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  

## Background

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

The Shoot Branching Gene-Phenotype Network generates values for intermediate traits (`Auxin`,`Strigolactone`,`Cytokinin`,`Sucrose` & 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.

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.

The whole divergent selection experiments were replicated 5 times, resulting in 1,200 populations with genotype and phenotype data.

### Data

##### Genotype

*TrueQtlInfo.csv*

Information on Causal Genomic Sites (Quantitative Trait Loci - QTL) & 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)

 *QtlMatrix.csv*

Information on Number of Gene Copies (Alleles) at each QTL for each individual

 - 1st Column: Individual ID

 - 2nd Column Onnwards: QTL Allele Counts

  *SnpMatrix.csv*

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

##### Phenotype

  *TraitData.csv*

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