LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces

Abstract

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.

CLIP Test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis

“…A QTL region of 0.1 (or 0.01) M containing 203 (or 263) equally spaced SNPs was then simulated to mimic 60 K (or 800 K) assay genotypes. Genotypes were simulated with the LDSO (Linkage Disequilibrium with Several Options) software (INRA, Jouy-en-Josas, France) (Ytournel et al , 2012). The initial SNP allele frequencies were drawn at random from a uniform distribution.…”

Using haplotypes for the prediction of allelic identity to fine-map QTL: characterization and properties

“…The 235 FLW chromosomes were included in N =200 gene-drop simulations, in a 25-generation pedigree for the FLW breed, using the LDSO software [40]. The pedigree was composed of 1594 founders, 3373 sires and 7100 dams.…”

XVth QTLMAS: simulated dataset

“…The parental generation (20 sires and 200 dams) was generated by a random choice of two gametes chosen in pools of 75. These 2x75 gamete pools were generated after a long history of random drift and mutation simulated by the LDSO software [ 3 ]. This history involved two steps: 1000 generations of a population comprising 1000 gametes, followed by a severe bottleneck with 150 gametes evolving during 30 generations.…”