References of "Szydlowski, Maciej"
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See detailEstimating myostatin gene effect on milk performance traits using estimated gene content for a large number of non-genotyped cows
Buske, Bernd; Vanrobays, Marie-Laure ULg; Szydlowski, Maciej et al

Conference (2011, August 29)

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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 detailEstimating myostatin gene effect on milk performance traits using estimated gene content for a large number of non-genotyped cows
Buske, Bernd ULg; Szydlowski, Maciej; Verkenne, Catherine et al

in Animal (2011), 5(1), 43-47

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See detailA robust method for simultaneous estimation of single gene and polygenic effects in dairy cows using externally estimated breeding values as prior information
Buske, Bernd ULg; Szydlowski, Maciej; Gengler, Nicolas ULg

in Journal of Animal Breeding & Genetics (2010), 127(4), 272-279

The aim of this study was to develop a robust method to estimate single gene and random polygenic animal effects simultaneously in a small field dataset with limited pedigree information. The new method ... [more ▼]

The aim of this study was to develop a robust method to estimate single gene and random polygenic animal effects simultaneously in a small field dataset with limited pedigree information. The new method was based on a Bayesian approach using additional prior information on the distribution of externally estimated breeding values. The field dataset consisted of 40 269 test-day records for milk performance traits for 1455 genotyped dairy cows for the 11 bp-deletion in the coding sequence of the myostatin gene. For all traits, estimated additive effects of the favoured wild-type allele (‘+’ allele) were smaller when applying the new method in comparison with the application of a conventional mixed inheritance test-day model. Dominance effects of the myostatin gene showed the same behaviour but were generally lower than additive effects. Robustness of methods was tested using a data-splitting technique, based on the correlation of estimated breeding values from two samples, with one-half of the data eliminated randomly from the first sample and the remaining data eliminated from the second sample. Results for 100 replicates showed that the correlation between split datasets when prior information included was higher than the conventional method. The new method led to more robust estimations for genetic effects and therefore has potential for use when only a small number of genotyped animals with field data and limited pedigree information are available. [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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