Although all the SNP packets that we examined were from regions that were generated with LD, LD was not strong in most of the regions and did not have an obvious effect on linkage analysis. However, strong LD existed between three markers in SNP packet 121: B03T2407, B03T2408, and C03R0221 with pair-wise D' > 0.95 and r2 > 0.38. The pair-wise LD as measured by D' and r2 for this packet is shown in Table 1.
