<abstract xmlns="http://www.w3.org/1999/xhtml">

<p><italic>SNPscan breeder</italic> is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of a trait of interest, different mating designs and different selection criteria, i.e. pheno-types, breeding values from progeny tests, marker-assisted selection (MAS) and genomic selection (GS). The impact of breeding population size, mating design, selection intensity, genetic architecture, heritability and selection criteria on genetic gains, kinship, inbreeding and genetic diversity can be evaluated to optimize the breeding program. A special feature is the possibility for post-hoc analysis of different strategies to identify causal SNPs and allele effects within the frame of genome-wide association studies (GWAS). The proportion of true and false positive SNPs and the correlation of estimated and true allelic effects can be measured and the overall impact of their use for MAS on the success of the breeding program can be tested.</p>
</abstract>

SNPscan breeder is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of a trait of interest, different mating designs and different selection criteria, i.e. pheno-types, breeding values from progeny tests, marker-assisted selection (MAS) and genomic selection (GS). The impact of breeding population size, mating design, selection intensity, genetic architecture, heritability and selection criteria on genetic gains, kinship, inbreeding and genetic diversity can be evaluated to optimize the breeding program. A special feature is the possibility for post-hoc analysis of different strategies to identify causal SNPs and allele effects within the frame of genome-wide association studies (GWAS). The proportion of true and false positive SNPs and the correlation of estimated and true allelic effects can be measured and the overall impact of their use for MAS on the success of the breeding program can be tested.

<italic>SNPscan breeder</italic> – a computer program to test genomic tools in breeding programs

Silvae Genetica

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

 – a computer program to test genomic tools in breeding programs

SNPscan breeder is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of...

SNPscan breeder – a computer program to test genomic tools in breeding programs

Published Online: Jul 16, 2023

Page range: 126 - 131

DOI: https://doi.org/10.2478/sg-2023-0013

Keywords
gBLUP, genetic gain, genomic selection, GWAS, mating design, marker-assisted selection, stochastic simulation

© 2023 Bernd Degen et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

SNPscan breeder – a computer program to test genomic tools in breeding programs

Published Online: Jul 16, 2023

Page range: 126 - 131

DOI: https://doi.org/10.2478/sg-2023-0013

KeywordsgBLUP, genetic gain, genomic selection, GWAS, mating design, marker-assisted selection, stochastic simulation

© 2023 Bernd Degen et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
gBLUP, genetic gain, genomic selection, GWAS, mating design, marker-assisted selection, stochastic simulation