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).