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1.
We have evaluated the use of genomic coancestry coefficients based on shared segments for the maintenance of genetic diversity through optimal contributions methodology for populations of three different Austrian cattle breeds. This coancestry measure has been compared with the genomic coancestry coefficient calculated on a SNP‐by‐SNP basis and with pedigree‐based coancestry. The regressions of the shared segments coancestry on the other two coefficients suggest that the former mainly reflect Identity By Descent but with the advantage over pedigree‐based coancestry of providing the realized Identity By Descent rather than an expectation. The effective population size estimated from the rate of coancestry based on shared segments was very similar to those obtained with the other coefficients and of small magnitude (from 26.24 to 111.90). This result highlights the importance of implementing active management strategies to control the increase of inbreeding and the loss of genetic diversity in livestock breeds, even when the population size is reasonably large. One problem for the implementation of coancestry based on shared segments is the need of estimating the gametic phases of the SNPs which, given the techniques used to obtain the genotypes, are a priori unknown. This study shows, through computer simulations, that using estimates of gametic phases for computing coancestry based on shared segments does not lead to a significant loss in the diversity maintained. This has been shown to be true even when the size of the population is very small as it is usually the case in populations subjected to conservation programmes.  相似文献   

2.
The preservation of the maximum genetic diversity in a population is one of the main objectives within a breed conservation programme. We applied the maximum variance total (MVT) method to a unique population in order to maximize the total genetic variance. The function maximization was performed by the annealing algorithm. We have selected the parents and the mating scheme at the same time simply maximizing the total genetic variance (a mate selection problem). The scenario was compared with a scenario of full-sib lines, a MVT scenario with a rate of inbreeding restriction, and with a minimum coancestry selection scenario. The MVT method produces sublines in a population attaining a similar scheme as the full-sib sublining that agrees with other authors that the maximum genetic diversity in a population (the lowest overall coancestry) is attained in the long term by subdividing it in as many isolated groups as possible. The application of a restriction on the rate of inbreeding jointly with the MVT method avoids the consequences of inbreeding depression and maintains the effective size at an acceptable minimum. The scenario of minimum coancestry selection gave higher effective size values, but a lower total genetic variance. A maximization of the total genetic variance ensures more genetic variation for extreme traits, which could be useful in case the population needs to adapt to a new environment/production system.  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.
We study here the effect of using genome-wide marker data versus genealogical data in population management for the maintenance of diversity in conservation schemes using optimal contributions. We re-examine the benefits of using molecular data for different population and genome sizes and compare different management strategies according to the group of individuals where we take decisions (parents or offspring). We also study the consequences of using estimated genealogical coancestries calculated from molecular information. Using genome-wide marker data performed usually better than using genealogical data or estimated genealogical coancestry to maintain expected and observed heterozygosity. Furthermore, when we could take decisions acting on the offspring, a larger heterozygosity was maintained than when we based our decisions on the potential parents.  相似文献   

5.
The issue of loss of animal genetic diversity, worldwide in general and in Canada in particular, has become noteworthy. The objective of this study was to analyze the trend in within‐breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective population sizes were 54, 47, 40, 46 and 66, respectively. Based on coancestry coefficients, the estimated effective population sizes in the last generation were 62, 76, 43, 61 and 76, respectively. The estimated percentage of genetic diversity lost within each breed over the last four decades was 6, 7, 11, 8 and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the five breeds ranged between 59.3% and 89.7%. The results indicate that each breed has lost genetic diversity over time and that the loss is gaining momentum due to increasing rates of inbreeding and reduced effective population sizes. Therefore, strategies to decrease rate of inbreeding and increase the effective population size are advised.  相似文献   

6.
In this article coefficients of kinship between and within populations are proposed as a tool to assess genetic diversity for conservation of genetic variation. However, pedigree-based kinships are often not available, especially between populations. A method of estimation of kinship from genetic marker data was applied to simulated data from random breeding populations in order to study the suitability of this method for livestock conservation plans. Average coefficients of kinship between populations can be estimated with low Mean Square Error of Prediction, although a bias will occur from alleles that are alike in state in the founder population. The bias is similar for all populations, so the ranking of populations will not be affected. Possible ways of diminishing this bias are discussed. The estimation of kinships between individuals is imprecise unless the number of marker loci is large (> 200). However, it allows distinction between highly related animals (full sibs, half sibs and equivalent relations) and animals that are not directly related if about 30–50 polymorphic marker genes are used. The marker-based estimates of kinship coefficients yielded higher correlations than genetic distance measures with pedigree-based kinships and thus to this measure of genetic diversity, although correlations were high overall. The relation between coefficients of kinship and genetic distances are discussed. Kinship-based diversity measures conserve the founder population allele frequencies, whereas genetic distances will conserve populations in which allele frequencies are the most different. Marker-based kinship estimates can be used for the selection of breeds and individuals as contributors to a genetic conservation programme.  相似文献   

7.
Recent studies have proposed the use of molecular coancestry coefficients as a measure of genetic variability and as a useful tool for conservation purposes. Using simulated data, molecular coancestry has been shown to become constant very quickly after separation of populations, leading to population diversity remaining constant. However, the use of molecular coancestry information to study the genetic relationships between breeds has not yet been widely explored. Here we analyze the polymorphism of 14 microsatellites in 222 unrelated individuals belonging to seven native Spanish breeds to ascertain the usefulness of molecular coancestry-based methodologies in providing information on their genetic relationships. Average kinship distance (D(k)) and average molecular coancestry coefficients (f(ij)) were compared with well-known genetic distances, such as between-breed Reynolds' distance (D(R)), Nei's standard distance (D(s)), and shared allele distance (D(AS)). Kinship distance and f(ij) have moderate to low correlations with the other genetic distances, showing that they provide different information: both D(k) and f(ij) account for the allele frequencies in the founder population, whereas D(R), D(s), and D(AS) characterize the short-term evolution of the populations. Furthermore, D(k) and f(ij) were only moderately correlated (-0.500). The present study used field data to confirm previous research pointing out the ability of molecular coancestry coefficients to assess genetic differentiation of an ancestral origin. In this respect, molecular coancestry-based parameters may be used with classical genetic parameters to obtain information on population dynamics in livestock breeds. This study additionally presents reliable evidence on the history of these sheep breeds.  相似文献   

8.
Controlling the increase of coancestry and inbreeding coefficients in selected populations is made possible through calculation of the optimal contributions allowed to breeding animals, given the current situation with regard to genetic diversity, and further, through optimal design of matings. The potential of such an approach for pig breeding was tested by retrospective optimization on the French Landrace population in reference to the matings actually carried out during a 21-week test period. The major constraint was that the average overall estimated breeding value (EBV) should be the same as the observed one, for not decreasing short-term genetic gain. Optimizing breeding allocations to boars would have led one to decrease coancestry and inbreeding coefficients by approximately 20%. This decrease would have even increased to approximately 30%, would have replacements and disposals been optimized after accounting for genetic variability, keeping the same constraint of genetic level identical to the observed one. These results showed the potential value, in the future, of completing each periodical calculation of EBVs by optimizations considering genetic variability and of releasing corresponding information to breeders, in order to enhance maintenance of genetic variability.  相似文献   

9.
Abstract

The Icelandic goat breed is a closed population consisting of around 700 animals kept in 45 herds. Several population bottlenecks are known to have occurred and the population has at least twice declined below 100 animals. Here the genetic diversity of the breed was estimated using pedigree information, D-loop sequencing and microsatellite markers. The annual rate of inbreeding was estimated as 3% and the effective population size as 5.1 animals. The effective population size based on molecular markers was estimated in the range of 4.1–8.8 individuals and mtDNA D-loop sequencing identified only three haplotypes. The results presented here show the population to be highly inbred, fragmented and the level of genetic variation among the lowest found in livestock. The results will be an important input into conservation planning for the Icelandic goat.  相似文献   

10.
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   

11.
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   

12.
Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.  相似文献   

13.
We introduce a simple method to estimate effective population size from increase in coancestry (Δc(jk)) for all pairs of individuals j and k in a reference subpopulation. An increase in pairwise coancestry for any pair of individuals j and k can be defined assuming that a hypothetical mating between them would give an individual with an inbreeding coefficient equal to c(jk), where c(jk) is the coancestry coefficient between the individuals j and k. The equivalent measure to discrete generations value (g(jk)) corresponding to the individual jk can be computed by averaging discrete equivalents generations of its parents (g(j) and g(k)). The mean increase in coancestry for all pairs of individuals in a reference subpopulation can be used to estimate a realized effective population size based on coancestries that would provide information on the effective size of a population under random mating. Performance of the new parameter was tested on simulated and empirical (horse) populations with different mating strategies and population structures. The routines needed to compute the introduced parameters have been included in a new version of the program ENDOG.  相似文献   

14.
基于SNP芯片监测通城猪的保种效果   总被引：1，自引：1，他引：0  
旨在基于SNP芯片信息分析通城猪保种群的群体结构和遗传多样性,对保种效果进行监测。本研究利用“中芯一号”50K SNP芯片对68头通城猪的全基因组SNP进行扫描,通过以下两方面评估保种效果：1）群体结构。通过群体分层、遗传距离、亲缘关系以及公猪基因组家系等分析,研究通城猪个体间的群体结构;2）遗传多样性。估算等位基因频率、有效等位基因数、多态信息含量、多态性标记比例、杂合度、核苷酸多样性等多态性和杂合性相关参数估计遗传多样性,分析有效群体含量和连续性纯合片段（runs of homozygosity,ROH）,综合评估保种效果。结果显示：1）保种群无明显分层,遗传距离为0.27,亲缘系数为0.17;2）基因组等位基因频率为0.77,有效等位基因数为1.52,多态信息含量均值为0.31,多态性标记比例为88.28%,观测杂合度为0.32,期望杂合度为0.31;20世代前通城猪有效群体含量为105头,当前世代有效群体含量为94头;ROH共计有184个,平均ROH长度为23.71 Mb,其中28.80%的长度在15~20 Mb之间;基因组近交系数为0.04%,具较低水平的近交程度。通城猪保种群是一个没有分层的纯种群体,具有丰富的遗传多样性,得到了有效保护。  相似文献   

15.
Artificial selection and high genetic gains in livestock breeds led to a loss of genetic diversity. Current genetic diversity conservation actions focus on long‐term maintenance of breeds under selection. Gene banks play a role in such actions by storing genetic materials for future use and the recent development of genomic information is facilitating characterization of gene bank material for better use. Using the Meuse‐Rhine‐Issel Dutch cattle breed as a case study, we inferred the potential role of germplasm of old individuals for genetic diversity conservation of the current population. First, we described the evolution of genetic merit and diversity over time and then we applied the optimal contribution (OC) strategy to select individuals for maximizing genetic diversity, or maximizing genetic merit while constraining loss of genetic diversity. In the past decades, genetic merit increased while genetic diversity decreased. Genetic merit and diversity were both higher in an OC scenario restricting the rate of inbreeding when old individuals were considered for selection, compared to considering only animals from the current population. Thus, our study shows that gene bank material, in the form of old individuals, has the potential to support long‐term maintenance and selection of breeds.  相似文献   

16.
In order to contribute to conservation of the endangered Kiso horse, we clarified their genetic information using 31 microsatellite DNAs, and genotyped 125 horses, 83% of the existing breed. First, we clarified the current status of the horses. The horses were confirmed to have experienced rapid loss of population causing a bottleneck, and their effective population size was much smaller than their census size. Moreover, the number of alleles (6.3), observed heterozygosity (0.674), and expected heterozygosity (0.662) were in the same range as other endangered horses all over the world. Therefore, although their inbreeding level was not so severe (F(is): -0.017), the Kiso horse is surely one of the endangered. Second, we obtained genetic information of individuals. This information allowed us to understand the genetic distance of individuals, and might help in development of a reproductive strategy concerning the genetic distance between the mating pairs. Moreover, there appeared to be 4 subpopulations of Kiso horse, and this result was in good agreement with their historical background. Third, we confirmed that the parentage test for identification using the 31 microsatellite DNAs was highly reliable (probability of exclusion: 0.999999993). This identification increases the reliability of stud certification, and is also helpful for effective management. Understanding the genetic diversity within the population and the relationships among individuals is important to ensuring effective management for maintenance of genetic variation, and this study may help in conservation of the endangered Kiso horse.  相似文献   

17.
The genetic relationship among individuals at one locus is characterized by nine coefficients of identity. The coefficients of inbreeding, coancestry and dominance (or fraternity) are just linear functions of them. Here, it is shown how they can be estimated using biallelic and triallelic markers using the method of moments, and comparisons are made with other methods based on molecular coancestry or molecular covariance. It is concluded that in the general case of dominance and inbreeding with biallelic markers, only the coefficients of inbreeding and coancestry can be estimated, but neither the single coefficients of identity nor the coefficient of dominance can be estimated. More than two alleles are required for a full estimation as illustrated with the triallelic situation.  相似文献   

18.
The African Penguin (Spheniscus demersus) has suffered population declines and is listed in the IUCN Red List as Endangered. The species is endemic to the coast of southern Africa, and breeding colonies are distributed on the south-western coast of Africa. Currently, African Penguins are being kept in zoo and aquarium facilities throughout South Africa. In this study, molecular genetic data based on 12 microsatellite markers from 1 119 African Penguin samples from four facilities were generated in order to determine the level of genetic variation, population structure and differentiation, and effective population size to assist in the development of an effective captive management plan. Expected heterozygosity ranged from 0.57 to 0.62, and allelic richness from 4.2 to 5.1. However, based on differences between first- and second-generation captive birds, we conclude that the ex situ population is at risk of losing genetic variability in the future and management programmes should include exchange of birds between captive facilities in order to induce gene flow and increase effective population size. Adding individuals from in situ populations should also be considered in the future in cases where these birds cannot be rehabilitated. Molecular genetic analyses of wild penguin populations should be carried out for comparison, and to ascertain to what degree ‘in situ genetic diversity’ is represented among ex situ populations. With regular resampling and analyses, the extent of the effect of processes such as genetic drift on diversity in the ex situ penguin populations will become evident.  相似文献   

19.
The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity.  相似文献   

20.
ABSTRACT

The Fjord horse originates from Norway but forms a global population due to several small populations in foreign countries. There exists no information about the additive relationship and the genetic variance between these subpopulations. By collecting blood samples from Norwegian and Swedish Fjord horses, a sample of 311 Norwegian and 102 Swedish horses gave 485,918 SNPs available for analysis. Their inbreeding coefficients were calculated and compared to the pairwise coancestry and the shared genomic segments. The effective population size was almost similar with the two methods in the Norwegian Fjord horse population (63 and 71), but very different in the Swedish population (269 and 1136) and unprecise due to a much smaller number of observations. The study showed that coancestry from shared genomic segments can be used to estimate additive genetic relationship and genetic variation within and between the global populations of the Fjord horse.  相似文献   

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