Genome-wide association study
GAPIT (v3) R package implemented FarmCPU (J. Wang & Zhang, 2021) method was used for the genome-wide association to fruit color phenotype. We ran LD pruning on QC passing SNP data to improve the computational efficiency of the GWAS analysis. LD pruning was executed with plink software (Purcell et al., 2007) using –indep-pairwise 500 50 0.99 option. We used the first four principal components (PCA) and Kinship matrix as covariates to correct population structure. PCA and Kinship matrix was generated by GAPIT using LD pruned SNPs data set. VanRaden algorithm in GAPIT R package used for calculating kinship. In this study, an FDR-adjusted p-value of 0.05 ( 5%) was used as a cut-off value for identifying the list of significant SNPs associated with date palm fruit’s color phenotype. QQ-plot and Manhattan plots were generated from the GWAS result using the R package CMPlot.