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Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

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Abstract

Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

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References

  • Benson G. 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580.

    Article  PubMed  CAS  Google Scholar 

  • Broman K. W. 2005 The genomes of recombinant inbred lines. Genetics 169, 1133–1146.

    Article  PubMed  CAS  Google Scholar 

  • Christensen S. A., Pratt D. B., Pratt C., Stevens M. R., Jellen E. N., Coleman C. E. et al. 2007 Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers. Plant. Genet. Res. 5, 82–95.

    Article  CAS  Google Scholar 

  • Cureton A. N., Burns M. J., Ford-Lloyd B. V. and Newbury H. J. 2002 Development of simple sequence repeat (SSR) markers for the assessment of gene flow between sea beet (Beta vulgaris ssp. maritima) populations. Mol. Ecol. Notes 2, 402–403.

    Article  CAS  Google Scholar 

  • Danielsen S., Bonifacio A. and Ames T. 2003 Diseases of quinoa (Chenopodium quinoa). Food Rev. Int. 19, 43–59.

    Article  Google Scholar 

  • Diwan N., McIntosh M. S. and Bauchan G. R. 1995 Methods of developing a core collection of annual Medicago species. Theor. Appl. Genet. 90, 755–761.

    Article  Google Scholar 

  • Franco J. 2003 Parasitic nematodes of quinoa in the Andean region of Bolivia. Food Rev. Int. 19, 77–85.

    Article  Google Scholar 

  • Hall M. C. and Willis J. H. 2005 Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence. Genetics 170, 375–386.

    Article  PubMed  CAS  Google Scholar 

  • Jacobsen S.-E. 2003 The Worldwide potential for quinoa (Chenopodium quinoa Willd.) potential. Food Rev. Int. 19, 167–177.

    Article  Google Scholar 

  • Jacobsen S.-E., Mujica A. and Jensen C. R. 2003 The resistance of quinoa (Chenopodium quinoa Willd.) to adverse abiotic factors. Food Rev. Int. 19, 99–109.

    Article  Google Scholar 

  • Konieczny A. and Ausubel F. M. 1993 A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4, 403–410.

    Article  PubMed  CAS  Google Scholar 

  • Lu H., Romero-Severson J. and Bernardo R. 2002 Chromosomal regions associated with segregation distortion in maize. Theor. Appl. Genet. 105, 622–628.

    Article  PubMed  CAS  Google Scholar 

  • Mason S. L., Stevens M. R., Jellen E. N., Bonifacio A., Fairbanks D. J., Coleman C. E. et al. 2005 Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.). Crop Sci. 45, 1618–1630.

    Article  CAS  Google Scholar 

  • Maughan P. J., Bonifacio A., Jellen E. N., Stevens M. R., Coleman C. E., Ricks M. et al. 2004 A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD, and SSR markers. Theor. Appl. Genet. 109, 1188–1195.

    Article  PubMed  CAS  Google Scholar 

  • Maughan P. J., Kolano B., Maluszynska J., Coles N. D., Bonifacio A., Rojas Beltran J. et al. 2006 Molecular and cytological characterization of ribosomal DNAs in Chenopodium quinoa and Chenopodium berlandieri. Genome (in press).

  • McCouch S. R., Teytelman L., Xu Y., Lobos K. B., Clare K., Walton M., Fu B. et al. 2002 Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9, 199–207.

    Article  PubMed  CAS  Google Scholar 

  • Mozo T., Dewar K., Dunn P., Ecker J. R., Fischer S., Kloska S. et al. 1999 A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genet. 22, 271–275.

    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  Google Scholar 

  • Ooijen J. W. van and Voorrips R. E. 2001 JoinMap 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen, Netherlands.

    Google Scholar 

  • Ott J. 1992 Strategies for characterizing highly polymorphic markers in human gene mapping. Am. J. Hum. Genet. 51, 283–290.

    PubMed  CAS  Google Scholar 

  • Paterson A. H., Lander E. S., Hewitt J. D., Peterson S., Lincoln S. E. and Tanksley S. D. 1988 Resolution of quantitative trait into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335, 721–726.

    Article  PubMed  CAS  Google Scholar 

  • Pearsall D. 1992 The origins of plant cultivation in South America. In The Origins of Agriculture An International Perspective (ed. C. W. Cowan and P. J. Watson), pp. 173–205. Smithsonian Institution Press, Washington.

    Google Scholar 

  • Prado R. E., Boero C., Gallard M. and Gonzalez J. A. 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 

  • Rae S. J., Aldam C., Dominguez I., Hoebrechts M., Barnes S. R. and Edwards K. J. 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 

  • Rasmussen C., Lagnaoui A. and Esbjerg P. 2003 Advances in the knowledge of quinoa pests. Food Rev. Int. 19, 61–75.

    Article  Google Scholar 

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

    Google Scholar 

  • Rozen S. and Skaletsky H. J. 2000 Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols: Methods in molecular biology (ed. S. Krawetz and S. Misener), pp. 365–386. Human Press, Totowa, NJ.

    Google Scholar 

  • Sambrook J., Fritsch E. E. and Maniatis T. 1989 Molecular cloning. A laboratory manual. 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

    Google Scholar 

  • Simmonds N. W. 1971 The breeding system of Chenopodium quinoa. I. Male sterility. Heredity 27, 73–82.

    Article  Google Scholar 

  • Stam P. 1993 Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J. 3, 739–744.

    Article  CAS  Google Scholar 

  • Staub J. E., Serquen F. C. and Gupta M. 1996 Genetic markers, map construction, and their application in plant breeding. HortScience 31, 729–741.

    CAS  Google Scholar 

  • Stevens M. R., Coleman C. E., Parkinson S. E., Maughan P. J., Zhang H. B., Balzotti M. R. et al. 2006 Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins. Theor. Appl. Genet. 112, 1593–1600.

    Article  PubMed  CAS  Google Scholar 

  • Tanksley S. D. and McCouch S. R. 1997 Seed bands and molecular maps: Unlocking genetic potential from the wild. Science 277, 1063–1066.

    Article  PubMed  CAS  Google Scholar 

  • Tapia M., Gandarillas H., Alandia S., Cardozo A., Mujica R., Ortiz R. et al. 1979 Quinua y kañiwa: Cultivos andinos. CIID-IICA. Bogotá, Colombia.

    Google Scholar 

  • Todd J. J. and Vodkin L. O. 1996 Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell 8, 687–699.

    Article  PubMed  CAS  Google Scholar 

  • Vacher J. J. 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 adaptation. Agric. Ecosyst. Environ. 68, 99–108.

    Article  Google Scholar 

  • Vos P., Hogers R., Bleeker M., Reijans M., Van de Lee T., Hornes M. et al. 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407–4414

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Weber J. L. 1990 Informativeness of human (dC-dA)n. (dG-dT)n polymorphisms. Genomics 7, 524–530.

    Article  PubMed  CAS  Google Scholar 

  • Wilson H. D. 1988 Quinoa biosystematics I: Domesticated populations. Econ. Bot. 42, 461–477

    Google Scholar 

  • Wilson H. and Manhart J. 1993 Crop/weed gene flow: Chenopodium quinoa Willd. and C. berlandieri Moq. Theor. Appl. Genet. 86, 642–648

    Article  Google Scholar 

  • Zamir D. and Tadmor Y. 1986 Unequal segregation of nuclear genes in plants. Bot. Gaz. 147, 355–358.

    Article  Google Scholar 

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Jarvis, D.E., Kopp, O.R., Jellen, E.N. et al. Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.). J Genet 87, 39–51 (2008). https://doi.org/10.1007/s12041-008-0006-6

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  • DOI: https://doi.org/10.1007/s12041-008-0006-6

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