Strategies to build high-density linkage maps of the porcine 60k SNP chip

F. Tortereau, B. Servin, J. Beever, A. Archibald, G. Rohrer, D. Milan, L. Schook, M.A.M. Groenen
Plant and Animal Genome XIX Conference, January 15-19, 2011, San Diego, CA


We present here two different strategies to compute high-density linkage maps based on the porcine 60k SNP chip that was genotyped on 4 different pedigrees with a total of 5600 animals. The first strategy uses the draft sequence as a reference order, the SNP being first mapped to it. The second strategy uses a physical map based on RH mapping as a reference order. Two radiation hybrid panels have been genotyped on the 60k chip, so physical maps could be computed. The two strategies are illustrated here with the analysis of one F2 pedigree. Based on the draft sequence,1403 SNP are predicted to be on SSC18. Of these SNPs 1040 could be mapped on SSC18 with this pedigree. The total length of the average map is estimated at 105cM. For the second strategy, 763 SNP are retained as being common to our linkage map and to the physical map. For this subset of SNPs, the length of the linkage map varied when the reference order used was build10 or the physical map. In case of build10 as the reference, the length of the average map is 100cM whereas it is only 92cM when the order is based on the physical map. Therefore, prior knowledge of the physical map facilitates the computation of linkage maps. Based on the RH order, a first linkage map was estimated and the remaining SNP could be integrated based on build10 information. Links between linkage map and sequence features will also be presented for this chromosome.