References of "Bömcke, Elisabeth"
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See detailNew method to combine molecular and pedigree relationships
Bömcke, Elisabeth ULg; Soyeurt, Hélène ULg; Szydlowski, Maciej et al

in Journal of Animal Science (2011), 89

Relationship coefficients are traditionally based on pedigree data. Today, with the development of molecular techniques, they are often completely replaced by coefficients calculated from molecular data ... [more ▼]

Relationship coefficients are traditionally based on pedigree data. Today, with the development of molecular techniques, they are often completely replaced by coefficients calculated from molecular data. Examples are relationships from microsatellites for biodiversity studies but also genomic relationships from SNP as currently used in genomic prediction of breeding values. There are, however, many situations in which optimal combination of both sources would be the best solutions. Obviously, this is the case for incompletely genotyped populations, but also when pedigree information is sparse. Also, markers, even dense ones, do not reflect the whole genome and therefore give only an incomplete picture of relationships. The main objective of this study was therefore to develop a method to calculate a relationship matrix by the combination of molecular and pedigree data. It will be useful for all situations where pedigree and molecular data are available. In this study, based on simulations of pedigree and marker data, we used partial least squares regression and linear regression to combine total allelic relationship coefficients calculated for each marker with additive relationship coefficients calculated from incomplete pedigree. The results showed that the greatest advantage of this method, compared with the one that replaces a part of the pedigree-based relationship matrix by a genomic relationship matrix, is that adding the partial pedigree data allows for the correction of the molecular coefficient for the ungenotyped part of the genome. [less ▲]

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See detailGenetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg; Cothran, E Gus

in Genetics and Molecular Biology (2011), 34

In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic ... [more ▼]

In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever. [less ▲]

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See detailForensic science technique applied for calculation of kinship index
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg

Poster (2010)

Implementing conservation strategies needs the knowledge of relationships inside the concerned population. The aim of this study was to find tools to help scientists and breeders to manage endangered ... [more ▼]

Implementing conservation strategies needs the knowledge of relationships inside the concerned population. The aim of this study was to find tools to help scientists and breeders to manage endangered populations or populations with missing pedigree information. The animal genetics literature often seems unaware of relevant developments in human genetics (and conversely). In this study, an approach called Familial Searching was tested. This is used in forensic science, in addition to matching DNA evidence directly to criminal profiles, to search for people (present in a database) who are related to an individual that left DNA evidence at a scene of crime. This method is based on the calculation of likelihood ratios (LR) between genotype of an individual and genotypes of each other individuals of the database. In order to decrease the number of comparisons, the available pedigree information was used as ‘local’ prior information, i.e. relating to specific pairs of individuals. General knowledge about the studied population (e.g., generation interval, sexual maturity) was considered as ‘global’ prior information. Including prior information reduced the number of comparisons from over 50%. Results showed that the parents were always classified into the 4 highest LR. This method simplified parentage verifications, it allowed the detection of 90% of false parentage (LR=0). It also allowed to create new links in the pedigree through detection of unregistered parents. The method was tested on the Skyros pony, an indigenous Greek breed. For this breed, partial pedigree information was available, and 99 individuals were genotyped at 16 microsatellite loci. The method allowed to check about 2500 possible parent-child combinations, three registered parentages were considered as incorrect and one non-recorded parentage was detected. The method will now be tested on other breed and with other markers, e.g. SNPs. [less ▲]

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See detailNew Method to Combine Pedigree and Molecular Relationships applied to Brandrood Cattle
Bömcke, Elisabeth ULg; Windig, J. J.; Gengler, Nicolas ULg

in 9th World Congress of Genetics Applied to Livestock Production: Leipzig, Germany (2010)

Relationship coefficients are traditionally based on pedigree data. Today, they are often replaced by coefficients calculated from molecular data, for example, microsatellites-based relationships for bio ... [more ▼]

Relationship coefficients are traditionally based on pedigree data. Today, they are often replaced by coefficients calculated from molecular data, for example, microsatellites-based relationships for bio-diversity studies or genomic relationships for prediction of breeding values. However, in many situations, optimal combination of both sources would be the best solutions; i.e. when population is incompletely genotyped or when pedigree information is sparse. Also even dense markers do not reflect the whole genome. The objective of this study was to applied a new method to calculate a relationship matrix by the combination of molecular and pedigree data on Brandrood cattle. The results showed that combining marker and pedigree information produced more accurate A-matrices what will be useful for future management of the breed genetic variability. [less ▲]

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See detailCalculate relationships using pedigree and marker information – What to combine into a single estimator?
Bömcke, Elisabeth ULg; Szydlowski, Maciej; Gengler, Nicolas ULg

in Book of Abstracts of the 60th Annual Meeeting of the European Association for Animal Production (2009, August)

The knowledge of relationships among individuals is an important topic in all fields of modern genetics, from selection to conservation. Estimation of relationships was traditionally based on pedigree ... [more ▼]

The knowledge of relationships among individuals is an important topic in all fields of modern genetics, from selection to conservation. Estimation of relationships was traditionally based on pedigree data. Today, molecular data can replace pedigrees. Numerous methods already exist. However, genotyping a complete population for a sufficient number of markers can be impossible, e.g., in case of local and/or rare breeds. Therefore, the idea was to combine these 2 sources of information into a new single relationship estimator. Based on simulations, the aim of this study was to determine what could be combined. Following the principle that things have to be similar to be combined, we compared first two coefficients that have the advantage to be similarly defined: the additive relationship coefficient (axy) calculated from pedigrees and the total allelic relationship (taxy) obtained from markers. The similarity between these two coefficients was measured by means of linear regression and correlations. In order to highlight the influence of inbreeding, Wright relationship coefficient (rped,xy) were also compared to taxy transformed into rmol,xy. The results showed that the correlation increases when the values are made independent from inbreeding. If the pedigree coefficients are considered as the true value, both molecular coefficients tended to overestimate the relationship among individuals. It can be expected because they do not distinguish identical-by-state and identical-by-descendent alleles. The influence of marker quality was also highlighted. In all cases, the correlation coefficient increased when only the more informative loci were used. Uninformative genetic markers potentially making animals appear more related than they were. [less ▲]

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See detailHow to combine pedigree and marker information into a single estimator for the calculation of relationships?
Bömcke, Elisabeth ULg; Soyeurt, Hélène ULg; Szydlowski, Maciej et al

in Book of Abstracts of the 60th Annual Meeeting of the European Association for Animal Production (2009, August)

Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data. In case of incomplete or missing ... [more ▼]

Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data. In case of incomplete or missing pedigree, they are replaced by coefficients calculated from molecular data when this information is available. However, genotyping a complete population for a sufficient number of markers can be impossible. The main objective of this study was therefore to develop a new method to estimate relationship by combining molecular with pedigree data. It will be useful for specific situations, where neither pedigree nor molecular data are complete. In a companion paper, the compatible coefficients were determined. In this study, based on simulations of pedigree and marker data, the method to combine the selected coefficients was determined. Various parameters were taken into account in the model: number and quality of the marker (e.g. marker informativeness), mutation rate, quality of the pedigree (e.g. generation-equivalents), … The combined estimator has several advantages. Especially, negative relationship values obtained in literature with molecular-based estimators in case of small inbred populations can be avoided. In conclusion, this combined estimator was originally developed for the management of an endangered horse population. It should also be a promising alternative to traditionally used estimators, e.g. for the management of small and/or rare breeds; especially in case of inbred populations, with both incomplete pedigree and partial molecular information. [less ▲]

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See detailCombine pedigree and marker information into a single estimator for the calculation of relationships
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg

Poster (2009, May)

Relationship coefficients are particularly useful to improve genetic management of endangered populations. Estimation of relationships was traditionally based on pedigree data but, today, numerous methods ... [more ▼]

Relationship coefficients are particularly useful to improve genetic management of endangered populations. Estimation of relationships was traditionally based on pedigree data but, today, numerous methods already exist to replace pedigrees by molecular data. However, genotyping a complete population for a sufficient number of markers can be impossible, e.g., in case of local and/or rare breeds. The idea was therefore to develop a new method to estimate relationship by combining molecular with pedigree data into a single estimator. Originally developed for the management of an endangered horse population, it will be useful for specific situations, where neither pedigree nor molecular data are complete. Two questions appeared: What and how to combine? Following the principle that things have to be similar to be combined, we compared two coefficients that have the advantage to be similarly defined: the additive relationship coefficient (axy) calculated from pedigrees and the total allelic relationship (taxy) obtained from markers. Wright relationship coefficient (rped,xy) were also compared to taxy, transformed into rmol,xy, to highlight the influence of inbreeding. The results showed the influence of inbreeding, of marker quality and the tendency of molecular coefficients to overestimate the relationship among individuals. The method to combine the selected coefficients was also determined. Various parameters were taken into account in the model: number of markers and quality (e.g. marker informativeness), mutation rate, pedigree quality (e.g. generation-equivalents), … The combined estimator has several advantages. Especially, negative relationship values obtained in literature with molecular-based estimators in case of small inbred populations can be avoided. [less ▲]

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See detailCombining microsatellite and pedigree data to estimate relationships among Skyros ponies.
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg

in Journal of Applied Genetics (2009), 50(2), 133-43

Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or ... [more ▼]

Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or inexistent pedigrees they are replaced by coefficients calculated from molecular data. The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyros pony breed, which consists of less than 200 individuals, divided into 3 main herds or subpopulations. In this study, relationships between individuals were estimated using traditional estimators as well as the newly developed method. For this purpose, 99 Skyros ponies were genotyped at 16 microsatellite loci. It appeared that the limitation of the most common molecular-based estimators is the use of weights that assume relationships equal to 0. The results showed that, as a consequence of this limitation, negative relationship values can be obtained in small inbred populations, for example. By contrast, the combined estimator gave no negative values. Using principal component analysis, the combined estimator also enabled a better graphic differentiation between the 3 subpopulations defined previously. In conclusion, this new estimator can be a promising alternative to traditionally used estimators, especially in inbred populations, with both incomplete pedigree and molecular information. [less ▲]

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See detailAnalysis of the Skyros pony breed: population structure and genetic variability
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg

Conference (2008, November)

Due to its geographic location, Greece is a crossroad between three continents and its mountainous landscape and numerous islands have lead to the creation of many small populations of distinct and ... [more ▼]

Due to its geographic location, Greece is a crossroad between three continents and its mountainous landscape and numerous islands have lead to the creation of many small populations of distinct and isolated breeds. On the basis of phenotypes and genotypes, seven native breeds were identified. The Skyros pony has a distinct phenotype from those of other breeds. This phenotypic difference seems to be linked to the fact that the Skyros pony is less genetically similar to the other Greek breed than the other breeds are to each other as shown in previous studies. Furthermore, the Skyros pony breed risk status is described as endangered according to the criteria of the Food and Agricultural Organization (DAD-IS). The main reason is that the population is concentrated only in three herds of reduced size. This study analyses the population structure and describes the genetic variability of the breed using 15 microsatellite markers and available genealogical information. The molecular characterization and the pedigree were also used to investigate the presence of bottleneck. Factorial correspondence analysis and analysis of molecular variance showed that the three herds seemed to be genetically distinct even if the genetic variance between herds was low (5.75%). For the whole population, the mean total number of allele per locus was 5.93. The average Polymorphism Information Content value was relatively high (~ 0.60) as the observed heterozygosity (0.64) and the expected heterozygosity (0.62). The comparison with other studies showed that these values were well within the range for domestic horses but were at the lower end of that range, i.e. with the values from breeds with small population size or recent bottlenecks. However, these values indicated a still substantial genetic diversity in the Skyros breed that could be useful for planning future breeding strategies for the breed conservation. This is consistent with the results of various bottleneck tests, which detected no evidence of bottleneck when considering the whole population but suggested that there was bottleneck in two of the three main herds of Skyros pony. Comparisons between DNA-based and pedigree-based results showed that the loss of genetic diversity has probably occurred before the beginning of breed registration. [less ▲]

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See detailGenetic variability of the Skyros pony breed and its relationship with other Greek and foreign horse breeds
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg; Cothran, E. G.

in Book of Abstracts of the 59th Annual Meeeting of the European Association for Animal Production (EAAP) (2008, August)

On the basis of phenotypes and genotypes, seven native breeds were identified in Greece. The Skyros pony is the more distinctive of these breeds. Using blood group and microsatellite loci, the aim of this ... [more ▼]

On the basis of phenotypes and genotypes, seven native breeds were identified in Greece. The Skyros pony is the more distinctive of these breeds. Using blood group and microsatellite loci, the aim of this study was to assess the genetic diversity of Skyros breed, using also available genealogical information, and to investigate its relationships with the other Greek and foreign horse breeds. Results showed that the Skyros breed presented similar level of genetic diversity to other European breeds. Comparisons between DNA-based and pedigree-based results showed that the loss of genetic diversity has probably occurred before the beginning of breed registration. However, the relatively high levels of heterozygosity and Polymorphism Information Content values indicated still sufficient residual genetic variability that could be useful for planning future breeding strategies for the breed conservation. Relationship study showed no association between genetic variation of native Greek breed and population size or degree of geographic isolation. Compared to other domestic breeds, most of the Greek breed showed closest relationships with Middle Eastern breeds, while the Skyros breed clustered surprisingly with Lithuanian horses. [less ▲]

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See detailApplication of forensic science technique to the management of an endangered horse population
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg

in Journal of Animal Science (2008), 86(E-suppl.2), 433

Implementing conservation strategies needs the knowledge of relationships inside the concerned population. The aim of the study was to find tools to help breeders to manage their horse population. The ... [more ▼]

Implementing conservation strategies needs the knowledge of relationships inside the concerned population. The aim of the study was to find tools to help breeders to manage their horse population. The Skyros pony is an indigenous Greek breed. The breed risk status is defined as critical-maintained according to the criteria from the Food and Agriculture Organization. Partial pedigree information is available, but its quality is poor as the average number of generation-equivalents is under 0.8 for the first known generation and under 1.4 for the second to the fifth. Further, 99 living individuals were genotyped at 16 microsatellite loci in order to check the registered parentage. For ungenotyped animals, conditional expectation of gene contents was calculated given molecular and pedigree data. As said in other studies, the animal genetics literature often seems unaware of relevant developments in human genetics (and conversely). In this study, an approach called Familial Searching was tested. This is used in forensic science, in addition to matching DNA evidence directly to criminal profiles, to search for people (present in a database) who are related to an individual that left DNA evidence at a scene of crime. This method is based on the calculation of likelihood ratios (LR) between genotype of an individual and genotypes of each other individuals of the database. The pedigree was used as ‘local’ prior information, i.e. relating to specific pairs of individuals. General knowledge about the studied population (generation interval, sexual maturity, …) was considered as ‘global’ prior information. Including prior information reduced the number of comparisons from over 50%. First results showed that the parents were always classified into the 5 highest LR. These results simplified parentage verifications, it allowed the detection of 90% of false parentage (LR=0). New links were created in the pedigree through detection of unregistered parents, what involved a reduction of the percentage of animals with one or both unknown parents and consequently an increase of the number of generation-equivalents. The pedigree of the breed was thus improved. [less ▲]

Detailed reference viewed: 39 (4 ULg)
See detailFirst approaches for a combined use of microsatellites and pedigree data to estimate relationships.
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg

in Book of Abstract of the 58th Annual Meeeting of the European Association for Animal Production (2007, August)

The main objective of conservation is the preservation of genetiv diversity. Among several tools recommended to measure genetic variability, relationships coefficients are often used. They can be ... [more ▼]

The main objective of conservation is the preservation of genetiv diversity. Among several tools recommended to measure genetic variability, relationships coefficients are often used. They can be estimated from pedigree but also from direct knowledge of hte genotype. The Skyros pony is an example of a small breed concerned by the management of genetic variability. However,the analysis of the pedigree showed its very poor quality. A part of the population was therefore genotyped for 16 microstellites and two estimators of relationships were tested: the Lynch & Ritland (L&R) (anly based on genotypes and described as having the best performances for all population comositionsof the mammal species) and a new estimator (developed for this study and combining pedigree and microsatellite information). In order to compare the results, a Principal Component Analysis (PCA) was performed. The new estimator explained a higher percentage of information within the 3 principal factors of the PCA (41.99%) than the L&R estimator (20.61%). The graphic PCA representation showed a better separation between the reference group and the rest of the populationin the case of the new estimator. The new estimator showed interesting preliminary results and results support interest in combining information in case of incomplete pedigrees and/or use of a limited number of markers. [less ▲]

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See detailConservation of animal genetic resources: Improvement of the relationship matrix
Bömcke, Elisabeth ULg

Master of advanced studies dissertation (2007)

The main objective of breed conservation is the preservation of genetic diversity. Relationship coefficients are one possibility to measure the genetic variability. With a total size lower than 200 ... [more ▼]

The main objective of breed conservation is the preservation of genetic diversity. Relationship coefficients are one possibility to measure the genetic variability. With a total size lower than 200 individuals, the Skyros small-horse may be called a small population. It is thus a good example of breed concerned by the management of genetic variability. Genetic variability within the Skyros breed was evaluated, at the genome level, using 16 microsatellites. The Factorial Correspondence Analysis of the molecular data showed that the population could be divided in three groups (Skyros, Thessaloniki and Corfu). A relatively high level of genetic variability within the breed was observed in terms of high values of mean effective number of alleles (3.2), observed heterozygosity (0.647), expected Levene’s heterozygosity (0.622), expected Nei’s heterozygosity (0.625), and polymorphism information content (0.598). This study demonstrated thus the existence of substantial genetic diversity in the Skyros small-horse population although two of the three sub-populations (Thessaloniki and Corfu) underwent a bottleneck. Finally, relationships were estimated using various estimators including a new one, which combines pedigree and markers information. Compared to the others, this combined estimator showed interesting results inter alia a higher correlation with genealogical relationship (0.889 or 0.883 according to the number and to the quality of the markers used). When the results are presented graphically, this estimator also allowed to do a better differentiation between the three sub-populations defined previously. [less ▲]

Detailed reference viewed: 35 (8 ULg)
See detailConservation of animal genetic resources in horses: The case of the Skyros small-horses
Bömcke, Elisabeth ULg

Master's dissertation (2006)

The main objective of conservation is the preservation of genetic diversity. Several tools are available to measure the genetic variability. In this study, we have used principally the relationship (and ... [more ▼]

The main objective of conservation is the preservation of genetic diversity. Several tools are available to measure the genetic variability. In this study, we have used principally the relationship (and inbreeding) coefficients and the information given by the study of genetic markers. With a total population size lower than 200 individuals, the Skyros small-horse may be called a small population. It is thus a good example of population concerned by the management of genetic variability. In this study, the ‘studbook’ of the Skyros small-horse comprising a total of 395 individuals was analyzed in order to evaluate its genetic variability amongst other things. Only 6 ancestors were necessary to explain 50% of the genetic variability of the breed. Then genetic diversity within the Skyros breed was evaluated, at the genome level, using 16 microsatellites. A relatively high level of genetic variability within the breed was observed in terms of high values of mean effective number of alleles (3.3), observed heterozygosity (0.635), expected Levene’s heterozygosity (0.642), expected Nei’s heterozygosity (0.639), and polymorphism information content (0.617). This study demonstrated the existence of substantial genetic diversity in the Skyros small-horse population. Finally, one part of a conservation program is the establishment of a good mating plan (coupling of less related individuals). Relationships were thus estimated using a new estimator, which combines pedigree and markers information. Compared to other estimators, this combined estimator showed interesting results (inter alia, higher percentage of information explained by the 3 principal factors in the principal components analysis (46.22%)). Hence, the resulting estimated relationships were used to make proposals for the management of the breed. [less ▲]

Detailed reference viewed: 62 (2 ULg)