Change search
ReferencesLink to record
Permanent link

Direct link
Investigating a complex genotype-phenotype map for the development of methods to predict genetic values based on genome-wide marker data – a simulation study for the livestock perspective
Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.ORCID iD: 0000-0002-7173-5579
2013 (English)In: Archiv für Tierzucht, ISSN 0003-9438, Vol. 56, no 38, 380-398 p.Article in journal (Refereed) Published
Abstract [en]

Phenotypic variation can partly be explained by genetic variation, such as variation in single nucleotide polymorphism (SNP) genotypes. Genomic selection methods seek to predict genetic values (breeding values) based on SNP genotypes. To develop and to optimize these methods, simulated data are often used, which follow a rather simple genotype-phenotype map. Is the conventional approach for data simulation in this field an appropriate basis to optimize such methods in view of experimental data? Here, we present an alternative approach, striving to simulate more realistic data based on a genotype-phenotype map which includes a simulated metabolome level. This level was used to simulate genetic values, implicitly including additive and non-additive genetic effects, whereas in a conventional approach additive and dominance effects were explicitly simulated and assembled to genetic values. For both simulation approaches, different scenarios regarding numbers of quantitative trait loci (QTLs) and SNPs were analysed using fastBayesB as prediction method. We observed that our alternative map showed a smaller prediction precision (at least 3.75 %) compared to the conventional approach in all investigated scenarios. The observed degree of linearity is at least 94.12 % of the conventional approach or less. Additionally, we present results for different simulated data and experimental data to allow a comparison on a purely conceptual level. Concluding, simulating a more complex genotype-phenotype map including a molecular level, allows to study processing of variation from the genetic to the phenotype level in more detail and may prepare the ground for modern methods of genomic selection.

Place, publisher, year, edition, pages
Dummerstorf, Germany: Leibniz Institute for Farm Animal Biology (FBN) , 2013. Vol. 56, no 38, 380-398 p.
Keyword [en]
genotype-phenotype map, metabolome, genetic value prediction
National Category
Bioinformatics and Systems Biology
URN: urn:nbn:se:oru:diva-40720DOI: 10.7482/0003-9438-56-038ISI: 000336968000002ScopusID: 2-s2.0-84882583369OAI: diva2:778528
Available from: 2015-01-10 Created: 2015-01-10 Last updated: 2015-06-02Bibliographically approved

Open Access in DiVA

fulltext(347 kB)45 downloads
File information
File name FULLTEXT01.pdfFile size 347 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full textScopus

Search in DiVA

By author/editor
Repsilber, Dirk
Bioinformatics and Systems Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 45 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 159 hits
ReferencesLink to record
Permanent link

Direct link