Skip to main content
SpringerLink
Log in

A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD, and SSR markers

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

Abstract

Quinoa (Chenopodium quinoa Willd.) is an important seed crop for human consumption in the Andean region of South America. It is the primary staple in areas too arid or saline for the major cereal crops. The objective of this project was to build the first genetic linkage map of quinoa. Selection of the mapping population was based on a preliminary genetic similarity analysis of four potential mapping parents. Breeding lines ‘Ku-2’ and ‘0654’, a Chilean lowland type and a Peruvian Altiplano type, respectively, showed a low similarity coefficient of 0.31 and were selected to form an F2 mapping population. The genetic map is based on 80 F2 individuals from this population and consists of 230 amplified length polymorphism (AFLP), 19 simple-sequence repeat (SSR), and six randomly amplified polymorphic DNA markers. The map spans 1,020 cM and contains 35 linkage groups with an average marker density of 4.0 cM per marker. Clustering of AFLP markers was not observed. Additionally, we report the primer sequences and map locations for 19 SSR markers that will be valuable tools for future quinoa genome analysis. This map provides a key starting point for genetic dissection of agronomically important characteristics of quinoa, including seed saponin content, grain yield, maturity, and resistance to disease, frost, and drought. Current efforts are geared towards the generation of more than 200 mapped SSR markers and the development of several recombinant-inbred mapping populations.

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

Similar content being viewed by others

References

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    CAS  Google Scholar 

  • Atienza SG, Satovia Z, Petersen KK, Dolstra O, Martin A (2002) Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers. Theor Appl Genet 105:946–952

    Article  CAS  PubMed  Google Scholar 

  • Barzen E, Mechelke W, Ritter E, Schulte-Kappert E, Salamini F (1995) An extended map of the sugar beet genome containing RFLP and RAPD loci. Theor Appl Genet 89:167–178

    Google Scholar 

  • Chauhan GS, Eskin NAM, Tkachuk R (1992) Nutrients and anitnutrients in quinoa seed. Cereal Chem 69:85–88

    CAS  Google Scholar 

  • Chauhan GS, Eskin NAM, Tkachuk R (1999) Effect of saponin extraction on quality of quinoa (Chenopodium quinoa Willd.). J Food Sci Technol 36:123–126

    CAS  Google Scholar 

  • Diwan N, McIntosh MS, Bauchan GR (1995) Methods of developing a core collection of annual Medicago species. Theor Appl Genet 90:775–761

    Google Scholar 

  • Fleming JE, Galwey NW (1995) Quinoa (Chenopodium quinoa). In: Williams JT (ed) Cereals and pseudocereals. Chapman and Hall, London, pp 3–83

  • Halldén C, Hjerdin A, Rading IM, Säll T, Fridlundh B, Johannisdottir G, Tuvesson S, Åkesson C, Nilsson N-O (1996) A high-density RFLP linkage map of sugar beet. Genome 39:634–645

    Google Scholar 

  • Hulbert SH, Ilott TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW (1988) Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms. Genetics 120:947–958

    CAS  PubMed  Google Scholar 

  • Jeuken M, van Wijk R, Peleman J, Lindhout P (2001) An integrated interspecific AFLP map of lettuce (Lactuca) based on two L. sativa × L. saligna F2 populations. Theor Appl Genet 103:638–647

    Article  CAS  Google Scholar 

  • Keim P, Schupp JM, Travis SE, Clayton K, Zhu T, Shi L, Ferreira A, Webb DM (1997) A high-density soybean genetic map based on AFLP markers. Crop Sci 37:537–543

    CAS  Google Scholar 

  • Lacape JM, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG, Burr B, Hau B (2003) A combined RFLP–SSR–AFLP map of tetraploid cotton based on a Gossypium hirsutum × Gossypium barbadense backcross population. Genome 46:612–626

    Article  CAS  PubMed  Google Scholar 

  • Lashermes P, Combes MC, Prakash NS, Trouslot P, Lorieux M, Charrier A (2001) Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses. Genome 44:589–596

    Article  CAS  PubMed  Google Scholar 

  • Lotti C, Salvi S, Pasqualone A, Tuberosa R, Blanco A (2000) Integration of AFLP markers into an RFLP-based map of durum wheat. Plant Breed 119:393–401

    Article  CAS  Google Scholar 

  • Ochoa J, Frinking HD, Jacobs TH (1999) Postulation of virulence groups and resistance factors in the quinoa/downy mildew pathosystem using material from Ecuador. Plant Pathol 48:425–430

    Article  Google Scholar 

  • Ooijen JW van, Voorrips RE (2001) JoinMap 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen

  • Patterson AH, Tanksley SD, Sorrells ME (1991) DNA markers in plant improvement. Adv Agron 46:39–90

    Google Scholar 

  • Pradhan AK, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D (2003) a high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers. Theor Appl Genet 106:607–614

    CAS  PubMed  Google Scholar 

  • Prado RE, Boero C, Gallard M, Gonzalez JA (2000) Effect of NaCl on germination, growth, and soluble sugar content in Chenopodium quinoa Willd. seeds. Bot Bull Acad Sci 41:27–34

    CAS  Google Scholar 

  • Qi X, Stam P Lindhout P (1998) Use of locus-specific AFLP markers to construct a high-density molecular map in barley. Theor Appl Genet 96:376–384

    Article  CAS  Google Scholar 

  • Rae SJ, Aldam C, Dominguez I, Hoebrechts M, Barnes SR, Edwards KJ (2000) Development and incorporation of microsatellite markers into the linkage map of sugar beet (Beta vulgaris spp.). Theor Appl Genet 100:1240–1248

    Article  CAS  Google Scholar 

  • Risi J, Galwey NW (1984) The Chenopodium grains of the Andes: Inca crops for modern agriculture. Adv Appl Biol 10:145–216

    Google Scholar 

  • Risi J, Galwey NW (1989) The pattern of genetic diversity in the Andean grain crop quinoa (Chenopodium quinoa Willd.). I. Associations between characteristics. Euphytica 41:147–162

    Google Scholar 

  • Rohlf FJ (2000) NTSYSpc 2.1: numerical taxonomy and multivariate analysis system. Exeter Software, New York

  • Ruales J, Nair BM (1993) Content of fat, vitamins and minerals in quinoa (Chenopodium quinoa Willd.) seeds. Food Chem 48:131–136

    Article  CAS  Google Scholar 

  • Ruas PM, Bonifacio A, Ruas CF, Fairbanks DJ, Andersen WR (1999) Genetic relationship among 19 accessions of six species of Chenopodium L., by randomly amplified polymorphic DNA fragments (RAPD). Euphytica 105:25–32

    Article  Google Scholar 

  • Sambrook J, Fritsch EE, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Sharma R, Aggarwal RAK, Kumar R, Mohapatra T, Sharma RP (2002) Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea). Genome 45:467–472

    Article  CAS  PubMed  Google Scholar 

  • Simmonds NW (1971) The breeding system of Chenopodium quinoa. I. Male sterility. Heredity 27:73–82

    Google Scholar 

  • Staub JE, Serquen FC, Gupta M (1996) Genetic markers, map construction, and their application in plant breeding. HortScience 31:729–741

    CAS  Google Scholar 

  • Tanksley SD, McCouch SR (1997) Seed bands and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066

    Article  CAS  PubMed  Google Scholar 

  • Tapia M, Gandarillas H, Alandia S, Cardozo A, Mujica R, Ortiz R, Otazu J, Rea J, Salas B, Zanabria E (1979) Quinua y kañiwa: Cultivos andinos. CIID-IICA. Bogota

  • Todd JJ, Vodkin LO (1996) Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell 8:687–699

    Article  CAS  PubMed  Google Scholar 

  • Vacher JJ (1998) Responses of two main Andean crops, quinoa (Chenopodium quinoa Willd.) and papa amarga (Solanum juzepezukii Buk.) to drought on the Bolivian Altiplano: significance of local adaption. Agric Ecosyst Environ 68:99–108

    Article  Google Scholar 

  • Vilanova S, Romero C, Abbott AG, Llácer, Badenes ML (2003) An apricot (Prunus armeniaca L.) F2 progeny linkage map based SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits. Theor Appl Genet 107:239–247

    Article  CAS  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker R, Reijans M, Van de Le T, HornesM, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    CAS  PubMed  Google Scholar 

  • Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lubbersted T, Xia XC, Stam P, Zabeau M, Kuiper M (1999) Two high-density AFLP linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921–935

    Article  CAS  Google Scholar 

  • Ward SM (2000) Allotetraploid segregation for single-gene morphological characters in quinoa (Chenopodium quinoa Willd.) Euphytica 116:11–16

    Google Scholar 

  • Ward SM (2001) A recessive allele inhibiting saponin synthesis in two lines of Bolivian quinoa (Chenopodium quinoa Willd.). Heredity 92:83–86

    Article  CAS  Google Scholar 

  • Willams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    CAS  PubMed  Google Scholar 

  • Wilson HD (1988) Quinoa biosystematics I: domesticated populations. Econ Bot 42:461–477

    Google Scholar 

  • Wood SG, Lawson LD, Fairbanks DJ, Robison LR, Andersen WR (1993) Seed lipid content and fatty acid composition of three quinoa cultivars. J Food Comp Anal 6:41–44

    Article  CAS  Google Scholar 

  • Yu YG, Saghai Maroof MA, Buss GR, Maughan PJ, Tolin SA (1994) RFLP and microsatellite mapping of a gene for soybean mosaic virus resistance. Phytopathology 84:60–64

    CAS  Google Scholar 

Download references

Acknowledgements

This research was supported with grants from the McKnight Foundation, the Holmes Family Foundation, and the Erza Taft Benson Agriculture and Food Institute. We thank Robert Jones, Eric Steward, and David Butler of Brigham Young University for their advice and technical assistance with the AFLP analysis.

Author information

Authors and Affiliations

  1. Department of Plant and Animal Sciences, Brigham Young University, Provo, UT, 84602, USA

    P. J. Maughan, E. N. Jellen, M. R. Stevens, C. E. Coleman, M. Ricks, S. L. Mason, D. E. Jarvis, B. W. Gardunia & D. J. Fairbanks

  2. The Foundation for the Promotion and Investigation of Andean Products (PROINPA), La Paz, Bolivia

    A. Bonifacio

Authors
  1. P. J. Maughan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Bonifacio
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. E. N. Jellen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. M. R. Stevens
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. C. E. Coleman
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. Ricks
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. S. L. Mason
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. D. E. Jarvis
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. B. W. Gardunia
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. D. J. Fairbanks
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to P. J. Maughan.

Additional information

Communicated by D. Hoisington

Rights and permissions

Reprints and permissions

About this article

Cite this article

Maughan, P.J., Bonifacio, A., Jellen, E.N. et al. A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD, and SSR markers. Theor Appl Genet 109, 1188–1195 (2004). https://doi.org/10.1007/s00122-004-1730-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-004-1730-9

Keywords

Search

Navigation