically low frequency were derived. The materials used were 68 781 animals born in 1955–1998 and their pedigree records traced back to the population in 1937 or before. The expected number of alleles retained in the population drastically decreased during the analyzed period, and reached to 57.9 in the population of 1998, which was only 3.3% of the total number of alleles assigned to founders. Detailed analysis of major founders with relatively high genetic contributions to the current population revealed that alleles from most of the major founders are now at high risk of future extinction. These results strongly suggest that for the management of genetic diversity, the genetic contributions of founders are not fully informative, and emphasize the importance of the detection of live animals having founder alleles with high extinction possibilities.  相似文献   

3.
The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (Nge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on Nge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.  相似文献   

4.
The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1 048 572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non‐founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non‐founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co‐ancestry and inbreeding, which would lead to better handling of the effective population size.  相似文献   

5.
The Catalonian donkey is one of the most endangered donkey breeds in the world. At present, five main subpopulations exist: AFRAC, which consists of many genetically connected Catalonian localities; Berga, which consists of a single herd located also in Catalunya but under private management; and three minor non‐Catalonian subpopulations (Huesca, Sevilla and Toledo). In this study, we analysed the pedigree information of the Catalonian donkey herdbook to assess the genetic diversity and population structure of the breed. We found that the Catalonian donkey has suffered an important loss of genetic diversity and moderate to high increases of inbreeding because of the abuse of a few individuals in matings. This scenario is mainly characterized by the fact that both the effective number of founders and ancestors for the whole population was 70.6 and 27, respectively, while the equivalent number of founders was 146.5 and the number of ancestors explaining overall genetic variability was 93. In addition, only 14% of animals born between the 1960s and 1970s were significantly represented in the pedigree. Our results also show that subpopulations where breeders exchanged reproductive individuals had low levels of inbreeding and average relatedness. One subpopulation, Berga, was reproductively isolated and showed high levels of inbreeding (F = 7.22%), with average relatedness (AR = 6.61%) playing an important role in increasing the values of these coefficients in the whole pedigree. Using genealogical F‐statistics we have found little evidence of population structuring (FST = 0.0083) with major genetic differences among non‐Catalonian subpopulations.  相似文献   

6.
Genetic variability of the dog breed Hanoverian Hound was analysed using a set of 16 microsatellites. The sample of 92 dogs was representative for the total current population [n = 334, inbreeding coefficient 9.2%, relationship coefficient 11.2%] with respect to the level and distribution of the inbreeding and relationship coefficients. All microsatellites used were in Hardy–Weinberg equilibrium. The average number of alleles was 6.4. The average observed heterozygosity (HO) was slightly higher than the expected heterozygosity (HE). Dinucleotide microsatellites exhibited lower polymorphism information content (PIC) than tetranucleotide microsatellites (0.52 versus 0.66). The average PIC was 0.61. The individual inbreeding coefficient was negatively related to the average HO of all microsatellites, whereas the proportion of genes from introducing of Hanoverian Hounds from abroad showed no relationships to HO. We found that the genetic variability in the Hanoverian Hounds analysed here was unexpectedly higher than that previously published for dog breeds of similar population size. Even in dog breeds of larger population size heterogyzosity was seldom higher than that observed here. The rather high genetic variability as quantified by polymorphic microsatellites in Hanoverian Hounds may be due to a large genetic variation in the founder animals of this breed and to the fact that this genetic diversity could be maintained despite genetic bottlenecks experienced by this breed in the 1920s and 1950s and despite the presence of high inbreeding and relationship coefficients for more than 50 years.  相似文献   

7.
In this study, we have investigated the genetic variability of three Italian cattle breeds, autochthonous of the Tuscany region (Chianina, Maremmana and Mucca Pisana), using the parameters based on probabilities of gene origin: f e, f a and N g. Compared with Chianina (N g=53.9) and Maremmana (N g=79.6), Mucca Pisana was found to be the genetically smaller (N g=10.1) and less diverse population. The genetic variability in Chianina population was lower than in Maremmana probably because of bottlenecks in its pedigree and genetic drift. However, the values found in these breeds were higher than those found in dairy cattle breeds, but lower than those found in beef cattle breeds.  相似文献   

8.
The genetic diversity of the Red Bororo and White Fulani cattle breeds of Cameroon and Nigeria was assessed with a panel of 32 markers. Estimates for the various indices of genetic diversity, total number of alleles (TNA), mean observed number of alleles (MNA), mean effective number of alleles (MNE), observed heterozygosity (H ob) and expected heterozygosity (H ex), were higher at microsatellite loci than at protein loci. Mean H ex values were above 71% at microsatellite loci in all the breeds and ranged from 37% to 41.6% at milk protein loci and from 40.9% to 45.6% at blood protein loci. The highest TNA and MNA of microsatellites were recorded for the Nigerian White Fulani. MNE of milk protein loci was highest in the Cameroonian Red Bororo, while TNA of blood protein loci was highest in the Cameroonian White Fulani. The high genetic diversity levels indicate the presence of the necessary ingredients for improvement breeding and conservation. Multi-locus estimates of within-population inbreeding (f), total inbreeding (F) and population differentiation (θ) of the breeds were significantly different from zero, except for θ of blood proteins. A high level of gene flow was found between the breeds (5.829). The phylogenetic relationship existing among the four breeds is greatly influenced by location. The high gene flow between the breeds may lead to a loss of genetic diversity through genetic uniformity and a reduction in opportunities for future breed development. We propose an improvement scheme with aims to prevent loss of genetic diversity, improve productivity and reduce uncontrolled genetic exchanges between breeds.  相似文献   

9.
Conservation of genetic diversity in farm animal species can be achieved by preventing extinction of breeds and by reducing genetic drift within breeds. It is suggested to use the expected number of alleles segregating in the species after a given time period as objective function in the design of conservation strategies. A formal approach is presented to predict this quantity based on marker information, accounting for extinction probability of breeds and effective population size within breeds as the major component of genetic drift. Based on this model, relative efficiency of different strategies of diversity conservation can be quantified. Formulas are given to derive the marginal expected number of alleles with respect to genetic drift within population and extinction probability, respectively. The suggested approach is illustrated with an example of 13 European cattle breeds. With the assumed parameters, drift is shown to be the major force leading to loss of alleles, and different breeds are prioritized for activities to reduce risk of extinction and for measures to reduce genetic drift, respectively. Although different aspects of the model need to be further refined, the suggested methodology provides a general and flexible tool to derive the optimum conservation strategy in various scenarios.  相似文献   

10.
Maintaining genetic diversity and inbreeding control are important in Japanese Black cattle production, especially in remote areas such as the islands of Okinawa Prefecture. Using a single-nucleotide polymorphism (SNP) array, we evaluated the genetic diversity and genomic inbreeding in Japanese Black cows from the islands of Okinawa Prefecture and compared them to those from other locations across Japan. Linkage disequilibrium decay was slower in cows in the islands of Okinawa Prefecture. The estimated effective population size declined over time in both populations. The genomic inbreeding coefficient (FROH) was estimated using long stretches of consecutive homozygous SNPs (runs of homozygosity; ROH). FROH was higher in the cows on the islands of Okinawa Prefecture than on other locations. In total, 818 ROH fragments, including those containing NCAPG and PLAG1, which are major quantitative trait loci for carcass weight in Japanese Black cattle, were present at significantly higher frequencies in cows in the islands of Okinawa Prefecture. This suggests that the ROH fragments are under strong selection and that cows in the islands of Okinawa Prefecture have low genetic diversity and high genomic inbreeding relative to those at other locations. SNP arrays are useful tools for evaluating genetic diversity and genomic inbreeding in cattle.  相似文献   

11.
Genetic contributions of nine historically important ancestors and allelic diversity in the Japanese Thoroughbred population were examined by applying the gene dropping simulation to the foals produced from 1978 to 2005. Full pedigree records traced to ancestors (base animals) born around 1890 were used for the simulation. Alleles originated from some of the historically important ancestors were found to be at risk of future extinction, although their genetic contributions to the foal population have increased during the last three decades. The proportion of surviving alleles to the total alleles assigned to the base animals was 8.0% in the foal population in 2005, suggesting that a large part of genetic variability contained in the base animals is extinct in the current population.  相似文献   

12.
In this study we examined the genetic diversity of yak populations in the northernmost part of their current global distribution. Five Mongolian and one Russian yak populations as well as one Chinese yak population from the Qinghai–Tibetan Plateau, the putative centre of yak domestication, were analysed with 15 microsatellite loci to determine the level of genetic variation within populations as well as the genetic differentiation and relationship between populations. A total of 116 microsatellite alleles were identified. The mean number of alleles per locus (MNA) across populations was 7.73 ± 1.98 and the mean expected heterozygosity (HE) was 0.696 ± 0.026. The relative magnitude of gene differentiation (FST) among populations was 4.1%, and all genetic differentiations (FST) between populations were significant (p < 0.001). A significant inbreeding effect (FIS) was detected in the Hovsgol yak (p < 0.01). There was no indication of a recent bottleneck in any of the populations studied. The results showed that yak populations in Mongolia and Russia have maintained high genetic diversity within populations and a low, although significant, genetic differentiation between populations. Both phylogenetic and principal component analyses support a close genetic relationship between the Gobi Altai, south Gobi and north Hangai populations, and between the Hovsgol and Buryatia populations respectively. Our results indicate that these yak populations should be considered as distinct genetic entities in respect of conservation and breeding programmes.  相似文献   

13.
The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average coancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.  相似文献   

14.
The effective number of breedable individuals is a crucial determinant for maintaining genetic variability within a population. The population of Bargur, the hill cattle of South India, has gone down drastically by more than 93 % in the past three decades, and only a few thousand animals are available at present. The present study was undertaken to evaluate Bargur cattle for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck event, if any, in this population. About 50 unrelated animals, true to the type, were sampled and genotyped at 25 microsatellite loci. The mean observed heterozygosity (0.808?±?0.023) was higher than the mean expected heterozygosity (0.762?±?0.008) with 15 out of 25 microsatellite loci exhibiting heterozygosity excess when assumed under Hardy–Weinberg equilibrium. To evaluate Bargur cattle for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM), stepwise mutation model (SMM) and two-phase model (TPM). The observed gene diversity (H e) and expected equilibrium gene diversity (H eq) were estimated under different models of microsatellite evolution. All the 25 loci were found to exhibit gene diversity excess under IAM and TPM, while 22 loci were having gene diversity excess under SMM. All the three statistical tests, viz., sign test, standardized differences test, and Wilcoxon sign rank test, revealed significant (P?<?0.01) deviation of Bargur cattle population from mutation-drift equilibrium under all the three models of mutation. Furthermore, the qualitative test of allele frequency distribution in Bargur cattle population revealed a strong mode shift from the normal L-shaped form suggesting that the population had experienced genetic bottleneck in the recent past. The occurrence of genetic bottleneck might have led to the loss of several rare alleles in the population, which point towards the need for efforts to conserve this important cattle germplasm. The present study is the first report in demonstrating the genetic basis of demographic bottleneck in an Indian cattle population.  相似文献   

15.
In the present study, microsatellite data on 24 loci were generated and utilized to evaluate the genetic architecture and mutation drift equilibrium of Marathwada buffaloes, a Central Indian population maintained under low input system. Sufficient allelic diversity was observed with a total of 109 alleles across different loci. The genetic diversity analysis of Marathwada buffaloes displayed moderate level of within breed variability in terms of mean number of alleles per locus (4.48) and heterozygosity values (Ho = 0.532, He = 0.624). The studied Indian buffalo population showed considerable heterozygote deficiency (FIS = 0.138) and deviation from HWE at many investigated loci. Three quantitative tests viz. sign test, standardized difference test and Wilcoxon sign rank test and a qualitative test for mode shift distortion of allelic frequencies were employed to evaluate mutation drift equilibrium under three different models of microsatellite evolution. The population was found to deviate significantly under IAM and TPM, while it was reverse under SMM. The qualitative test for mode shift supported the results under SMM indicating the absence of genetic bottleneck in the recent past in Marathwada buffaloes.  相似文献   

16.
The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability of the Mazandaran native fowls in Iran by quantifying the pedigree completeness index, effective population size, genetic diversity, inbreeding level, and individual increase in inbreeding. The pedigree completeness analysis showed 3.31 full, 10.19 maximum, and 6.30 equivalent generations. The effective number of founders (f e) was 131, representing 5% of the potential number of founders. The effective number of ancestors (f a) was 81, and the genetic contribution of the 37 most influent ancestors explained 50% of the genetic variability in the population. The ratio f e/f a (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.62. The inbreeding coefficient increased over generations and the average was 1.93%. The average relatedness coefficient between individuals of the population was estimated to be 2.59%. The effective population size, based on the number of full generations, was 56. Family size analysis showed that fewer males than females were used, resulting in the observed levels of inbreeding. Average inbreeding coefficient in the Mazandaran native fowls can be regarded to be below critical levels. However, considering the relationship coefficients of individuals is recommended to aid maintaining genetic diversity of Mazandaran native fowls.  相似文献   

17.
Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise FST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.  相似文献   

18.
Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (Ho) and expected (He) heterozygosity, individual coancestry coefficients (f and fm), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (fa), effective population size (Ne and Ne(m)) and founder genome equivalents (Ng and Ng(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (fm, Mk and Ng(m)). However, Ho and He showed the highest values for C1 and the molecular heterozygote deficiency within population (FIS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.  相似文献   

19.
The genetic structure of three Indian sheep breeds from two different geographical locations (Nali, Chokla from north‐western arid and semi‐arid region; Garole from eastern saline marshy region) of India was investigated by means of 11 ovine‐specific microsatellite markers as proposed in FAOs MoDAD programme. Microsatellite analysis revealed high allelic and gene diversity in all the three breeds. Nali sheep showed higher mean number of alleles and gene diversity (6.27 and 0.65) than Chokla (5.63 and 0.64) and Garole (5.63 and 0.59). High within population inbreeding estimates observed in the three breeds (FIS, Chokla = 0.286, Nali = 0.284, Garole = 0.227) reflected deficit of heterozygotes. The overall estimates for F‐statistics were significantly (p < 0.05) different from zero. High values of FST (0.183) across all the loci revealed substantial degree of breed differentiation. Based on pair wise FST and Nm between different breeds, Nali and Chokla (FST = 6.62% and Nm = 4.80) were observed to be the closest followed by Garole and Nali (FST = 20.9% and Nm = 1.80), and Garole and Chokla (FST = 21.4% and Nm = 1.71). In addition, genetic distance estimates, phylogeny analysis and individual assignment test used to evaluate interbreed genetic proximity and population structure also revealed substantial genetic differentiation between Garole and the other two Rajasthani (Nali and Chokla) sheep. This divergent status of Garole sheep indicated genetic uniqueness of this breed suggesting higher priority for its conservation.  相似文献   

20.
Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (fa) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis () is 168, whereas the genetic effective population size (Neg) computed the decay of linkage disequilibrium (r2) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had fa of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz ( = 98 and Neg = 49). Interestingly, the r2 data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed.  相似文献   

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