In order to match up the genetic positions of all microsatellite and SNP markers, 38 microsatellite markers in Map03 and 58 microsatellite markers in Marshfield were excluded because of their missing physical positions. ∼200,000 SNPs with low minor allele frequency (≤5%) were excluded. In consideration of any possible impact from linkage disequilibrium (LD), we exclude ∼1,500 SNPs that are within 1,000 base pairs flanking each microsatellite marker. We use equation (2) to create the common map for these microsatellite and SNP markers. A comparison of the numbers of microsatellite and SNP markers before and after cleaning is given in Table 6 . Figure 4 shows the distribution of these cleaned markers in EA families. With these cleaned and mapped markers, we create new pedigrees with the LinkageMS and CIDRSNP data combined together. One combined pedigree has indtotal individuals (in rows) with (mrkMS+mrkSNP) markers (in columns). Missing SNPs of (indtotal - indcommon) individuals were inferred by MERLIN. ( Figure 1 ).
