pSBVB

pSBVB simulates genotype and phenotype data to evaluate and optimize genomic selection strategies in polyploid species by modeling inheritance from founder SNP or sequence data with specified causal variants, heritabilities, and pedigrees.

Key Features:

• Versatile simulation of polyploid phenotypes: Simulates complex phenotypes across a wide range of genetic architectures specific to polyploid species.
• Founder genotype input: Accepts founder population genotype data as single nucleotide polymorphisms (SNPs) or sequence data.
• Causal variants and heritabilities: Requires a list of causal variants per trait along with their heritabilities for trait simulation.
• Pedigree-based simulation: Uses pedigree information to propagate genotypes and phenotypes through related individuals.
• Recombination rate specification: Allows specification of recombination rates between homeologous chromosomes for application to both allo- and autopolyploid species.
• Output generation: Produces phenotype and genotype data for all individuals in the pedigree and can generate genomic relationship matrices using exact or approximate genotype values.
• Evaluation of genomic selection strategies: Enables simulation across varying SNP densities, genetic architectures, and population sizes to assess and compare genomic selection approaches.

Scientific Applications:

• Plant breeding evaluation: Assess the potential benefits and outcomes of genomic selection in complex polyploid crop genomes, including tetraploid potatoes and octoploid strawberries.
• Benchmarking selection strategies: Compare efficacy of different genomic selection strategies under varying SNP densities, genetic architectures, and population sizes.
• Association study design optimization: Aid optimization of experimental designs for association studies in polyploid species.

Methodology:

Implements a gene-dropping approach that simulates inheritance of causal variants across pedigrees while incorporating founder genotype data and user-specified recombination rates between homeologous chromosomes.