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

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

Comparing Host Plant Resistance, Engineered Resistance, and Insecticide Treatment for Control of Colorado Potato Beetle and Potato Leafhopper in Potatoes

The Colorado potato beetle, Leptinotarsa decemlineata (Say) Order Coleoptera and the potato leafhopper, Empoasca fabae (Harris) Order Homoptera, are the major insect pests of potato in eastern North America. In two years of field trials, we compared the effectiveness of three pest management options for the control of Colorado potato beetle and potato leafhopper: natural host plant resistance (glandular trichomes), engineered resistance (Bacillus thuringiensis [Bt] Berliner cry3A gene) and a susceptible potato cultivar (Superior) with an at-planting application of the insecticide thiamethoxam. Similar and acceptable control of the Colorado potato beetle larvae was obtained with the Bt-cry3A lines and the thiamethoxam treated “Superior” variety. The glandular trichome cultivar had significantly less Colorado potato beetle damage than did the untreated “Superior” in 2004, although damage was significantly greater than in the Bt-cry3A lines and the insecticide-treated potatoes for both years, and was the only treatment that consistently had very little potato leafhopper damage. These data demonstrate that although each type of host plant resistance mechanism (Bt-cry3A or glandular trichomes) was as effective as the chemical control against one of the insects, neither provides adequate resistance to both Colorado potato beetle and potato leaf hopper

Position and size of blocks with distorted segregation.

<p>Position and size of blocks with distorted segregation.</p

Comparison of four diploid potato linkage maps: D84 and DRH maps (SNP based) and the ultra-high density (UHD) maps (AFLP-based [5]).

z<p>The number of co-segregating markers in the UHD maps was calculated by subtracting the number of filled bins from the number of markers used for map construction.</p

Graph of chromosome 10 (D84) showing the genetic location (cM) and the physical position (Mb) of 98 markers, and the estimated local recombination.

<p><b>A.</b> Chromosome 10 from population D84 demonstrating poor concordance between physical and genetic position. <b>B.</b> Chromosome 10 from population D84 after correcting the order and orientation of the superscaffolds in the pseudomolecules.</p

Comparison of markers mapped in two diploid populations, DRH and D84.

z<p>Includes co-segregating markers plus mapped markers; 14 ungrouped markers and their 15 co-segregating markers from population DRH were not included in this list.</p>y<p>Length spanned by the northern- and southern-most markers.</p>x<p>Total length.</p

Summary of disconcordant markers for each of the mapping populations.

z<p>Chromosome as determined by the pseudomolecules generated by the Potato Genome Sequencing Consortium.</p>y<p>SNP c2_37964 mapped to two pseudomolecule locations which were both disconcordant with the linkage map positions in DRH and D84 and is therefore included twice in this table.</p>x<p>Based on the number of segregating markers per chromosome.</p

Distribution of mapped markers in DRH, D84 and the Infinium 8303 Potato Array.

<p>Distribution of mapped markers in DRH, D84 and the Infinium 8303 Potato Array.</p

Graphs of DRH SNP marker position (cM) vs. D84 SNP marker position (cM) for all 12 potato chromosomes.

<p>Graphs of DRH SNP marker position (cM) vs. D84 SNP marker position (cM) for all 12 potato chromosomes.</p