Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth


Key message

Generation of a dense SNP-based linkage map of a diploid potato population and identification of major QTLs for tuber shape and eye depth on chromosomes 2 and 10.


This paper reports the construction of a genetic map of a highly heterozygous full-sib diploid potato population (06H1) based on the use of a set of 8,303 single nucleotide polymorphism (SNP) markers. The map contains 1,355 distinct loci and 2,157 SNPs, 802 of which co-segregate with other markers. We find high levels of collinearity between the 12 chromosomal maps with a recently improved version of the potato genome assembly, with the expected genetic clustering in centromeric regions. The linkage maps are used in combination with highly detailed phenotypic assessments conducted over two growing seasons to perform quantitative trait loci analysis of two important potato traits, tuber shape and eye depth. The major loci segregating for tuber shape in 06H1 map to loci on chromosomes 2 and 10, with smaller effects mapping to three other chromosomes. A major locus for tuber eye depth co-locates with the tuber shape locus on chromosome 10. To assess when tuber shape is established in the developing tuber, we have performed staged observations of tuber formation. Our observations suggest that tuber shape is determined very early in tuber development.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. Bonierbale MW, Plaisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120:1095–1103

  2. Bradshaw JE, Hackett CA, Lowe R, McLean K, Stewart HE, Tierney I, Vilaro MDR, Bryan GJ (2006) Detection of a quantitative trait locus for both foliage and tuber resistance to late blight Phytophthora infestans (Mont.) de Bary on chromosome 4 of a dihaploid potato clone (Solanum tuberosum subsp tuberosum). Theor Appl Genet 113:943–951

  3. Bryan G, McLean K, Bradshaw J, De Jong W, Phillips M, Castelli L, Waugh R (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

  4. Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PLoS ONE 7:e36347

  5. Graham J, Hackett CA, Smith K, Woodhead M, MacKenzie K, Tierney I, Cooke D, Bayer M, Jennings N (2011) Towards an understanding of the nature of resistance to Phytophthora root rot in red raspberry. Theor Appl Genet 123:585–601

  6. Hackett CA, McLean K, Bryan GJ (2013) Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PloS One 8. doi:10.1371/journal.pone.0063939

  7. Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR (2011) Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genom 12:302

  8. Kloosterman B, Abelenda JA, Carretero Gomez MdM, Oortwijn M, de Boer JM, Kowitwanich K, Horvath BM, van Eck HJ, Smaczniak C, Prat S, Visser RGF, Bachem CWB (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495:246–250

  9. Li XQ, De Jong H, De Jong DM, De Jong WS (2005) Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes. Theor Appl Genet 110:1068–1073

  10. Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D (2001) Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics 157:1369–1385

  11. Maris B (1966) The modifiability of characters important in potato breeding. Euphytica 15:18–31

  12. Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–197

  13. Rezvoy C, Charif D, Gueguen L, Marais GAB (2007) MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics 23:2188–2189

  14. Sharma SK, Bolser D, de Boer J, Sonderkaer M, Amoros W, Carboni MF, D’Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejia N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RGF, Bachem CWB, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JME, Milbourne D, Martin DMA, Bryan GJ (2013) Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3-genes genomes. Genetics 3:2031–2047

  15. Sliwka J, Wasilewicz-Flis I, Jakuczun H, Gebhardt C (2008) Tagging quantitative trait loci for dormancy, tuber shape, regularity of tuber shape, eye depth and flesh colour in diploid potato originated from six Solanum species. Plant Breeding 127:49–55

  16. Uitdewilligen JGAML, Wolters A-MA, D’Hoop BB, Borm TJA, Visser RGF, van Eck HJ (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8(5):e62355

  17. van Eck HJ (2007) Genetics of morphological and tuber traits. In: Vreugdenhil D (ed) Potato biology and biotechnology: advances and perspectives. Elsevier, Amsterdam, pp 91–115

  18. van Eck HJ, Jacobs JME, Stam P, Ton J, Stiekema WJ, Jacobsen E (1994) Multiple alleles for tuber shape in diploid potato detected by qualitative and quantitative genetic analysis using RFLPs. Genetics 137:303

  19. Van Ooijen JW (2006) JoinMap 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands

  20. Van Ooijen JW (2009) MapQTL 6, Software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, Wageningen, Netherlands

  21. van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort J, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087

  22. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

Download references


We gratefully acknowledge the financial support of the The Scottish Government and Mylnefield Research Services. We also acknowledge the assistance of the potato field trialling team at The James Hutton Institute. We thank Julie Graham and Joanne Russell for critical comments on the manuscript.

Conflict of interest

The authors declare they have no conflicts of interest.

Author information

Correspondence to Glenn J. Bryan.

Additional information

Communicated by Herman J. van Eck.

Electronic Supplementary Material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Prashar, A., Hornyik, C., Young, V. et al. Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth. Theor Appl Genet 127, 2159–2171 (2014). https://doi.org/10.1007/s00122-014-2369-9

Download citation


  • Quantitative Trait Locus
  • Quantitative Trait Locus Analysis
  • Single Nucleotide Polymorphism Marker
  • Quantitative Trait Locus Region
  • Tuber Shape