LDSO

The use of Linkage Disequilibrium (LD) greatly increased over the last decades. It has become a classical tool for the detection of QTL by using fine-mapping methods (Meuwissen and Goddard, 2000; Boitard et al. 2006) or genome-wide association studies (Hayes et al. 2009, Pausch et al. 2011). LD is also the key point of the genomic selection (Meuwissen et al. 2001). Finally LD is also used for studying the population histories, for instance to evaluate the evolution of the population sizes over the time (Hayes et al. 2003) or the effects of natural and artificial selection through the identification of selective sweeps (Fan et al. 2010). Simulations are necessary to evaluate the new methods that can be developed for any method using LD.

LDSO (Linkage Disequilibrium with Several Options) is a completely self-contained program written in Fortran90. It is a complete computer program for simulations of whole diploid population histories under various historical scenarios based on the gene-dropping method (MacCluer et al. 1986). The random number generator from L'Ecuyer (1996) was used. The genetic history of one or two populations can be simulated; the output files can deliver various statistics (inbreeding rates, allele frequencies, linkage disequilibrium) on these populations for generations wished by the user. Evolutionary forces that are classically found in livestock populations, such as mutation, selection, changes in the population size or random drift, can be taken into account. This allows the simulation of a wide-range of natural or experimental livestock populations, possibly by making use of a real pedigree. A set of parameters has to be provided by the user using simple text files. The possibility of genotyping errors and missing data is also envisaged.

LDSO has been tested on :
Win / g95
Unix, Linux OS / gfortran, ifort

Author : F. Ytournel

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Reference : Ytournel F, Teyssèdre S, Roldan D, Erbe M, Simianer H, Boichard D, Gilbert H, Druet T, Legarra A. LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces. J Anim Breed Genet. 2012 Oct;129(5):417-21. doi: 10.1111/j.1439-0388.2011.00986.x. Epub 2012 Jan 23. PMID: 22963363. https://doi.org/10.1111/j.1439-0388.2011.00986.x