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Journal Article

A compendium of genome-wide sequence reads from NBS (nucleotide binding site) domains of resistance genes in the common potato


Prakash,  Celine
Max Planck Research Group Biological Clocks (Kaiser), Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Prakash, C., Trognitz, F. C., Venhuizen, P., von Haeseler, A., & Trognitz, B. (2020). A compendium of genome-wide sequence reads from NBS (nucleotide binding site) domains of resistance genes in the common potato. Scientific Reports, 10: 11392. doi:10.1038/s41598-020-67848-z.

Cite as: https://hdl.handle.net/21.11116/0000-000A-184D-6
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.