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.