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Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers

Published online by Cambridge University Press:  01 August 2007

S. A. Christensen ,
D. B. Pratt ,
C. Pratt ,
P. T. Nelson ,
M. R. Stevens ,
E. N. Jellen ,
C. E. Coleman ,
D. J. Fairbanks ,
A. Bonifacio  and
P. J. Maughan
S. A. Christensen
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
D. B. Pratt
Affiliation:
Stephen F. Austin State University, Department of Biology, Nacogdoches, TX 75961, USA
C. Pratt
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
P. T. Nelson
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
M. R. Stevens
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
E. N. Jellen
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
C. E. Coleman
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
D. J. Fairbanks
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
A. Bonifacio
Affiliation:
Fundacion PROINPA, Casilla Postal 4285, Cochabamba, Bolivia
P. J. Maughan*
Affiliation:
Brigham Young University, Department of Plant & Animal Sciences, 275 WIDB, Provo, UT 84602, USA
*
*Corresponding author. E-mail: [email protected]
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Abstract

Quinoa (Chenopodium quinoa Willd.) is a staple food crop for millions of impoverished rural inhabitants of Andean South America where it has been cultivated for millennia. Interest in quinoa, due largely to its superior nutritional characteristics, is fuelling a growing export market and has led to an increased focus on genetic research and the development of quinoa breeding programmes throughout South America. The success of these breeding programmes will rely heavily on the development of core germplasm collections and germplasm conservation. We report the development of a set of fluorescence-tagged microsatellite molecular markers that can be used to characterize genetic diversity within quinoa germplasm and we use this set of 36 microsatellites markers to genetically characterize the diversity of 121 accessions of C. quinoa held in the USDA germplasm bank, 22 accessions from the CIP-FAO international nursery collection and eight accessions representing parents from genetic mapping populations. A total of 420 alleles were detected among the quinoa accessions with an average of 11 alleles detected per microsatellite locus. Genetic heterogeneity was observed in 32% of the quinoa accessions at a given locus and suggests that many of these accessions represent heterogeneous seed lots or landraces. Both unweighted pair-group method with arithmetic averages (UPGMA) and principle components analysis (PCA) analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina and extreme northeastern Chile. The other main cluster contained accessions from both the lowlands of Chile and a set of USDA accessions with no known passport data, collected by Emigdio Ballón. Using the patterns of genetic diversity detected within the C. quinoa accessions we discuss hypotheses regarding quinoa's centre of diversity, including highland and lowland ecotype clustering patterns, origin of lowland varieties, origin of domestication, and diversity levels in the USDA and CIP-FAO collections.

Keywords

Chenopodium quinoagenetic diversitymicrosatellitesSSRs
Type
Research Article
Information
Plant Genetic Resources , Volume 5 , Issue 2 , August 2007 , pp. 82 - 95
Copyright
Copyright © NIAB 2007

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References

Aellen, P (1929) Beitrag zur systematic der Chenopodium—Arten Amerikas, vorweigend auf Grund der Sammlung des United States National Museum in Washington, D.C. Feddes Repertorium Specierum Novarum Regni Vegetabilis 26: 31–67, 119–160.CrossRefGoogle Scholar
Cusack, DF (1984) Quinua: grain of the Incas. Ecologist 14: 21–31.Google Scholar
Dean, RE, Dahlberg, JA, Hopkins, MS, Mitchell, SE and Kresovich, S (1999) Genetic redundancy and diversity among ‘orange’ accessions in the US National Sorghum Collection as assessed with simple sequence repeat (SSR) markers. Crop Science 39: 1215–1221.CrossRefGoogle Scholar
Diwan, N and Cregan, PB (1997) Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean. Theoretical and Applied Genetics 95: 723–733.CrossRefGoogle Scholar
Elder, JK and Southern, EM (1987) Computer-aided analysis of one dimensional restriction fragment gels. In: Bishop, MJ and Rawlings, CJ (eds) Nucleic Acid and Protein Sequence Analysis —A Practical Approach. Oxford: IRL Press, pp. 165–172.Google Scholar
Gandarillas, H (1979) Genética y orígen. In: Tapia, ME (ed.) Quinua y Kañiwa: Cultivos Andinos. Bogota: Instituto Interamericano de Ciencias Agrícolas, pp. 45–64.Google Scholar
Gupta, PK and Varshney, RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with special emphasis on bread wheat. Euphytica 113: 163–185.CrossRefGoogle Scholar
Hokanson, SC, Szewc-McFadden, AK, Lamboy, WF and McFerson, JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus ×  domestica Borkh. core subset collection. Theoretical and Applied Genetics 97: 671–683.CrossRefGoogle Scholar
Jacobsen, SE (2000) Quinoa—research and development at the International Potato Center (CIP). Paper presented at the Annual Meeting of the Consultative Directorate of CONDESAN, November, pp. 1–5 Lima, peru.Google Scholar
Jain, S, Jain, RK and McCouch Lima, Peru, SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theoretical and Applied Genetics 109: 965–977.CrossRefGoogle ScholarPubMed
Mace, ES and Godwin, ID (2002) Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta). Genome 45: 823–832.CrossRefGoogle ScholarPubMed
Mason, SL, Stevens, MR, Jellen, EN, Bonifacio, A, Fairbanks, DJ, Coleman, CE, McCarty, RR, Rasmussen, AG and Maughan, PJ (2005) Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.). Crop Science 45: 1618–1630.CrossRefGoogle Scholar
Maughan, PJ, Saghai Maroof, MA, Buss, GR and Huestis, GM (1996) Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis. Theoretical and Applied Genetics 93: 392–401.CrossRefGoogle ScholarPubMed
McGregor, CE, van Treuren, R, Hoekstra, R and van Hintum, TJL (2002) Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation. Theoretical and Applied Genetics 104: 146–156.CrossRefGoogle Scholar
Mujica, A, Jacobsen, SE, Izquierdo, J and Marathee, JP (1998) Prueba Americana y Europea de quinoa (Chenopodium quinoa Willd.). Puno: FAO, Libro de Campo.Google Scholar
Nelson, DC (1968) Taxonomy and origins of Chenopodium quinoa and Chenopodium nuttalliae. PhD Thesis, Indiana University.Google Scholar
Ortiz, R, Ruiz-Tapia, EN and Mujica-Sanchez, A (1998) Sampling strategy for a core collection of Peruvian quinoa germplasm. Theoretical and Applied Genetics 96: 475–483.CrossRefGoogle ScholarPubMed
Ott, J (1992) Strategies for characterizing highly polymorphic markers in human gene mapping. American Journal of Human Genetics 51: 283–290.Google ScholarPubMed
Pratt, DB and Clark, LG (2001) Amaranthus rudis and A. tuberculatus—one species or two? Journal of the Torrey Botanical Society 128: 282–296.CrossRefGoogle Scholar
Risi, JC and Galwey, NW (1984) The Chenopodium grains of the Andes: Inca crops for modern agriculture. Advances in Applied Biology 10: 145–216.Google Scholar
Roa, NK (2004) Plant genetic resources: advancing conservation and use through biotechnology. African Journal of Biotechnology 3: 136–145.Google Scholar
Rohlf, FJ (2000) NTSYSpc 2.1: Numerical Taxonomy and Multivariate Analysis System. New York: Exeter Software.Google Scholar
Rojas, W, Barriga, P and Figueroa, H (2000) Multivariate analysis of the genetic diversity of Bolivian quinoa germplasm. Plant Genetic Resources Newsletter 122: 16–23.Google Scholar
Ruales, J and Nair, BM (1992) Nutritional quality of the protein in quinoa (Chenopodium quinoa, Willd) seeds. Plant Foods and Human Nutrition 42: 1–11.CrossRefGoogle ScholarPubMed
Ruales, J, de Grijalva, Y, Lopez-Jaramillo, P and Nair, BM (2002) The nutritional quality of an infant food from quinoa and its effect on the plasma level of insulin-like growth factor-1 (IGF-1) in undernourished children. International Journal of Food Science and Nutrition 53: 143–154.CrossRefGoogle ScholarPubMed
Sambrook, J, Fritsch, EF and Maniatis, T (1989) Molecular Cloning: A Laboratory Manual. 2nd edn. New York: Cold Spring Harbor Press.Google Scholar
Simmonds, NW (1965) The grain chenopods of the tropical American highlands. Economic Botany 19: 223–235.CrossRefGoogle Scholar
Simmonds, NW (1971) The breeding system of Chenopodium quinoa. I. Male sterility. Heredity 27: 73–82.CrossRefGoogle Scholar
Tang, S, Kishore, VK and Knapp, SJ (2003) PCR-multiplexes for a genome wide framework of simple sequence repeat marker loci in cultivated sunflower. Theoretical and Applied Genetics 107: 6–19.CrossRefGoogle ScholarPubMed
Tapia, ME (1979) Historia y distribción geográfica. In: Tapia, ME (ed.) Quinua y Kañiwa: Cultivos Andinos. Bogota: Instituto Interamericano de Ciencias Agrícolas, pp. 11–19.Google Scholar
Tapia, ME, Mujica, SA and Canahua, A (1980) Orígen, distribución geográfica, y sistemas de producción en quinua. Primera Reunion Sobre Genética y Fitomejoramiento de la Quinua. Puno: Universidad Nacional Técnica del Altiplano, Instituto Boliviano de Technologia Agropecuaria, Instituto Interamericana de Ciencias Agricolas, Centro de Investicación Internacional para el Desarollo, pp. A1–A8.Google Scholar
Todd, JJ and Vodkin, LO (1996) Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell 8: 687–699.CrossRefGoogle ScholarPubMed
Tommasini, L, Batley, J, Arnold, GM, Cooke, RJ, Donini, P, Lee, D, Law, JR, Lowe, C, Moule, C, Trick, M and Edwards, KJ (2003) The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties. Theoretical and Applied Genetics 106: 1091–1101.CrossRefGoogle ScholarPubMed
Ward, SM (2000) Allotetraploid segregation for single-gene morphological characters in quinoa (Chenopodium quinoa Willd.). Euphytica 116: 11–16.CrossRefGoogle Scholar
Wilson, HD (1988a) Quinoa biosystematics I: domesticated populations. Economic Botany 42: 461–477.CrossRefGoogle Scholar
Wilson, HD (1988b) Quinoa biosystematics II: free living populations. Economic Botany 42: 478–494.CrossRefGoogle Scholar