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.