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1000 Titel
  • Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs
1000 Autor/in
  1. Hampel, Alexander |
  2. Teuscher, Friedrich |
  3. Gomez-Raya, Luis |
  4. Doschoris, Michael |
  5. Wittenburg, Dörte |
1000 Erscheinungsjahr 2018
1000 LeibnizOpen
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2018-06-05
1000 Erschienen in
1000 Quellenangabe
  • 9:186
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2018
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.3389/fgene.2018.00186 |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996054/ |
1000 Ergänzendes Material
  • https://www.frontiersin.org/articles/10.3389/fgene.2018.00186/full#h12 |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation maximization algorithm has been proposed for estimating these parameters in half-sibs without phasing the progeny. It, however, overlooks the fact that the underlying likelihood function may have two maxima. The magnitudes of the maxima depend on the maternal allele frequencies at the investigated marker pair. Which maximum the algorithm converges to depends on the chosen start values. We present a stepwise procedure in which the relationship between the two modes is exploited. The expectation maximization algorithm for the parameter estimation is applied twice using different start values, followed by a decision process to assess the most likely estimate. This approach was validated using simulated genotypes of half-sibs. It was also applied to a dairy cattle dataset consisting of multiple half-sib families and 39,780 marker genotypes, leading to estimates for 12,759,713 intrachromosomal marker pairs. Furthermore, the proper order of markers was verified by studying the mean of estimated recombination rates in a window adjacent to the investigated locus as well as in a window at its most distant chromosome end. Putatively misplaced markers or marker clusters were detected by comparing the results with the revised bovine genome assembly UMD 3.1.1. In total, 40 markers were identified as candidates of misplacement. This outcome may help improving the physical order of markers which is also required for refining the bovine genetic map.
1000 Sacherschließung
lokal linkage analysis
lokal expectation maximization algorithm
lokal likelihood function
lokal genome assembly
lokal allele frequency
1000 Fachgruppe
  1. Biologie |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/creator/SGFtcGVsLCBBbGV4YW5kZXI=|https://frl.publisso.de/adhoc/creator/VGV1c2NoZXIsIEZyaWVkcmljaA==|https://frl.publisso.de/adhoc/creator/R29tZXotUmF5YSwgTHVpcw==|http://orcid.org/0000-0001-7458-0886|http://orcid.org/0000-0002-3639-2574
1000 Label
1000 Förderer
  1. German Federal Ministry of Education and Research (BMBF) |
  2. Leibniz Institute for Farm Animal Biology (FBN) |
1000 Fördernummer
  1. -
  2. -
1000 Förderprogramm
  1. -
  2. Open Access Fund
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer German Federal Ministry of Education and Research (BMBF) |
    1000 Förderprogramm -
    1000 Fördernummer -
  2. 1000 joinedFunding-child
    1000 Förderer Leibniz Institute for Farm Animal Biology (FBN) |
    1000 Förderprogramm Open Access Fund
    1000 Fördernummer -
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6410251.rdf
1000 Erstellt am 2018-09-18T08:47:21.820+0200
1000 Erstellt von 122
1000 beschreibt frl:6410251
1000 Bearbeitet von 122
1000 Zuletzt bearbeitet Thu Jan 30 16:53:31 CET 2020
1000 Objekt bearb. Tue Sep 18 08:48:23 CEST 2018
1000 Vgl. frl:6410251
1000 Oai Id
  1. oai:frl.publisso.de:frl:6410251 |
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