DHOEM: a statistical simulation software for simulating new markers in real SNP marker data

Jacquin Laval, Cao Tuong-Vi, Grenier Cécile, Ahmadi Nourollah. 2015. DHOEM: a statistical simulation software for simulating new markers in real SNP marker data. BMC Bioinformatics, 16 (404), 8 p.

https://doi.org/10.1186/s12859-015-0830-7

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Quartile : Q1, Sujet : MATHEMATICAL & COMPUTATIONAL BIOLOGY / Quartile : Q2, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q3, Sujet : BIOCHEMICAL RESEARCH METHODS

Résumé : Background Numerous simulation tools based on specific assumptions have been proposed to simulate populations. Here we present a simulation tool named DHOEM (densification of haplotypes by loess regression and maximum likelihood) which is free from population assumptions and simulates new markers in real SNP marker data. The main objective of DHOEM is to generate a new population, which incorporates real and simulated SNP by statistical learning from an initial population, which match the realized features of the latter. Results To demonstrate DHOEM's abilities, we used a sample of 704 haplotypes for 12 chromosomes with 8336 SNP from a synthetic population, used for breeding upland rice in Latin America. The distributions of allele frequencies, pairwise SNP LD coefficients and data structures, before and after marker densification of the associated marker data set, were shown to be in relatively good agreement at moderate degrees of marker densification. DHOEM is a user-friendly tool that allows the user to specify the level of marker density desired, with a user defined minor allele frequency (MAF) limit, which is produced in a reasonable computation time. Conclusions DHOEM is a user-friendly and useful tool for simulation and methodological studies in quantitative genetics and breeding.

Mots-clés Agrovoc : modèle de simulation, modèle mathématique, génétique des populations, amélioration des plantes, étude de cas, Oryza sativa, allèle, halophyte, équilibre génétique, fréquence allélique, génomique, sélection, riz pluvial