Stochastic Simulation of Divergent Selection Experiment on a Gene-Phenotype Network: A Case Study of Shoot Branching in Plants

# Stochastic Simulation of Divergent Selection Experiment on a Gene-Phenotype Network: A Case Study of Shoot Branching in Plants <br> ## Background <br> General Background Information on the specification of the Gene-Phenotype Network for Shoot Branching can be found in this publication: https://doi.org/10.1093/insilicoplants/diac006 <br> The Shoot Branching Gene-Phenotype Network generates values for intermediate traits (`Auxin`,`Strigolactone`,`Cytokinin`,`Sucrose` &amp; the `Integrator Signal`) and the end-point trait, `Time Bud Outgrowth`, that was under direct selection in the simuations. Starting from a common segregating population of genotypes (F2 - cycle1 folders), individuals were selected for either `Faster` or `Slower` Time to Bud Outgrowth for 30 selection cycles which created two seperate selection lines. <br> The heritability, the ratio of genetic variance to error variance, of the `Time Bud Outgrowth` trait under direct selection was varied (`H2 = 1.0, 0.7, 0.5, 0.3`) to assess implications of the accuracy of selection decisison on the seleciton trajectories of the gene-phenotype network. <br> The whole divergent selection experiments were replicated 5 times, resulting in 1,200 populations with genotype and phenotype data. <br> ### Data <br> ##### Genotype <br> *TrueQtlInfo.csv* <br> Information on Causal Genomic Sites (Quantitative Trait Loci - QTL) &amp; their Effect Sizes on Gene-Phenotype Network; - Column 1: Intermediate Trait Infuenced by each QTL - Column 2: QTL Order - Column 3: Effect Size of each QTL - Column 4: Location Information of each QTL (ChromosomeNumber_WithinChromosomeIndex) <br> *QtlMatrix.csv* <br> Information on Number of Gene Copies (Alleles) at each QTL for each individual - 1st Column: Individual ID - 2nd Column Onnwards: QTL Allele Counts <br> *SnpMatrix.csv* <br> Information on Number of Gene Copies (Alleles) at each SNP (Non-Causal Genomic Sites) for each individual - 1st Column: Individual ID - 2nd Column Onnwards: SNP Allele Counts <br> ##### Phenotype <br> *TraitData.csv* <br> Trait Records for each individual - Column 1: Individual ID - Column 2: Selection Direction on Time to Bud Outhgrowth - Column 3-6: Additive Genetic Values (Sum of QTL Allele Counts x QTL Effect Size) for Intermediate Traits - Column 7-11: Total Genetic Values (Sum of Additive Genetic Values + Interaction Effects) for Intermediate Traits - Column 12: Total Genetic Values for Time to Bud Outgrowth - Column 13: Phenotypes (Total Genetic Values + Error) for Time to Bud Outgrowth <br>