Integration of Two Diploid Potato Linkage Maps with the Potato Physical Map

To assess the quality of the potato genome sequence and the utility of the SolCAP 8303 Infinium array, we developed and mapped two diploid potato populations (DRH and D84, n=92 for each) using the genotype data from the array.  Over 4400 SNPs were mapped (1960 in DRH and 2454 in D84 with 787 in common) resulting in map sizes of 966 (DRH) and 787 (D84) cM, covering 633.8 (DRH) and (641.6) Mb of genome sequence.  Of the mapped SNPs, 33.5% were in candidate genes, 4.5% were previously mapped markers, and 61% were selected based on distribution across the genome.  Distorted segregation ratios occurred in blocks of SNPs in both linkage maps, accounting for 6% (DRH) and 21% (D84) of mapped SNPs.  SNPs with distorted segregation ratios were unique to each population with blocks on chromosomes IX and XII in DRH and III, IV, VI and VIII in D84.  Chromosome assignment of SNPs based on linkage mapping differed from that based on alignment with the PGSC pseudomolecules for only 1% of the mapped SNPs.  Some disconcordant SNPs could be attributed to paralogs.  There were 126 (DRH) and 226 (D84) mapped SNPs not anchored to the pseudomolecules.  The remarkable consensus between the linkage maps and the pseudomolecules demonstrates both the quality of the potato genome sequence and the functionality of the SolCAP 8303 Infinuim array.  The broad genome coverage of the SolCAP 8303 Infinium array compared to other marker types enables many downstream applications.