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

Abstract

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.

Abstract

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.

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Acknowledgments

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.

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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

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Keywords

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