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1.
旨在对中国地方鸡品种的遗传多样性与种群结构进行分析。本研究使用Affymetrix Axiom 600K高密度鸡基因分型芯片对来自8个品种的157只地方鸡及233只商品鸡进行基因分型,以品种作为分组来计算各分组的观测杂合度、期望杂合度、次等位基因频率、近交系数及核苷酸多样性分析地方鸡群体的遗传多样性,利用进化树、主成分分析、群体结构、MDS等方法分析鸡群体的群体结构,基于状态同源(IBS)和群体分化系数(Fst)分析种群内部与种群之间的亲缘关系,利用长纯合片段(runs of homozygosity, ROH)估算得到基于ROH的近交系数。结果表明,各群体的观测杂合度均高于期望杂合度,次等位基因频率在0.175~0.236之间,近交系数在0.018~0.205之间,核苷酸多样性在0~6×10-4之间,进化树与主成分分析表明品种间出现了明显的群体分化,地方鸡群体与商品鸡群的MDS分析发现我国地方鸡与商业肉鸡品种的遗传距离较近;IBS遗传距离在0.092 9~0.319 9之间;各品种成对Fst分析表明,群体间呈现中高分化程度(0.09~0.22);此次分析共得到了...  相似文献   

2.
The aim of this study was to research the population structure and genetic diversity of the Nova Scotia Duck Tolling Retriever (NS) and the Lancashire Heeler (LH) dog breeds. Data consisted of nearly all the worldwide registration history for both breeds, including 28 668 NS and 4 782 LH individuals. A reference population, including the females born between 1999 and 2008, was defined for genetic analyses for each breed. Average depth of the pedigrees known for the reference population dogs was 12.9 complete generation equivalents in the NS and 6.0 in the LH. Only a small fraction of the born dogs were used later for breeding. Effective number of founders was 9.8 in the NS and 15.2 in the LH. More than 50% of the genetic diversity in the reference population was explained by two ancestors in the NS and five in the LH. Average inbreeding coefficients in the reference populations were 0.26 in the NS and 0.10 in the LH. Average kinships were 0.26 and 0.08 and realised effective population sizes 18 and 28, respectively. Failure to use available genetic resources for sustainable breeding has resulted in depletion of genetic variation in both breeds. To increase genetic variation, a larger proportion of the dogs should be used in reproduction and the contributions of reproducing animals should be equalized. In the LH, it is necessary to use the unregistered farm dogs in breeding. In the NS, crosses with another breed are needed.  相似文献   

3.
样本量和性比对微卫星分析中群体遗传多样性指标的影响   总被引:12,自引:1,他引:12  
以4个中国地方鸡品种遗传多样性的微卫星分析数据为例,分析样本量和性比对微卫星分析中群体遗传多样性指标的影响。结果表明:当样本量超过20后,期望杂合度值趋于稳定,样本量与期望杂合度无显著相关,而与平均等位基因数呈正相关,在微卫星分析中性比对群体遗传多样性指标不表现出显著影响;微卫星位点多态性的高低直接影响到检测所需的样本量,在使用平均等位基因数分析群体遗传多样性时,应该充分考虑样本量对检测结果的影响;期望杂合度受样本量变动的影响较小,可作为度量群体遗传多样性的一个最适参数,而且样本量以20~25较为适宜。  相似文献   

4.
Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to the reduction of genetic diversity. Estimates of marginal contributions of ancestors suggest that the bottlenecks arose mainly because related stallions had been used for breeding. A tendency for an increase in inbreeding coefficients was observed. F‐statistics revealed that a small effective population size majorly contributed to this increase, although non‐random mating in particular regions also contributed. Because the bottlenecks are thought to have reduced the effective population size, our results imply that mitigation of bottlenecks is important for conservation. To this end, breeding should involve genetically diverse stallions. In addition, to prevent non‐random mating observed in particular regions, efforts should be made to plan mating with consideration of kinships.  相似文献   

5.
选用来源于牛和绵羊的27个微卫星DNA标记,对山东省4个地方山羊品种进行遗传多样性分析,通过计算等位基因频率、多态信息含量、不同标记的平均杂和度、总群体杂合度、亚群体杂合度、群体杂合度、基因分化系数、不同群体的F-统计量、基因流动数、不同群体间的基因流动个数和遗传距离并进行聚类分析,评估其种内变异和种间变异的关系,以群体平均杂合度、F-统计量和遗传分化系数为基础,结合四个山羊种群的实际生存状况,提出避免近交和种群间杂交符合山东山羊种群实际状况的保种模式。研究结果可为山东地方种质特性研究提供基础数据,为山东地方山羊种群的合理保护利用提供科学依据。  相似文献   

6.
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   

7.
Population structure and genetic diversity in the Portuguese native breeds of pigs Alentejano (AL), Bísaro (BI), and Malhado de Alcoba?a (MA) and the exotic breeds Duroc (DU), Landrace (LR), Large White (LW), and Pietrain were analyzed by typing 22 microsatellite markers in 249 individuals. In general, the markers used were greatly polymorphic, with mean total and effective number of alleles per locus of 10.68 and 4.33, respectively, and an expected heterozygosity of 0.667 across loci. The effective number of alleles per locus and expected heterozygosity were greatest in BI, LR, and AL, and least in DU. Private alleles were found in 9 of the 22 markers analyzed, mostly in AL, but also in the other breeds, with the exception of LW. The proportion of loci not in Hardy-Weinberg equilibrium in each breed analyzed ranged between 0.23 (AL) and 0.41 (BI, LW, and Pietrain), mostly because of a less than expected number of heterozygotes in those loci. With the exception of MA, all breeds showed a significant deficit in heterozygosity (F(IS); P < 0.05), which was more pronounced in BI (F(IS) = 0.175) and AL (F(IS) = 0.139), suggesting that inbreeding is a major concern, especially in these breeds that have gone through a genetic bottleneck in the recent past. The analysis of relationships among breeds, assessed by different methods, indicates that DU and AL are the more distanced breeds relative to the others, with the closest relationship being observed between LR and MA. The degree of differentiation between subpopulations (F(ST)) indicates that 0.184 of the total genetic variability can be attributed to differences among breeds. The analysis of individual distances based on allele sharing indicates that animals of the same breed generally cluster together, but subdivision is observed in the BI and LR breeds. Furthermore, the analysis of population structure indicates there is very little admixture among breeds, with each one being identified with a single ancestral population. The results of this study confirm that native breeds of pigs represent a very interesting reservoir of allelic diversity, even though the current levels of inbreeding raise concerns. Therefore, appropriate conservation efforts should be undertaken, such as adopting strategies aimed at minimizing inbreeding, to avoid further losses of genetic diversity.  相似文献   

8.
To understand molecular genetic characteristics of Korean pigs, the genetic relationships of nine pig breeds including two Korean pigs (Korean native pig and Korean wild pig), three Chinese pigs (Min pig, Xiang pig, and Wuzhishan pig), and four European breeds (Berkshire, Duroc, Landrace, and Yorkshire) were characterized from a 16-microsatellite loci analysis. The mean heterozygosity within breeds ranged from 0.494 to 0.703. Across multiple loci, significant deviation from Hardy-Weinberg equilibrium was observed in most pig breeds, except for two Chinese pigs (Min pig and Wuzhishan pig). This deviation was in the direction of heterozygote deficit. Across population loci, 36 of 144 significantly deviated (P < 0.05) from Hardy-Weinberg equilibrium. The mean FST, a measure of genetic divergence among subpopulations, of all loci indicated that 26.1% of total variation could be attributed to the breed difference. Relationship trees based on the Nei's DA genetic distance and scatter diagram from principal component analysis consistently displayed pronounced genetic differentiation among the Korean wild pig, Xiang pig, and Wuzhishan pig. Individual assignment test using a Bayesian method showed 100% success in assigning Korean and Chinese individual pigs into their correct breeds of origin and 100% exclusion success from all alternative reference populations at P < 0.001. These findings indicate that the Korean native pig has been experiencing progressive interbreeding with Western pig breeds after originating from a North China pig breed with a black coat color. Considering the close genetic relationship of Korean pigs to the Western breeds such as Berkshire and Landrace, our findings can be used as valuable genetic information for the preservation and further genetic improvement of the Korean native pig.  相似文献   

9.
试验旨在研究地方绵羊品种的遗传变异,为种质资源评价、保护和利用提供理论数据。利用5个微卫星标记分析4个地方绵羊品种的遗传多样性,根据等位基因组成及频率进行群体遗传统计分析;基于品种间标准遗传距离(Ds)和Nei氏遗传距离,分别构建UPGMA系统发生树。4个地方绵羊品种共检测到70个等位基因,各位点等位基因数(Na)在10~18之间;4个地方绵羊品种平均有效等位基因数(Ne)为3.81~5.68个,平均多态信息含量(PIC)为0.6152~0.7373,平均遗传杂合度(H)为0.6711~0.7820;4个地方绵羊品种间遗传分化系数为0.0847,标准遗传距离(Ds)和Nei氏遗传距离晋中绵羊与乌珠穆沁羊为最大(0.5775、0.6126),小尾寒羊与乌珠穆沁羊为最小(0.1542、0.1955),首先小尾寒羊与乌珠穆沁羊聚为一类,晋中绵羊与广灵大尾羊聚为另一类,然后两类聚在一起形成一大类。结果表明,4个地方绵羊品种遗传变异大、多样性丰富;品种间遗传分化小,但小尾寒羊和乌珠穆沁羊与晋中绵羊和广灵大尾羊间已有明显分化。选择的5个微卫星座位均为高度多态位点,可作为有效遗传标记用于绵羊品种遗传多样性和系统发生关系分析。各地方绵羊品种分子聚类关系与其形成史、分化及地理分布基本一致。  相似文献   

10.
为阐明保山猪、迪庆藏猪、高贡黎山猪、丽江猪、明光小耳猪、滇南小耳猪、撒坝猪、大河猪、昭通猪、大河乌猪10个云南省优良地方猪种的群体遗传多样性和遗传结构,本试验参考ArkDB数据库中家猪14条染色体上的15对微卫星引物,对549个云南地方猪个体的耳组织样品进行了检测分析,计算各微卫星座位等位基因数(Na)、有效等位基因数(Ne)、Shannon's信息指数(I)、表观杂合度(Ho)、期望杂合度(He)、F-统计量(Fis、Fit、Fst)、基因流(Nm)、群体遗传距离等相关参数及多态信息含量(PIC),采用NTsys 2.10软件构建聚类树,并采用STRUCTRUE 2.3.3软件评估群体遗传结构。结果显示:15个微卫星座位共检测到293个等位基因,各座位等位基因数在5~38个之间,平均等位基因数为19个,平均有效等位基因数8.3682个;10个云南地方猪群体的Shannon多样性、表观杂合度、期望杂合度和多态信息含量分别在1.4374~2.0317、0.6389~0.7756、0.7021~0.8281和0.6647~0.7993之间。各座位单个群体内近交系数(Fis)、总群体近交系数(Fit)、群体间遗传分化系数(Fst)的变化范围分别为-0.0678~0.4594、0.0618~0.5567和0.0713~0.1801;群体间Fst平均值为0.1101,处于中度遗传分化状态,有11.01%的遗传变异来自于群体间,大部分遗传变异来自于群体内;每个座位基因流程度较高,变化范围在1.6392~3.2551之间,平均值为2.0214。基于Nei氏遗传距离构建UPGMA系统发生树显示,高黎贡山猪与迪庆藏猪聚为一支,并与丽江猪、保山猪和明光小耳猪聚为一大支,其结果得到了STRUCTURE分析的验证。综上所述,10个云南地方猪种遗传多样性丰富,群体内有近交现象,群体间处于中度遗传分化,存在着一定的基因交流。  相似文献   

11.
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   

12.
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   

13.
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   

14.
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   

15.
中国地方鸭品种资源的分子遗传多样性   总被引:14,自引:3,他引:14  
通过筛选的28个多态性较好的微卫星标记,检测了我国24个地方鸭品种的遗传多样性。利用等位基因频率计算了各群体的遗传参数和群体间的遗传距离,采用邻接法构建了聚类图,并进行了系统发生分析。结果表明:28个微卫星座位在我国家鸭群体中的多态信息含量除APL23和APL79为中度多态外,其他座位均为高度多态座位,可以作为有效的遗传标记用于鸭种之间遗传多样性分析和系统发生关系的分析;我国所有家鸭群体平均杂合度(0.569)低于国内的家鸡和家鹅,其遗传多样性相对贫乏;聚类结果分析表明了各家鸭品种的分子系统发生关系与其育成史、分化及地理分布比较一致。  相似文献   

16.
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   

17.
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   

18.
The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean FIS values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.  相似文献   

19.
遗传多样性的研究主要包括形态学水平,染色体水平、蛋白质水平、DNA水平等。中国地方鸡种类繁多,研究地方鸡种的遗传多样性,不仅能加强生物多样性的保护,同时对起源、进化、分类鉴定及遗传育种等都有重要意义。20世纪80年代以来,分子生物学技术的快速发展为遗传多样性检测提供了更直接、更精确的方法,即直接通过分析DNA水平的序列变化检测动物遗传多样性。DNA分析方法成为目前最有效的遗传分析方法,避免了根据表型性推断基因型时可能产生的误差。作者对目前中国各种鸡群的遗传多样性在DNA水平的研究进行了综述,旨在发掘地方鸡种的优良基因,为地方鸡种的分子育种、改良提供参考。  相似文献   

20.
Abstract

To examine the genetic variation in two endangered Norwegian horse breeds, the pedigree structures were investigated, and key parameters such as inbreeding coefficients, effective population size, effective number of founders, effective number of ancestors and effective number of founder genomes were calculated. The data consisted of 31,142 individuals of the D?le horse and 1973 individuals of the Nordland/Lyngen horse, for which the complete generation equivalent was 10.5 and 7.2, respectively. In both breeds, the pedigree data were more than 98.5% complete in the fourth generation, allowing the rate of inbreeding and the effective population size to be precisely estimated, actually measuring the fractional loss of heterozygosity, comparable across generations (not so for the other measures). The level of inbreeding was about 12% in both breeds, with a rather wavy pattern during the past 50 years in the D?le. Considering the last generations only, the effective population size was found to be 152 in the D?le and 42 in the Nordland/Lyngen. For both populations selection in the future should be based on optimal contribution.  相似文献   

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