carrot-diallel

Synopsis

This repository contains data and corresponding code to perform diallel analysis of shoot growth in carrots. Scripts include analyses using Griffing's Method I Model I (Griffing 1956) and BayesDiallel (Lenarcic et al. 2012, Crowley et al. 2014).

Data sets (.csv)

1. parentalData.csv
   phenotypic data for parents used to construct the diallel
2. diallelRawData.csv
   phenotypic observations for diallel progenies, includes variables for year, replication, male parent, and female parent
3. Diallel tau prior.csv
   prior information for BayesDiallel

Scripts

• 01_diallel_parental_means.R
  computes and plots means + 95% confidence intervals for parent phenotypes

• 02_missing_data_heatmap.R
  plots phenotypic values and location of missing data by cross, year, and replication

• 03_phenotypic_correlations.R
  calculates and plots Pearson's correlations for phenotypes

• 04_impute_missing_data.R
  uses mice package to impute missing data (see van Buuren and Groothuis-Oudshoorn 2011); generates imputed datasets for pooled diallel analysis

• 05_pooled_diallel_analysis.R
  computes Griffing's ANOVA and effect estimates (i.e. GCA, SCA, reciprocal) for each imputed dataset and combines results. Calls functions from three other scripts (listed below)

  • 05A_diallel_analysis_functions.R
    modified diallele1 function from plantbreeding package (Rosyara 2014); allows calculation of Griffing's ANOVA with multiple environments; includes additional edits to SCA calculation from G. Ramstein
  • 05B_calcSCA.R
    function to calculate SCA estimates for multiple environments and pooling
  • 05C_calcRecip.R
    function to calculate reciprocal effect estimates for multiple environments and pooling
  • 05D_pool_Griffing_Method3.R
    Griffing's ANOVA using method III (without parents) to estimate Baker's ratio

• 06_GGE_biplots.R
  GGE biplots for diallel phenotypes & parents following Frutos et al. (2014)

• 07_BayesDiallel_fulldiallelanalyze.R
  applies and stores AFD objects from DiallelAnalyzer function in BayesDiallel

• 08_read_AFD_objects.R
  reads in AFD objects for subsequent analyses in BayesDiallel

• 09_BayesDiallel_plots.R
  plots observed vs. expected phenotypes, highest posterior density (HPD) intervals, and strawplots (see Lenarcic et al. 2012 and BayesDiallel documentation)

• 10_create_psq_df.R
  exports table of posterior PSq values (diallel variance projection [VarP] in Crowley et al. 2014) for all traits

• 11_VarP_plot.R
  plots relative contribution of inhertiance classes to VarP

• 12_degree_of_dominance.R
  uses BayesDiallel AFD results to estimate the degree of dominance and the dominance index for crosses in a diallel (see Maurizio et al. 2018)

• 13_BayesDiallel_fulldiallelanalyze_by_env.R
  applies and stores AFD objects for each environment

• 14_read_AFD_by_env.R
  reads in AFD objects by environment

• 15_ranks_by_environment.R
  estimates and hybrid rankings in each environment

• 16_plot_ranks_by_environment.R
  plots hybrid rankings by environment

References

Crowley JJ, Kim Y, Lenarcic AB, Quackenbush CR, Barrick C, Adkins DE, Shaw GS, Miller DR, Pardo Manuel de Villena F, Sullivan PF, Valdar W (2014) Genetics of adverse reactions to haloperidol in a mouse diallel: A drug-placebo experiment and Bayesian causal analysis. Genetics 196(1):321-47.

Frutos E, Purificación Galindo M (2014) An interactive biplot implementation in R for modeling genotype-by-environment interaction. Stoch Environ Res Risk Assess 28:1629-1641.

Griffing B (1956) Concept of general and specific combining ability in relation to diallel crossing systems. Aust. J. Biol. Sci. 9:463-493.

Lenarcic AB, Svenson KL, Churchill GA, Valdar W (2012) A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190:413-435. doi: 10.1534/genetics.111.132563

Maurizio PM et al (2018) Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. G3 doi:10.1534/g3.117.300438

Rosyara U (2014) plantbreeding: Analysis and visualization of data from plant breeding and genetics experiments. http://R-Forge.R-project.org/projects/plantbreeding/

van Buuren S and Groothuis-Outshoorn K (2011) mice: multivariate imputation by chained equations in R. J. Stat. Softw. 45:1-67

BayesDiallel website: http://valdarlab.unc.edu/software/bayesdiallel/BayesDiallel.html