Abstract
SolariX is a compendium of DNA sequence tags from the nucleotide binding site (NBS) domain of disease resistance genes of the common potato, Solanum tuberosum Group Tuberosum. The sequences, which we call NBS tags, for nearly all NBS domains from 91 genomes—representing a wide range of historical and contemporary potato cultivars, 24 breeding programs and 200 years—were generated using just 16 amplification primers and high-throughput sequencing. The NBS tags were mapped to 587 NBS domains on the draft potato genome DM, where we detected an average, over all the samples, of 26 nucleotide polymorphisms on each locus. The total number of NBS domains observed, differed between potato cultivars. However, both modern and old cultivars possessed comparable levels of variability, and neither the individual breeder or country nor the generation or time appeared to correlate with the NBS domain frequencies. Our attempts to detect haplotypes (i.e., sets of linked nucleotide polymorphisms) frequently yielded more than the possible 4 alleles per domain indicating potential locus intermixing during the mapping of NBS tags to the DM reference genome. Mapping inaccuracies were likely a consequence of the differences of each cultivar to the reference genome used, coupled with high levels of NBS domain sequence similarity. We illustrate that the SolariX database is useful to search for polymorphism linked with NBS-LRR R gene alleles conferring specific disease resistance and to develop molecular markers for selection.
Highlights
The common potato (Solanum tuberosum Group Tuberosum) was created in Europe
An resistance genes (R genes) will be maintained in the breeding pool, and the number of different resistance alleles accumulated would increase with every new generation of potato cultivars
As most R genes contain both nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains, conserved motifs from both NBS and LRR domains have been efficiently employed to identify the majority of plant NBS-LRR R g enes[12,13,14,15,16]
Summary
The common potato (Solanum tuberosum Group Tuberosum) was created in Europe. It has gone through considerable genetic bottlenecks, including the initial selection for adaptation to long-day prior to its first cropping in continental Europe[1] as well as the epiphytotics of late blight in 1845–47 and wart around 1910 (reviewed in Ross[2]). A common breeding scheme has been to cross a Group Tuberosum parental cultivar with a genebank accession of tuberous Solanum, either wild or domesticated, selected for a specific disease resistance. Jupe et al.[13], using close to 50,000, 120-mer biotinylated RNA oligos, enriched fragments putatively containing NBS-LRR domains from the genomic DNA of one Group Tuberosum cultivar and detected a total of 755 R genes containing NBS and LRR domains. Jupe and colleagues’[13 755] R genes refer to the potato’s current, publicly available sequenced genome (version 4.03) of the diploid (doubled monoploid) S. tuberosum Group Phureja clone (clonal cultivar) DM 1–3 516 R4415. S. phureja was, considered in pre-molecular taxonomy treatments as a separate s pecies[4]
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call