SNPscan breeder

Computer program SNPscan breeder

Advances in DNA sequencing techniques allow the sequencing of whole genomes of hundreds if not thousands of individuals. These data combined with precise phenotype data enable the identification of causal single nucleotide polymorphisms (SNPs) of traits with complex architecture. The old dream of merging quantitative genetics and genomics is getting reality. This offers enormous opportunities, especially in breeding. The simulation program SNPscan has been created to estimate, optimise and realise these opportunities.

The computer programSNPscan breeder has been developed to simulate SNPs of whole genomes for many individuals in populations in order to:

• simulate phenotypes based on concrete genetic architectures and a given level of heritability (number of SNPs with positive and negative effect alleles, distribution of SNPs in the genome)
• develop and test sample strategies for genome wide association studies (GWAS)
• predict phenotypes and validate them with empirical data
• test and optimise different breeding strategies based on pedigree data, genomic prediction and GWAS data
• develop and test sampling strategies for genetic inventories for population genomic studies

SnpScan breeder has been programmed with Visual Studio 2019 as a vb.net application and compiled as 64-bit versions for the operating system Microsoft Windows (Windows 11 and former versions).

The recent version SNPscan breeder, and a user’s manual  can be downloaded here:

64 bit version SNPscan breeder (last updated: 14/07/23)

User’s manual (last updated: 13/07/23)

The older version SNPscan 1.0, a user’s manual and tutorial videos can be downloaded here:

64 bit version SNPscan (last updated: 24/02/23)

User’s manual (last updated: 24/02/23)

Introduction - video (last updated: 28/02/23)

Generation of genomes and genetic architecture - video (last updated: 24/08/22)

Forward simulation - video (last updated: 26/02/23)

Genomic selection - video (last updated: 26/02/23)

GWAS with SNPscan results - video (last updated: 27/08/22)