Candidate gene and variant analysis
±150 kb region on both sides of significant SNPs (total 300 kb) were
considered as potential regions for possible candidate genes and variant
analysis. Possible gene sequences and coordinates were mapped from the
potential region using the GFF3 gene annotation file (PDK50.gff3) of the
PDK50 reference genome. Gene ontology of mapped gene sequences was
performed using Blast2Go software (Conesa & Götz, 2008). Literature
search and Blast2Go results were used to identify the function of the
candidate genes. All SNPs and INDELs from the potential regions were
annotated using SNPeff software. LD R^2 value of each SNP from the
candidate region was calculated against the significant SNPs from the
GWAS result using PLINK software. Amino acid substitution effects on the
protein function of the candidate SNPs were analysed using SIFT (Sim et
al., 2012).