Linkage disequilibrium analysis and haplotype construction
The degree of linkage disequilibrium between the SNPs was analyzed using SHEsis software[7] and expressed as D′ and r2, with larger values of D′ and r2indicating a higher degree of linkage disequilibrium between the two associated SNPs. Values of D′ > 0.9 and r2 > 0.33 are generally considered to indicate highly interlocked genes. If D′ ≥ 0.8, the SNPs were considered to be sites for the construction of haplotypes; haplotype frequencies < 0.03 were not included in the statistical analysis.