Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence

Abstract

To facilitate genome-guided breeding in potato, we developed an 8303 Single Nucleotide Polymorphism (SNP) marker array using potato genome and transcriptome resources. To validate the Infinium 8303 Potato Array, we developed linkage maps from two diploid populations (DRH and D84) and compared these maps with the assembled potato genome sequence. Both populations used the doubled monoploid reference genotype DM1-3 516 R44 as the female parent but had different heterozygous diploid male parents (RH89-039-16 and 84SD22). Over 4,400 markers were mapped (1,960 in DRH and 2,454 in D84, 787 in common) resulting in map sizes of 965 (DRH) and 792 (D84) cM, covering 87% (DRH) and 88% (D84) of genome sequence length. Of the mapped markers, 33.5% were in candidate genes selected for the array, 4.5% were markers from existing genetic maps, and 61% were selected based on distribution across the genome. Markers with distorted segregation ratios occurred in blocks in both linkage maps, accounting for 4% (DRH) and 9% (D84) of mapped markers. Markers with distorted segregation ratios were unique to each population with blocks on chromosomes 9 and 12 in DRH and 3, 4, 6 and 8 in D84. Chromosome assignment of markers based on linkage mapping differed from sequence alignment with the Potato Genome Sequencing Consortium (PGSC) pseudomolecules for 1% of the mapped markers with some disconcordant markers attributable to paralogs. In total, 126 (DRH) and 226 (D84) mapped markers were not anchored to the pseudomolecules and provide new scaffold anchoring data to improve the potato genome assembly. The high degree of concordance between the linkage maps and the pseudomolecules demonstrates both the quality of the potato genome sequence and the functionality of the Infinium 8303 Potato Array. The broad genome coverage of the Infinium 8303 Potato Array compared to other marker sets will enable numerous downstream applications.

The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map

“…An example of the four homolog maps of chromosome 1 in parent 2 is shown in Figure 1. In total, 30 mapped markers were found to have a discrepancy between their assignment to a linkage group in this population and their assigned chromosome on the physical sequence (Felcher et al 2012;Vos et al 2015). Of these, two SolCAP markers (solcap_snp_c2_42265 and solcap_snp_c2_32337) were found to have positions at two physical locations but mapped to a single genetic position.…”

“…When compared to previously published centromere boundaries (Sharma et al 2013), the results do not correspond precisely for chromosomes 4, 5, 7, 9, 10, 11, and 12. It is possible that the discrepancies are due to the fact that our estimates are based on a tetraploid population rather than a diploid one (Felcher et al 2012;Sharma et al 2013) because the method used to determine the boundaries was essentially the same. Table S2 provides our estimates for the centromere bounds used in the calculation of relative distance from the centromere for the DR analysis.…”

“…Of these SNPs, 4179 also form part of the SolCap SNP array (Felcher et al 2012). The arrays were processed according to the manufacturer's protocol at ServiceXS, Leiden, The Netherlands.…”

“…Of these, two SolCAP markers (solcap_snp_c2_42265 and solcap_snp_c2_32337) were found to have positions at two physical locations but mapped to a single genetic position. A further 25 mapped markers were found to have an unknown physical position from the published data sets of marker positions (Felcher et al 2012;Vos et al 2015). We provide a list of these markers with their mapped positions in Table S1.…”

“…This is partly due to the lack of software to perform linkage mapping and QTL analysis in polyploids but is also due to the complicated nature of autopolyploid genomes and genetics. The software program TetraploidMap (Hackett and Luo 2003) is a notable exception to this but is constrained by the relatively low numbers of markers it can handle (currently 800 is the maximum) and the need to manually assign marker phase, which may become infeasible with large data sets.One autopolyploid species in which large advances in genetic analysis have been made is tetraploid potato (Solanum tuberosum L.), in terms of the availability of a high-quality reference sequence (Potato Genome Sequencing Consortium 2011), many published linkage maps (Meyer et al 1998;van Os et al 2006;Felcher et al 2012;Hackett et al 2013) as well as methods for performing linkage mapping at the polyploid level (Luo et al 2001;Bradshaw et al 2004;Hackett et al 2013). In comparison with other economically important autotetraploid species such as alfalfa, rose, and leek, the pairing behavior of potato is thought to be relatively well understood, with random bivalent pairing during prophase I of meiosis being generally assumed (Swaminathan and Howard 1953;Milbourne et al 2009).…”