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1.
Up to now, prioritization of animals for conservation has been mainly based on pedigree information; however, genomic information may improve prioritization. In this study, we used two Holstein populations to investigate the consequences for genetic diversity when animals are prioritized with optimal contributions based on pedigree or genomic data and whether consequences are different at the chromosomal level. Selection with genomic kinships resulted in a higher conserved diversity, but differences were small. Largest differences were found when few animals were prioritized and when pedigree errors were present. We found more differences at the chromosomal level, where selection based on genomic kinships resulted in a higher conserved diversity for most chromosomes, but for some chromosomes, pedigree-based selection resulted in a higher conserved diversity. To optimize conservation strategies, genomic information can help to improve the selection of animals for conservation in those situations where pedigree information is unreliable or absent or when we want to conserve diversity at specific genome regions.  相似文献   

2.
Considering the effects of selection, dominance, epistasis and linkage, a stochastic computer simulation was performed to study how well inbreeding coefficients calculated from pedigree (fped) and genotypic frequencies (fhet) correspond to the inbreeding coefficient that is defined as the proportion of autozygous loci in the modelled genome (i.e. the level of autozygosity, faut). Although in random mating populations all three inbreeding coefficients show almost (with slight deviations in models with two loci) the same expectation, they represent three separate variables. First, faut, fped and fhet responded differently to selection, dominance, epistasis and linkage. Second, they did not have the same standard deviations, which means that the effects of random drift, especially in models under selection, were not affecting all three coefficients in the same way. Finally, they were not always defined in the same domain. With selection as the most important factor responsible for the observed discrepancies, the bias (discrepancy) was present in both directions, thus leading to overestimation or underestimation of the observed level of autozygosity depending on the genetic model, linkage and initial gene frequency. Variation of the autozygosity level (between replicates) was increased notably in models with additive inheritance under selection and was an additional potential source of bias. Thus, when the trait is, to a large extent, controlled by a finite number of loci and when selection is present, the bias in the estimation of the autozygosity is likely to occur and caution is necessary whenever conclusions are based on inbreeding coefficients estimated from the pedigree or decrease in heterozygosity.  相似文献   

3.
The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20–122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within‐breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. The mean molecular coancestry of the entire population examined was 0.205, Losino being the breed that contributed most. In addition to Nei's standard and Reynolds’ genetic distances, pair‐wise kinship distance and molecular coancestry were estimated. Remarkably similar breed rankings were obtained with all methods. Clustering analysis provided an accurate representation of the current genetic relationships among the breeds. Determining coancestry is useful for analysing genetic diversity distribution between and within breeds and provides a good framework for jointly analysing molecular markers and pedigree information. An integrated analysis was undertaken to obtain information on the population dynamics in western Mediterranean native horse populations, and to better determine conservation priorities.  相似文献   

4.
The aim of the current study was to investigate whether multiple oral dosing of valacyclovir could result in plasma concentrations exceeding the EC50-value of acyclovir against equine herpesvirus 1 (EHV1) during the majority of the treatment period. Additionally, we wanted to determine the concentration of acyclovir in nasal mucus and cerebrospinal fluid (CSF). Valacyclovir was administered to four horses and two ponies, three times daily, at a dosage of 40 mg/kg, for four consecutive days. Blood was collected prior to each administration and 1 h after dosing. Nasal mucus samples and CSF were collected once during treatment; 1 h after the last administration. This dosage regimen resulted in plasma concentrations that were higher than the EC50-value of 1.7 μg/mL, i.e. EC50 of an isolate highly susceptible to acyclovir, for 80% of the treatment period; and higher than the EC50-value of 3.0 μg/mL, i.e. EC50 of an isolate less susceptible to acyclovir, for 60% of the treatment period. Concentration in nasal mucus samples and CSF was 0.36–1.17 μg/mL and 0.11–0.23 μg/mL, respectively. This study illustrates that multiple dosing of valacyclovir may result in a therapeutic benefit as plasma concentrations could be maintained above the EC50-value of acyclovir against EHV1 for more than 50% of the treatment period. Acyclovir could be detected in both nasal mucus samples and CSF. However, these concentrations were lower than the EC50.  相似文献   

5.
The Martina Franca (MF) donkey, an ancient native breed of Apulia, was mostly famous for mule production. The breed was at serious risk of extinction in the 1980s following the decrease in demand for draft animals because they were increasingly replaced by agricultural machinery. Much has been done in the last few decades to safeguard the existing donkey breeds, but the situation remains critical. Successful implementation of conservation measures includes an evaluation of the present degree of breed endangerment, so the aim of this work was to analyze the demographic and genetic parameters of this breed to suggest effective conservation strategies. With a current breed register counting less than 500 recorded animals, the pedigree data set included 1,658 MF donkeys born between 1929 and 2006. Analyses were carried out on the whole data set as well as on a smaller one consisting of 422 living animals. Demographic and genetic variability parameters were evaluated using the ENDOG (v4.6) software. The pedigree completeness level was evaluated as well as the generation length, which was calculated for each of the 4 gametic pathways. This information was obtained from animal birth date records together with those of their fathers and mothers. The effective number of founders (f(e)), the effective number of ancestors (f(a)), the founder genome (f(g)), individual inbreeding (F), average relatedness (AR), and the rate of inbreeding per generation were analyzed to describe the genetic variability of the population. Because pedigree depth and completeness were appropriate, especially regarding the current population, the parameters defining genetic variability, namely, f(e), f(a), f(g), F, and AR, could be reliably estimated. Analysis of these parameters highlighted the endangerment status of the MF donkey. Our special concern was with the increased percentage of males and females exhibiting increased AR values. Moreover, the effective size of the current population, 48.08, is slightly less than the range of the minimum effective size, and the rates of inbreeding per generation found in the current MF population exceed the maximum recommended level of 1%. Such a scenario heightens concerns over the endangered status of the MF breed and calls for proper conservation measures and breeding strategies, such as selecting individuals for mating when relationships are below 12.5%.  相似文献   

6.
The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.  相似文献   

7.
Genetic relationships between Swiss sheep breeds were estimated on the basis of microsatellite analysis. In addition to the Swiss breeds wild-type Mouflon was included in this investigation. Polymerase chain reaction amplifications of 31 ovine, bovine and caprine microsatellites were performed in a total of 307 animals representing eight populations. The average heterozygosity within each population was high in the domestic breeds (0.60–0.71) and lower in Mouflon 0.45. The average coefficient of gene differentiation G ST over all loci was 0.17, i.e. a small part of the variability at the 31 microsatellite loci analysed must be ascribed to between-breed variability. Genetic distances between breeds were obtained, which were used to construct a phylogenetic tree. Microsatellites developed from closely related species of cattle and goat are useful for estimating genetic relationships among sheep breeds.  相似文献   

8.
The water buffalo plays a key role in the socio-economy of South-East Asia as it is the main draught power for paddy rice cultivation. While in the Indian subcontinent the water buffalo is the riverine type, in South-East Asia the majority of buffaloes are of the swamp type. In the poor remote northern province of Ha Giang in Vietnam, improvement of the swamp buffalo breed may be one of the best ways to increase sustainability of farming systems. Therefore, analysis of the genetic structure of the province buffalo population is a prerequisite to any conservation or improvement project. A total of 1122 animals were described for 11 body and horn measurements for morphometric characterization. From this sample set, 744 animals were genotyped for 17 microsatellite markers. Also 17 animals from southern provinces of Vietnam were genotyped as a comparative sample. The results showed that genetic diversity as well as inbreeding value in the Ha Giang was high. The F ST values within the province and across Vietnam were low indicating that most of the population variation is explained by individual variability. Bayesian clustering analysis did not highlight the presence of subdivided populations. These results are useful for the implementation of a conservation and improvement strategy of the swamp buffalo in order to guarantee the householders' needs for sustainability of the farming system in the Ha Giang province.  相似文献   

9.
基于SRAP和SSR分子标记分析了青藏高原东南缘8个老芒麦自然居群遗传变异及群体遗传结构,获得下述结果:1)16对SRAP引物在90个单株中共扩增出384条可统计条带,其中多态性条带334条,占86.98%;16个SSR位点共检测出等位变异221个,平均每个位点13.8个,其中具有多态性的位点数192个,占86.88%。2)2种分子标记检测到老芒麦居群水平的基因多样性(He)分别为0.1092和0.1296,而物种水平的基因多样性达0.2434和0.3732。3)基于2种标记的Nei氏遗传分化指数Gst(0.5525和0.5158)表明老芒麦居群出现了较大程度的遗传分化,居群间的基因流非常有限,分别为0.4050和0.4694,老芒麦的遗传变异主要分布在居群间,居群内变异相对较小,Shannon多样性指数和分子方差变异(AMOVA)分析显示了相似的结果。4)基于聚类分析结果表明各居群间存在较为明显的地理分化,8个居群分化为采集地范围内的南、北和中部3个分支。通过对老芒麦遗传多样性和遗传结构的分析提出了对该物种遗传多样性的保护策略。  相似文献   

10.
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   

11.
旨在对广灵县优种驴场保种群体进行调查的基础上构建分子系谱,并对其种群的遗传结构进行分析。本研究采集保种群成年、体况良好的广灵驴（体重350~400 kg）颈静脉血10 mL（n=107）,其中公驴13份,母驴94份,抗凝处理后提取全血DNA。采用12个微卫星标记进行荧光PCR扩增后,用ABI3730测序仪进行分型。分型结果采用Cervus 2.0和Pedigraph 2.4软件构建分子系谱,同时采用STRUCTURE2.3和Fstat软件计算群体遗传参数,采用R语言的hclust函数绘制7头公驴及其后代的系统发生NJ树（邻接树）。结果,对107头种驴进行了分子系谱构建,找到了30头子代的父亲和7头子代的母亲,系谱可靠性>90%;微卫星标记的平均观测杂合度（HObs）和多态信息含量（PIC）分别为0.676 5和0.593 9,标记遗传多样性较高;NJ树对7个公驴家系进行了聚类;群体分化系数（FST）为0.184,群体平均近交系数（FIT）为0.033,群体内近交系数（FIS）为-0.238,且群体处于哈代-温伯格平衡状态,存在很弱的近交。本研究建立了广灵驴保种群可靠性较高的分子系谱并对其遗传结构进行了分析,证明该群体遗传多态性较高,群体近交系数较低,处于较好的保种状态,具有较大的品种资源开发潜力。  相似文献   

12.
Blanca Cacereña cattle is the most threatened Spanish bovine breed. Although a Conservation Plan, exists, the little reproductive success and some chromosome abnormality were observed in the breed making it advisable to extend the genetic basis of the animals opening up the recorded herd book to new animals from local farms. However, the crossing with meat breeds like Charolais cattle is used to improve the commercial product. We used 30 microsatellites to determine the Charolais genetic influence in the current herds by the identification of the hybrids and to recognize new “purebred” animals in the “Blanca Cacereña” population. Blood samples were taken from animals of Blanca Cacereña bovine breed (112 animals with pedigree and 68 without pedigree), Charolais breed (60 animals) as a breed used commercially in crosses with Blanca Cacereña, and Retinta breed (60 animals) as a reference population. STRUCTURE analyses were performed with or without prior population information to assign individuals to breed, identifying admixed individuals, and inferring their ancestry. We have found that 37/68 animals without pedigree were purebred. Our results will be useful to manage a conservation plan of the breed, preserving the characteristic genetic pool and avoiding its extinction.  相似文献   

13.
Inbreeding depression is caused by increased homozygosity in the genome and merges two genetic mechanisms, a higher impact from recessive mutations and the waste of overdominance contributions. It is of major concern for the conservation of endangered populations of plants and animals, as major abnormalities are more frequent in inbred families than in outcrosses. Nevertheless, we lack appropriate analytical methods to estimate the hidden inbreeding depression load (IDL) in the genome of each individual. Here, a new mixed linear model approach has been developed to account for the inbreeding depression‐related background of each individual in the pedigree. Within this context, inbred descendants contributed relevant information to predict the IDL contained in the genome of a given ancestor; moreover, known relationships spread these predictions to the remaining individuals in the pedigree, even if not contributing inbred offspring. Results obtained from the analysis of weaning weight in the MARET rabbit population demonstrated that the genetic background of inbreeding depression distributed heterogeneously across individuals and inherited generation by generation. Moreover, this approach was clearly preferred in terms of model fit and complexity when compared with classical approaches to inbreeding depression. This methodology must be viewed as a new tool for a better understanding of inbreeding in domestic and wild populations.  相似文献   

14.
Limiting the inbreeding rate (?F) while maximizing genetic gain for any trait of economic interest is especially important in small populations of local breeds, like the Menorca Horse. In this breed, dressage performance is important for the profitability of the breed and should be accounted in the selection criterion. The aim of this study was to assess if a breeding programme aiming at improved dressage performance is feasible in such a small breed. To perform the analysis, animals that were currently available for breeding (between 3 and 20 years) were used. Selection was based on the estimated breeding values for dressage obtained by BLUP. The pedigree and molecular coancestry between potential breeding horses was used (separately or in combination) to account for the restriction on ?F. Results show that it is possible to avoid large increases in inbreeding while obtaining acceptable levels of genetic gain (i.e. a ?F of 1% would imply a maximum loss in genetic gain of 2%). Thus, the Menorca Horse population is suitable for a management procedure which jointly optimizes the response to selection and the levels of variability and inbreeding (Optimal Contribution selection). Regarding the source of information used to calculate the relationships, molecular information would provide a greater range of solutions to increase genetic gain than using pedigree coancestry (gain was 1–4% higher for the same levels of restriction on the increase in inbreeding).  相似文献   

15.
The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32?% of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50?% of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8?% for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64?%. The average relatedness coefficient between individuals of the population was estimated to be 2.05?%??the highest individual coefficient was 10.31?%. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help breeders and farmers adopt better precautionary measures against inbreeding depression and other deleterious genetic effects.  相似文献   

16.
Zebu breeds play an important role in cattle production systems in Brazil. To assess the genetic variability from animals in the Herd Books of Nelore, Gir and Guzerat breeds, generation intervals, inbreeding, effective population size and parameters of gene origin (effective number of founders, ancestors and founder genomes) were calculated using pedigree records from 1938 to 1998. Breed subdivision was quantified by Wright's F -statistics. Calculations were separately carried out for consecutive 4-year intervals in the period 1979–98. Generation interval was around 8 years for the three breeds. Total inbreeding increased in all the breeds reaching values of 2.13%, 2.28% and 1.75%. Effective population size decreased from 85 to 68 in Nelore, from 70 to 45 in Gir and remained nearly constant around 104 in Guzerat. The quantities assessing the number of contributing ancestors decreased with time in all the breeds, and in the last analysed period the most important ancestor accounted for 14%, 3.1% and 4.1% in Nelore, Gir and Guzerat, respectively. Results indicate that the studied breeds are suffering from a loss of genetic variability which can result in negative effects on breeding and conservation purposes.  相似文献   

17.
Beta2-adrenoceptor agonists are used as bronchodilators in both humans and horses. Of these drugs, clenbuterol is the one most frequently used when treating chronic obstructive pulmonary disease in the horse, while salbutamol and terbutaline are used in the treatment of human asthma. Little is known of the properties of the latter two drugs in equine medicine.
  We have compared salbutamol and terbutaline with clenbuterol in relation to their ability to relax muscle strips from equine tracheal muscle, pre- contracted with 40 n m carbachol, in tissue chambers. The affinities of these drugs to the β2-adrenoceptors in homogenates of the same muscle tissue were also examined. These experiments were performed with radioligand binding studies using the very potent β-adrenoceptor antagonist 125I-cyanopindolol.
  The three drugs were almost equipotent in relaxing the muscle strips. The EC50-values for salbutamol, terbutaline and clenbuterol were 5.6, 13.8 and 2.1 n m , respectively, and all three drugs relaxed the preparations completely. In the competitive binding study, however, the Kd-value of clenbuterol was much lower (24 n m ) than that of salbutamol and terbutaline (1100 n m and 3900 n m , respectively). The amount of receptors bound at the EC50-value of clenbuterol was 8% compared to less than 1% for salbutamol and terbutaline. This indicates a lower intrinsic efficacy of clenbuterol than of the other two drugs. The β-adrenoceptor density was 45 ± 14.3 fmol/mg protein (mean ± SD) and the Kd-value of 125I-cyanopindolol was 11.4 ± 3.3 p m .  相似文献   

18.
Strips of tracheal smooth muscle from 12 horses were contracted by carbachol in tissue baths under isometric conditions. This contraction (≅50% of maximum: EC50) was relaxed completely with adrenoceptor drugs. The only exception was clenbuterol, where the degree of relaxation was ≅90%. In all horses the EC50-value for isoprenaline (mean 1.6 × 10−8M) was less than that for adrenaline (mean 9.6 × 10− 8M) and noradrenaline (mean 1. 8 × 10- 6M). The potency ratio was 1 < 6 < 110 which indicates that the β2-subtype dominates among the β-adrenoceptors of equine airways. All preparations were also very sensitive to the specific and potent β2-receptor agonists clenbuterol (mean 5.7 × 10− 9M) and procaterol (mean 3.6 × 10−10M). No differences in EC50-values due to age, sex and breed were observed in this material. The standard deviation of the mean EC50-values seems to be larger for the specific β2-adrenoceptor agonists than for the unspecific. A reason for this could be differences in the pattern of the β-adrenoceptor population.  相似文献   

19.
Joint Nordic (Denmark, Finland, Sweden) genetic evaluation of female fertility is currently based on the multiple trait multilactation animal model (BLUP). Here, single step genomic model (ssGBLUP) was applied for the Nordic Red dairy cattle fertility evaluation. The 11 traits comprised of nonreturn rate and days from first to last insemination in heifers and first three parities, and days from calving to first insemination in the first three parities. Traits had low heritabilities (0.015–0.04), but moderately high genetic correlations between the parities (0.60–0.88). Phenotypic data included 4,226,715 animals with records and pedigree 5,445,392 animals. Unknown parents were assigned into 332 phantom parent groups (PPG). In mixed model equations animals were associated with PPG effects through the pedigree or both the pedigree and genomic information. Genotype information of 46,914 SNPs was available for 33,969 animals in the pedigree. When PPG used pedigree information only, BLUP converged after 2,420 iterations whereas the ssGBLUP evaluation needed over ten thousand iterations. When the PPG effects were solved accounting both the pedigree and the genomic information, the ssGBLUP model converged after 2,406 iterations. Also, with the latter model breeding values by ssGBLUP and BLUP became more consistent and genetic trends followed each other well. Models were validated using forward prediction of the young bulls. Reliabilities and variance inflation of predicted genomic breeding values (values for parent averages in brackets) for the 11 traits ranged 0.22–0.31 (0.10–0.27) and 0.81–0.95 (0.83–1.06), respectively. The ssGBLUP model gave always higher validation reliabilities than BLUP, but largest increases were for the cow fertility traits.  相似文献   

20.
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