Advertisement

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

Abstract

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.

Abstract

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.

Keywords

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.

Notes

Acknowledgments

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)

References

  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 120:1095–1103PubMedCentralPubMedGoogle Scholar
  2. Bradshaw JE, Pande B, Bryan GJ, Hackett CA, McLean K, Stewart HE, Waugh R (2004) Interval mapping of quantitative trait loci for resistance to late blight [Phytophthora infestans (Mont.) de Bary], height and maturity in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum). Genetics 168:983–995PubMedCentralPubMedCrossRefGoogle Scholar
  3. Breithaupt DE, Bamedi A (2002) Carotenoids and carotenoid esters in potatoes (Solanum tuberosum L.): new insights into an ancient vegetable. J Agric Food Chem 50:7175–7181PubMedCrossRefGoogle Scholar
  4. Brown CR, Edwards CG, Yang CP, Dean BB (1993) Orange flesh trait in potato: inheritance and carotenoid content. J Am Soc Hort Sci 118:145–150Google Scholar
  5. Brown CR, Kim TS, Ganga Z, Haynes K, De Jong D, Jahn M, Paran I, De Jong W (2006) Segregation of total carotenoid in high level potato germplasm and its relationship to beta-carotene hydroxylase polymorphism. Am J Pot Res 83:365–372CrossRefGoogle Scholar
  6. Bruno AK, Wetzel CM (2004) The early light-inducible protein (ELIP) gene is expressed during the chloroplast-to-chromoplast transition in ripening tomato fruit. J Exp Bot 55:2541–2548PubMedCrossRefGoogle Scholar
  7. Campbell R, Ducreux LJM, Morris WL, Morris JA, Suttle JC, Ramsay G, Bryan GJ, Hedley PE, Taylor MA (2010) The metabolic and developmental roles of carotenoid cleavage dioxygenase 4 from potato (Solanum tuberosum L). Plant Physiol 154:656–664PubMedCentralPubMedCrossRefGoogle Scholar
  8. Cazzonelli CI, Cuttriss AJ, Cossetto SB, Pye W, Crisp P, Whelan J, Finnegan EJ, Turnbull C, Pogson BJ (2009) Regulation of carotenoid composition and shoot branching in arabidopsis by a chromatin modifying histone methyltransferase, SDG8. Plant Cell 21:39–53PubMedCentralPubMedCrossRefGoogle Scholar
  9. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedCentralPubMedGoogle Scholar
  10. Cuevas HE, Staub JE, Simon PW, Zalapa JE, McCreight JD (2008) Mapping of genetic loci that regulate quantity of beta-carotene in fruit of US Western Shipping melon (Cucumis melo L.). Theor Appl Genet 117:1345–1359PubMedCrossRefGoogle Scholar
  11. DellaPenna D, Pogson BJ (2006) Vitamin synthesis in plants: tocopherols and carotenoids. Annu Rev Plant Biol 57:711–738PubMedCrossRefGoogle Scholar
  12. Ducreux LJ, Morris WL, Prosser IM, Morris JA, Beale MH, Wright F, Shepherd T, Bryan GJ, Hedley PE, Taylor MA (2008) Expression profiling of potato germplasm differentiated in quality traits leads to the identification of candidate flavour and texture genes. J Exp Bot 59(15):4219–4231PubMedCentralPubMedCrossRefGoogle Scholar
  13. Fraser PD, Bramley PM (2004) The biosynthesis and nutritional uses of carotenoids. Prog Lipid Res 43:228–265PubMedCrossRefGoogle Scholar
  14. Giuliano G, Tavazza R, Diretto G, Beyer P, Taylor M (2008) Metabolic engineering of carotenoid biosynthesis in higher plants. Trends Biotechnol 26:139–145PubMedCrossRefGoogle Scholar
  15. Haynes KG (2010) Genotype-environment interactions for potato tuber carotenoid content. J Amer Soc Hort Sci 135(3):250–258Google Scholar
  16. Hirschberg J (2001) Carotenoid biosynthesis in flowering plants. Curr Opin Plant Biol 4:210–218PubMedCrossRefGoogle Scholar
  17. Kloosterman B, De Koeyer D, Griffiths R, Flinn B, Steuernagel B, Scholz U, Sonnewald S, Sonnewald U, Bryan GJ, Bánfalvi Z, Hammond JP, Geigenberger P, Nielsen KL, Visser RGF, Bachem CWB (2008) The potato transcriptome: a new look at transcriptional changes during tuber development using the POCI array. Comp Funct Genom 8:329–340CrossRefGoogle Scholar
  18. Kloosterman B, Oortwijn M, uit de Willigen J, America T, de Vos R, Visser, RGF Bachem CWB (2010) From QTL to candidate gene: Genetical genomics of simple and complex traits in potato using a pooling strategy. BMC Genomics 11:158Google Scholar
  19. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  20. Li L, Paolillo DJ, Parthasarathy MV, Dimuzio EM, Garvin DF (2001) A novel gene mutation that confers abnormal patterns of beta-carotene accumulation in cauliflower (Brassica oleracea var. botrytis). Plant J 26:59–67PubMedCrossRefGoogle Scholar
  21. Liu YS, Gur A, Ronen G, Causse M, Damidaux R, Buret M, Hirschberg J, Zamir D (2003) There is more to tomato fruit colour than candidate carotenoid genes. Plant Biotechnol J 1:195–207PubMedCrossRefGoogle Scholar
  22. Livak KJ (1997) “Relative quantification of gene expression” User Bulletin No.2: ABI PRISM 7700 Sequence detection system. PE Applied Biosystems, Foster CityGoogle Scholar
  23. Lu W, Haynes K, Wiley E, Clevidence B (2001) Carotenoid content and color in diploid potatoes. J Am Soc Hortic Sci 126:722–726Google Scholar
  24. Morris WL, Ducreux L, Griffiths DW, Stewart D, Davies HV, Taylor MA (2004) Carotenogenesis during tuber development and storage in potato. J Exp Bot 55:975–982PubMedCrossRefGoogle Scholar
  25. Nesterenko S, Sink KC (2003) Carotenoid profiles of potato breeding lines and selected cultivars. HortScience 38(6):1173–1177Google Scholar
  26. Ohmiya A, Kishimoto S, Aida R, Yoshioka S, Sumitomo K (2006) Carotenoid cleavage dioxygenase (CmCCD4a) contributes to white color formation in chrysanthemum petals. Plant Physiol 142:1193–1201PubMedCentralPubMedCrossRefGoogle Scholar
  27. Römer S, Lubeck J, Kauder F, Steiger S, Adomat C, Sandmann G (2002) Genetic engineering of a zeaxanthin-rich potato by antisense inactivation and co-suppression of carotenoid epoxidation. Metab Eng 4:263–272PubMedCrossRefGoogle Scholar
  28. Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor J, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722CrossRefGoogle Scholar
  29. Sharma SK, Bolser D, de Boer J, Sonderkaer M, Amoros W, Federico Carboni M, D’Ambrosio JM, de la Cruz G, De Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall DF, 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 Genet 3.11:2031–2047Google Scholar
  30. Shepherd LVT, McNicol JW, Razzo R, Taylor MA, Davies HV (2006) Assessing the potential for unintended effects in genetically modified potatoes perturbed in metabolic and developmental processes. Targeted analysis of key nutrients and anti-nutrients. Trans Res 15:409–425CrossRefGoogle Scholar
  31. Stushnoff C, Ducreux LJM, Hancock RD, Hedley PE, Holm D, McDougall GJ, McNicol JW, Morris J, Morris WL, Sungurtas J, Verrall SR, Zuber T, Taylor MA (2010) Flavonoid profiling and transcriptome analysis reveals new gene-metabolite correlations in tubers of Solanum tubersoum L. J Exp Bot 61:1225–1238PubMedCentralPubMedCrossRefGoogle Scholar
  32. Taylor M, Ramsay G (2005) Carotenoid biosynthesis in plant storage organs: recent advances and prospects for improving plant food quality. Physiol Plant 124(2):143–151CrossRefGoogle Scholar
  33. The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefGoogle Scholar
  34. Thorup TA, Tanyolac B, Livingstone KD, Popovsky S, Paran I, Jahn M (2000) Candidate gene analysis of organ pigentation loci in the Solanaceae. Pro Nat Acad Sci USA 97:11192–11197CrossRefGoogle Scholar
  35. Tian L, Pang Y, Dixon RA (2008) Biosynthesis and genetic engineering of proanthocyanidins and (iso)flavonoids. Phytochem Rev 7:445–465CrossRefGoogle Scholar
  36. Van Eck J, Conlin B, Garvin DF, Mason H, Navarre DA, Brown CR (2007) Enhancing beta-carotene content in potato by RNAi-mediated silencing of the beta-carotene hydroxylase gene. Amer J Potato Res 84:331–342CrossRefGoogle Scholar
  37. Van Ooijen JW (2004) MapQTL® 5, Software for the mapping of quantitative trait loci in experimental populations. Kyazma B.V. Wageningen, NetherlandsGoogle Scholar
  38. Van Ooijen JW (2006) JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V. Wageningen, NetherlandsGoogle Scholar
  39. Welsch R, Maass D, Voegel T, DellaPenna D, Beyer P (2008) The transcription factor RAP2.2 and its interacting partner SINAT2—stable elements in the carotenogenesis of Arabidopsis leaves. Plant Physiol 145:1073–1085CrossRefGoogle Scholar
  40. Wolters AMA, Uitdewilligen JGAML, Kloosterman BA, Hutten RCB, Visser RGF, van Eck HJ (2010) Identification of alleles of carotenoid pathway genes important for zeaxanthin accumulation in potato tubers. Plant Mol Biol 73:659–671PubMedCentralPubMedCrossRefGoogle Scholar
  41. Zhou X, McQuinn R, Fei Z, Wolters AA, Van Eck J, Brown C, Giovannoni JJ, Li L (2011) Regulatory control of high levels of carotenoid accumulation in potato tubers. Plant Cell Environ 34:1020–1030PubMedCrossRefGoogle Scholar

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

Personalised recommendations