GWAS_Unfolding_p279_PechRouge_2024.Rmd

R Markdown script of the GWAS analysis for leaf unfolding. Three types of GWAS were performed: - An SNP-by-SNP model implemented in R/MM4LMM version 2.1.0 (Laporte et al., 2022) based on a linear mixed model was used to test the significance of the effect of each SNP, - A multi-locus mixed model MLMM (Segura et al., 2012), which jointly analyses all SNPs to handle LD while selecting a subset of SNPs with a stepwise regression procedure,) - A SNP selection in a Bayesian setting (Flutre et al., 2022) fitted with the variational algorithm implemented in R/varbvs version 2.5.7 (Carbonetto & Stephens, 2012).