Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 May 17:15:1384401.
doi: 10.3389/fpls.2024.1384401. eCollection 2024.

A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines

Julien Leuenberger  1   2 , Sanjeev Kumar Sharma  3 , Karen McLean  3 , Roland Pellé  1 , Aurélie Bérard  4 , Marie-Laure Lesage  1 , Danièle Porhel  1 , Marie-Ange Dantec  1 , Jean-Eric Chauvin  1 , Glenn J Bryan  3 , Marie-Laure Pilet-Nayel  1 , Marie-Claire Kerlan  1 , Florence Esnault  1
Affiliations

A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines

Julien Leuenberger et al. Front Plant Sci. .
No abstract available

Keywords: SolCAP DNA array; analysis pipeline; genomic dataset; genotyping by sequencing; potato; pre-breeding clones.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
GBS Data Processing Pipeline. Each square represents a processing step; the analysis method and the parameters used are indicated on the left side and on the right side of the scheme, respectively.
Figure 2
Figure 2
(A) Heatmap Depicting Concordance and Discordance in genotype calls of the SNPs in common between GBS and SolCAP array. Red (False): discordance, Blue (True): concordance, Grey (NA): missing data, (B) Distribution of the 26,384 identified SNPs along the chromosomes of Potato. Color scale from blue representing a density of 0 to 25 markers per 100 kb to red representing a density of 175 to 200 markers per 100 kb.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Asano K., Kobayashi A., Tsuda S., Nishinaka M., Tamiya S. (2012). DNA marker-assisted evaluation of potato genotypes for potential resistance to potato cyst nematode pathotypes not yet invading into Japan. Breed Sci. 62, 142–150. doi: 10.1270/jsbbs.62.142 - DOI - PMC - PubMed
    1. Bastien M., Boudhrioua C., Fortin G., Belzile F. (2018). Exploring the potential and limitations of genotyping-by-sequencing for SNP discovery and genotyping in tetraploid potato. Genome 61, 449–456. doi: 10.1139/gen-2017-0236 - DOI - PubMed
    1. Black W., Mastenbroek C., Mills W. R., Peterson L. C. (1953). A proposal for an international nomenclature of races of Phytophthora infestans and of genes controlling immunity in Solanum demissum derivatives. Euphytica 2, 173–178.
    1. Bryan G., McLean K., Bradshaw J., De Jong W., Phillips M., Castelli L., et al. . (2002). Mapping QTLs for resistance to the cyst nematode Globodera pallida derived from the wild potato species Solanum vernei. Theor. Appl. Genet. 105, 68–77. doi: 10.1007/s00122-002-0873-9 - DOI - PubMed
    1. Carley C. A. S., Coombs J. J., Douches D. S., Bethke P. C., Palta J. P., Novy R. G., et al. . (2017). Automated tetraploid genotype calling by hierarchical clustering. Theor. Appl. Genet. 130, 717–726. doi: 10.1007/s00122-016-2845-5 - DOI - PubMed

LinkOut - more resources