Theoretical and Applied Genetics

, Volume 109, Issue 6, pp 1188–1195 | Cite as

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

  • P. J. Maughan
  • A. Bonifacio
  • E. N. Jellen
  • M. R. Stevens
  • C. E. Coleman
  • M. Ricks
  • S. L. Mason
  • D. E. Jarvis
  • B. W. Gardunia
  • D. J. Fairbanks
Original Paper

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.

References

  1. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218Google Scholar
  2. Atienza SG, Satovia Z, Petersen KK, Dolstra O, Martin A (2002) Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers. Theor Appl Genet 105:946–952CrossRefPubMedGoogle Scholar
  3. 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 89:167–178Google Scholar
  4. Chauhan GS, Eskin NAM, Tkachuk R (1992) Nutrients and anitnutrients in quinoa seed. Cereal Chem 69:85–88Google Scholar
  5. Chauhan GS, Eskin NAM, Tkachuk R (1999) Effect of saponin extraction on quality of quinoa (Chenopodium quinoa Willd.). J Food Sci Technol 36:123–126Google Scholar
  6. Diwan N, McIntosh MS, Bauchan GR (1995) Methods of developing a core collection of annual Medicago species. Theor Appl Genet 90:775–761Google Scholar
  7. Fleming JE, Galwey NW (1995) Quinoa (Chenopodium quinoa). In: Williams JT (ed) Cereals and pseudocereals. Chapman and Hall, London, pp 3–83Google Scholar
  8. 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 39:634–645Google Scholar
  9. 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 120:947–958PubMedGoogle Scholar
  10. 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 103:638–647CrossRefGoogle Scholar
  11. 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 37:537–543Google Scholar
  12. 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 46:612–626CrossRefPubMedGoogle Scholar
  13. 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 44:589–596CrossRefPubMedGoogle Scholar
  14. 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 119:393–401CrossRefGoogle Scholar
  15. 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 48:425–430CrossRefGoogle Scholar
  16. Ooijen JW van, Voorrips RE (2001) JoinMap 3.0, software for the calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  17. Patterson AH, Tanksley SD, Sorrells ME (1991) DNA markers in plant improvement. Adv Agron 46:39–90Google Scholar
  18. 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 106:607–614PubMedGoogle Scholar
  19. 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 41:27–34Google Scholar
  20. 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 96:376–384CrossRefGoogle Scholar
  21. 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 100:1240–1248CrossRefGoogle Scholar
  22. Risi J, Galwey NW (1984) The Chenopodium grains of the Andes: Inca crops for modern agriculture. Adv Appl Biol 10:145–216Google Scholar
  23. Risi J, Galwey NW (1989) The pattern of genetic diversity in the Andean grain crop quinoa (Chenopodium quinoa Willd.). I. Associations between characteristics. Euphytica 41:147–162Google Scholar
  24. Rohlf FJ (2000) NTSYSpc 2.1: numerical taxonomy and multivariate analysis system. Exeter Software, New YorkGoogle Scholar
  25. Ruales J, Nair BM (1993) Content of fat, vitamins and minerals in quinoa (Chenopodium quinoa Willd.) seeds. Food Chem 48:131–136CrossRefGoogle Scholar
  26. 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 105:25–32CrossRefGoogle Scholar
  27. Sambrook J, Fritsch EE, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  28. 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 45:467–472CrossRefPubMedGoogle Scholar
  29. Simmonds NW (1971) The breeding system of Chenopodium quinoa. I. Male sterility. Heredity 27:73–82Google Scholar
  30. Staub JE, Serquen FC, Gupta M (1996) Genetic markers, map construction, and their application in plant breeding. HortScience 31:729–741Google Scholar
  31. Tanksley SD, McCouch SR (1997) Seed bands and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066CrossRefPubMedGoogle Scholar
  32. 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. BogotaGoogle Scholar
  33. Todd JJ, Vodkin LO (1996) Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell 8:687–699CrossRefPubMedGoogle Scholar
  34. 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 68:99–108CrossRefGoogle Scholar
  35. 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 107:239–247CrossRefPubMedGoogle Scholar
  36. 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 23:4407–4414PubMedGoogle Scholar
  37. 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 99:921–935CrossRefGoogle Scholar
  38. Ward SM (2000) Allotetraploid segregation for single-gene morphological characters in quinoa (Chenopodium quinoa Willd.) Euphytica 116:11–16Google Scholar
  39. Ward SM (2001) A recessive allele inhibiting saponin synthesis in two lines of Bolivian quinoa (Chenopodium quinoa Willd.). Heredity 92:83–86CrossRefGoogle Scholar
  40. 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 18:6531–6535PubMedGoogle Scholar
  41. Wilson HD (1988) Quinoa biosystematics I: domesticated populations. Econ Bot 42:461–477Google Scholar
  42. 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 6:41–44CrossRefGoogle Scholar
  43. 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 84:60–64Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • P. J. Maughan
    • 1
  • A. Bonifacio
    • 2
  • E. N. Jellen
    • 1
  • M. R. Stevens
    • 1
  • C. E. Coleman
    • 1
  • M. Ricks
    • 1
  • S. L. Mason
    • 1
  • D. E. Jarvis
    • 1
  • B. W. Gardunia
    • 1
  • D. J. Fairbanks
    • 1
  1. 1.Department of Plant and Animal SciencesBrigham Young UniversityProvoUSA
  2. 2.The Foundation for the Promotion and Investigation of Andean Products (PROINPA)La PazBolivia

Personalised recommendations