Theoretical and Applied Genetics

, Volume 127, Issue 9, pp 1917–1933 | Cite as

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.)

  • Raymond Campbell
  • Simon D. A. Pont
  • Jenny A. Morris
  • Gaynor McKenzie
  • Sanjeev Kumar Sharma
  • Pete E. Hedley
  • Gavin Ramsay
  • Glenn J. Bryan
  • Mark A. TaylorEmail author
Original Paper


Key message

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9.


The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient ‘genetical genomics’ analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.


Quantitative Trait Locus Carotenoid Amplify Fragment Length Polymorphism Zeaxanthin Quantitative Trait Locus Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was funded by the Scottish Government Rural and Environmental Research and Analysis Directorate, EU-SOL project number PL 016214 and EU-FP7 METAPRO 244348. The authors would also like to thank Christine Hackett of Biomathematics and Statistics, Scotland for assistance and advice on linkage and QTL analysis.

Conflict of interest

The authors declare they have no conflicts of interest.

Supplementary material

122_2014_2349_MOESM1_ESM.pdf (273 kb)
Online Resource I. The James Hutton Institute in-house visual tuber flesh colour standard scoring chart. The illustration represents the tuber flesh colour attributed individual colour scores. (PDF 272 kb)
122_2014_2349_MOESM2_ESM.pdf (314 kb)
Online Resource II. Chy2 haplotype assay. Figure shows the sequence variations in the second intron of the full length nucleotide sequence within the 3 alleles. Primer sequences are highlighted in red text. Amplicon sizes; allele 1, 213 bp; allele 2, 207 bp; allele 3, 206 bp. (PDF 314 kb)
122_2014_2349_MOESM3_ESM.png (2 mb)
Online Resource IIIa. Population 01H15 genetic maps. (PNG 2036 kb)
122_2014_2349_MOESM4_ESM.png (2.1 mb)
Online Resource IIIb. Population 03TR2 genetic maps. (PNG 2169 kb)
122_2014_2349_MOESM5_ESM.pdf (150 kb)
Online Resource IV. 01H15 and 03TR2 parental Zep amplicon sequences elucidated using the allele assay and primer sequences described by Wolters et al (2010). (PDF 150 kb)
122_2014_2349_MOESM6_ESM.pdf (101 kb)
Online Resource V. Microarray experiment 1 dataset. Comparison of 03TR2 clones bulked according to tuber carotenoid content. The developing and mature stage expression data are presented compared to wild type (P <0.05). The physical map position and gene annotation are presented for each individual microarray probe. (PDF 101 kb)
122_2014_2349_MOESM7_ESM.pdf (124 kb)
Online Resource VI. Tuber carotenoid contents (µg g-1 DW) of individual 03TR2 clones in two seasons selected for bulked microarray analysis. Rhombus, low carotenoid bulk replicate 1; Square, low carotenoid bulk replicate 2; Triangle, high carotenoid bulk replicate 1; Circle, high bulk replicate 2. (PDF 124 kb)
122_2014_2349_MOESM8_ESM.pdf (39 kb)
Online Resource VII. Physical map locations of the known carotenoid biosynthetic genes. The transcript ID, gene ID and superscaffold location are annotated according to The Potato Genome Browser version 4.03. (PDF 39 kb)
122_2014_2349_MOESM9_ESM.pdf (170 kb)
Online Resource VIII. Microarray experiment 2 dataset. Comparison of 03TR2 clones bulked according to Chy2 allele dosage and tuber carotenoid content. The developing and mature stage expression data are presented compared to wild type (P <0.05). The physical map position and gene annotation are presented for each individual microarray probe. (PDF 169 kb)
122_2014_2349_MOESM10_ESM.pdf (44 kb)
Online Resource IX. Sugar content of select 03TR2 clones containing varying levels of tuber carotenoid contents. (a) Total tuber sugar content, (b) tuber glucose content, (c) tuber fructose content, (d) tuber sucrose content. Values shown are the means of three technical extractions of a two sample bulk powder. Error bars indicate the standard error. (PDF 43 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Raymond Campbell
    • 1
  • Simon D. A. Pont
    • 2
  • Jenny A. Morris
    • 1
  • Gaynor McKenzie
    • 1
  • Sanjeev Kumar Sharma
    • 1
  • Pete E. Hedley
    • 1
  • Gavin Ramsay
    • 1
  • Glenn J. Bryan
    • 1
  • Mark A. Taylor
    • 1
    Email author
  1. 1.Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
  2. 2.Environmental and Biochemical SciencesThe James Hutton InstituteDundeeUK

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