Skip to main content
SpringerLink
Log in

Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of carrot (Daucus carota L. ssp. sativus). The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean π sil = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F ST = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r 2 = 0.635) within the 700–1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Aguade M (2001) Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes, in Arabidopsis thaliana. Mol Biol Evol 18:1–9

    PubMed  CAS  Google Scholar 

  • Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:e60

    Article  PubMed  CAS  Google Scholar 

  • Bang H, Kim S, Leskovar D, King S (2007) Development of a codominant CAPS marker for allelic selection between canary yellow and red watermelon based on SNP in lycopene β-cyclase (LCYB) gene. Mol Breed 20:63–72

    Article  CAS  Google Scholar 

  • Banga O (1963) Main types of the western carotene carrot and their origin. W.E.J. Tjeenk Willink, Zwolle

    Google Scholar 

  • Beaumont MA (2005) Adaptation and speciation: what can F ST tell us? Trends Ecol Evol 20:435–440

    Article  PubMed  Google Scholar 

  • Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171. Université de Montpellier II, Montpellier (France)

    Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  PubMed  CAS  Google Scholar 

  • Bradeen JM, Bach IC, Briard M, Le Clerc V, Grzebelus D, Senalik DA, Simon PW (2002) Molecular diversity analysis of cultivated carrot (Daucus carota L.) and wild Daucus populations reveals a genetically nonstructured composition. J Am Soc Hortic Sci 127:383–391

    CAS  Google Scholar 

  • Briard M, Le Clerc V, Grzebelus D, Senalik D, Simon P (2000) Modified protocols for rapid carrot genomic DNA extraction and AFLP™ analysis using silver stain or radioisotopes. Plant Mol Biol Rep 18:235–241

    Article  CAS  Google Scholar 

  • Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31:818–824

    Google Scholar 

  • Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3:e163

    Article  CAS  Google Scholar 

  • Clotault J, Peltier D, Berruyer R, Thomas M, Briard M, Geoffriau E (2008) Expression of carotenoid biosynthesis genes during carrot root development. J Exp Bot 59:3563–3573

    Article  PubMed  CAS  Google Scholar 

  • Corander J, Waldmann P, Sillanpaa MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163:367–374

    PubMed  CAS  Google Scholar 

  • Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997–1004

    Article  PubMed  CAS  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  PubMed  CAS  Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  PubMed  CAS  Google Scholar 

  • Glémin S, Bazin E, Charlesworth D (2006) Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proc R Soc B 273:3011–3019

    Article  PubMed  CAS  Google Scholar 

  • Grzebelus D, Baranski R, Kotlinska T, Michalik B (2002) Assessment of genetic diversity in a carrot (Daucus carota L.) germplasm collection. Plant Genet Resour Newslett 130:51–53

    Google Scholar 

  • Gupta P, Rustgi S, Kulwal P (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485

    Article  PubMed  CAS  Google Scholar 

  • Haasl RJ, Payseur BA (2010) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity. doi:10.1038/hdy.2010.21

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330–333

    Article  PubMed  CAS  Google Scholar 

  • Hill WG (1974) Estimation of linkage disequilibrium in randomly mating populations. Heredity 33:229–239

    Article  PubMed  CAS  Google Scholar 

  • Hudson RR (2000) A new statistic for detecting genetic differentiation. Genetics 155:2011–2014

    PubMed  CAS  Google Scholar 

  • Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147–164

    PubMed  CAS  Google Scholar 

  • Hudson RR, Slatkin M, Maddison WP (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132:583–589

    PubMed  CAS  Google Scholar 

  • Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169:945–953

    Article  PubMed  CAS  Google Scholar 

  • Ingvarsson PK (2008) Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180:329

    Article  PubMed  Google Scholar 

  • Isaacson T, Ronen G, Zamir D, Hirschberg J (2002) Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of β-carotene and xanthophylls in plants. Plant Cell 14:333–342

    Article  PubMed  CAS  Google Scholar 

  • Just BJ, Santos CAF, Fonseca MEN, Boiteux LS, Oloizia BB, Simon PW (2007) Carotenoid biosynthesis structural genes in carrot (Daucus carota): isolation, sequence-characterization, single nucleotide polymorphism (SNP) markers and genome mapping. Theor Appl Genet 114:693–704

    Article  PubMed  CAS  Google Scholar 

  • Just BJ, Santos CAF, Yandell BS, Simon PW (2009) Major QTL for carrot color are positionally associated with carotenoid biosynthetic genes and interact epistatically in a domesticated × wild carrot cross. Theor Appl Genet 119:1155–1169

    Article  PubMed  Google Scholar 

  • Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39:1151–1155

    Article  PubMed  CAS  Google Scholar 

  • Kraakman ATW, Niks RE, Van den Berg P, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446

    Article  PubMed  CAS  Google Scholar 

  • Kwak M, Gepts P (2009) Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118:979–992

    Article  PubMed  CAS  Google Scholar 

  • Latch EK, Dharmarajan G, Glaubitz JC, Rhodes OE (2006) Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conserv Genet 7:295–302

    Article  Google Scholar 

  • Laufer B (1919) The carrot. In: Sino-Iranica: Chinese contributions to the history of civilization in ancient Iran with special reference to the history of cultivated plants and products. Field Museum of Natural History, Chicago, pp 451–454

  • Le Clerc V (2001) Etude de la diversité génétique chez la carotte (Daucus carota L.): mise au point de stratégies d’analyse et de régénération des ressources génétiques. Ph.D. Thesis. Université d’Angers

  • Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Version 1.1 edn. University of Connecticut, Hartford

    Google Scholar 

  • Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15:271–290

    Article  CAS  Google Scholar 

  • Mackevic VI (1929) The carrot of Afghanistan. Bull Appl Bot Genet Plant Br 20:517–562

    Google Scholar 

  • Malysheva-Otto L, Ganal M, Roder M (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genet 7:6

    Article  PubMed  CAS  Google Scholar 

  • Nakajima Y, Yamamoto T, Oeda K (1997) Genetic variation of mitochondrial and nuclear genomes in carrots revealed by random amplified polymorphic DNA (RAPD). Euphytica 95:259–267

    Article  CAS  Google Scholar 

  • Nakajima Y, Oeda K, Yamamoto T (1998) Characterization of genetic diversity of nuclear and mitochondrial genomes in Daucus varieties by RAPD and AFLP. Plant Cell Rep 17:848–853

    Article  CAS  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    PubMed  CAS  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nicolle C, Simon G, Rock E, Amouroux P, Remesy C (2004) Genetic variability influences carotenoid, vitamin, phenolic, and mineral content in white, yellow, purple, orange, and dark-orange carrot cultivars. J Am Soc Hortic Sci 129:523–529

    CAS  Google Scholar 

  • Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190–193

    Article  PubMed  CAS  Google Scholar 

  • Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:e196

    Article  PubMed  CAS  Google Scholar 

  • Palaisa KA, Morgante M, Williams M, Rafalski A (2003) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15:1795–1806

    Article  PubMed  CAS  Google Scholar 

  • Palaisa K, Morgante M, Tingey S, Rafalski A (2004) Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc Natl Acad Sci USA 101:9885–9890

    Article  PubMed  CAS  Google Scholar 

  • Park H, Kreunen SS, Cuttriss AJ, DellaPenna D, Pogson BJ (2002) Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis. Plant Cell 14:321–332

    Article  PubMed  CAS  Google Scholar 

  • Pollak E (1987) On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics 117:353–360

    PubMed  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Price EW, Carbone I (2005) SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21:402–404

    Article  PubMed  CAS  Google Scholar 

  • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909

    Article  PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000a) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000b) Association mapping in structured populations. Am J Hum Genet 67:170–181

    Article  PubMed  CAS  Google Scholar 

  • Rafalski A, Morgante M (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 20:103–111

    Article  PubMed  CAS  Google Scholar 

  • Reimer S, Pozniak CJ, Clarke FR, Clarke JM, Somers DJ, Knox RE, Singh AK (2008) Association mapping of yellow pigment in an elite collection of durum wheat cultivars and breeding lines. Genome 51:1016–1025

    Article  PubMed  CAS  Google Scholar 

  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484

    Article  PubMed  CAS  Google Scholar 

  • Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138

    Article  Google Scholar 

  • Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497

    Article  PubMed  CAS  Google Scholar 

  • Santos CAF, Simon PW (2002) QTL analyses reveal clustered loci for accumulation of major provitamin A carotenes and lycopene in carrot roots. Mol Genet Genomics 268:122–129

    Article  PubMed  CAS  Google Scholar 

  • Schmid K, Törjék O, Meyer R, Schmuths H, Hoffmann M, Altmann T (2006) Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers. Theor Appl Genet 112:1104–1114

    Article  PubMed  CAS  Google Scholar 

  • Shim SI, Jørgensen RB (2000) Genetic structure in cultivated and wild carrots (Daucus carota L.) revealed by AFLP analysis. Theor Appl Genet 101:227–233

    Article  CAS  Google Scholar 

  • Shinohara S (1984) Introduction and variety development in Japan. In: Vegetable seed production technology of Japan elucidated with respective variety development histories, particulars. Shinohara’s Authorized Agricultural Consulting Engineer Office 4-7-7, Tokyo, pp 273–282

  • Simon PW (2000) Domestication, historical development, and modern breeding of carrot. Plant Breed Rev 19:157–190

    Google Scholar 

  • Small E (1978) A numerical taxonomic analysis of the Daucus carota complex. Can J Bot 56:248–276

    Article  Google Scholar 

  • St. Pierre MD, Bayer RJ (1991) The impact of domestication on the genetic variability in the orange carrot, cultivated Daucus carota ssp. sativus and the genetic homogeneity of various cultivars. Theor Appl Genet 82:249–253

    Article  Google Scholar 

  • St. Pierre MD, Bayer RJ, Weis IM (1990) An isozyme-based assessment of the genetic variability within the Daucus carota complex (Apiaceae: Caucalideae). Can J Bot 68:2449–2457

    CAS  Google Scholar 

  • Sun T, Simon PW, Tanumihardjo SA (2009) Antioxidant phytochemicals and antioxidant capacity of biofortified carrots (Daucus carota L.) of various colors. J Agric Food Chem 57:4142–4147

    Article  CAS  Google Scholar 

  • Surles RL, Weng N, Simon PW, Tanumihardjo SA (2004) Carotenoid profiles and consumer sensory evaluation of specialty carrots (Daucus carota. L.) of various colors. J Agric Food Chem 52:3417–3421

    Article  PubMed  CAS  Google Scholar 

  • Tenaillon MI, U’Ren J, Tenaillon O, Gaut BS (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21:1214–1225

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • van Tienderen PH, de Haan AA, van der Linden CG, Vosman B (2002) Biodiversity assessment using markers for ecologically important traits. Trends Ecol Evol 17:577–582

    Article  Google Scholar 

  • Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276

    Article  PubMed  CAS  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Wright SI, Lauga B, Charlesworth D (2003) Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Mol Ecol 12:1247–1263

    Article  PubMed  CAS  Google Scholar 

  • Xing Y, Frei U, Schejbel B, Asp T, Lübberstedt T (2007) Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne. BMC Plant Biol 7:43

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We would like to thank Françoise Gros and Marie-France Le Cunff, of the ‘Plate-forme de séquençage & de génotypage’ (IFR26, Nantes) for sequencing PCR products. We are grateful to Domenica Manicacci for providing script for LD decay analysis. We wish to thank Gérard Simon for his critical reading of this paper. This study was supported by grants from the region Pays de la Loire. This project is part of collaboration with Vilmorin SA, Clause Vegetable Seeds and Diana Naturals. Jérémy Clotault is a PhD student funded by the French Ministry of Research. Ethical standards: Authors declare that the experiments carried out comply with the current laws of the country in which they were performed, i.e., France.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Agrocampus Ouest, INHP, IFR 149 Quasav, UMR 1259 GenHort, 2 Rue Le Nôtre, 49045, Angers, France

    Jérémy Clotault, Emmanuel Geoffriau & Mathilde Briard

  2. Clause Vegetable Seeds, 49070, Beaucouzé, France

    Eric Lionneton

  3. Université d’Angers, IFR 149 Quasav, UMR 1259 GenHort, 49045, Angers, France

    Didier Peltier

Authors
  1. Jérémy Clotault
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Emmanuel Geoffriau
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eric Lionneton
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mathilde Briard
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Didier Peltier
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Emmanuel Geoffriau.

Additional information

Communicated by M. Havey.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (1166 kb)

Supplementary material 2 (28.5 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Clotault, J., Geoffriau, E., Lionneton, E. et al. Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot. Theor Appl Genet 121, 659–672 (2010). https://doi.org/10.1007/s00122-010-1338-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-010-1338-1

Keywords

Search

Navigation