Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers
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.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Quinoa accessions cluster into highland and lowland ecotypes, representing genetically distinct groups.
“Quinoa germplasm studies have revealed that quinoa accessions cluster into highland and lowland ecotypes, representing genetically distinct groups.7, 27, 28”
Northern Chilean quinoa varieties are genetically and morphologically distinct from Central-Southern ecotypes.
“Northern Chilean varieties are genetically and morphologically distinct from Central-Southern ecotypes.7, 27, 28”
Cites
Molecular Cloning: A Laboratory Manual
Sambrook, J., Fritsch, E., & Maniatis, T. (1989) · UCLA - Biblioteca de Ciencias de la Salud · Cited by 133,589 · see citing works
Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684 · see citing works
Gupta, P. K., & Varshney, R. K. (2000) · Euphytica · doi:10.1023/a:1003910819967 · Cited by 882 · see citing works
Hokanson, S. C., Szewc‐McFadden, A. K., Lamboy, W. F., et al. (1998) · Theoretical and Applied Genetics · doi:10.1007/s001220050943 · Cited by 360 · see citing works
Plant genetic resources: Advancing conservation and use through biotechnology
Kameswara Rao, N. (2003) · AFRICAN JOURNAL OF BIOTECHNOLOGY · doi:10.5897/ajb2004.000-2025 · Cited by 294 · see citing works
Maughan, P. J., Maroof, M. A. S., Buss, G. R., et al. (1996) · Theoretical and Applied Genetics · doi:10.1007/bf00223181 · Cited by 281 · see citing works
Self-citationStrategies for characterizing highly polymorphic markers in human gene mapping.
Ott, J. (1992) · PubMed · Cited by 236 · see citing works
Diwan, N., & Cregan, P. B. (1997) · Theoretical and Applied Genetics · doi:10.1007/s001220050618 · Cited by 234 · see citing works
Nutritional quality of the protein in quinoa (Chenopodium quinoa, Willd) seeds
Ruales, J., & Nair, B. M. (1992) · Plant Foods for Human Nutrition · doi:10.1007/bf02196067 · Cited by 212 · see citing works
Todd, J. J., & Vodkin, L. O. (1996) · The Plant Cell · doi:10.1105/tpc.8.4.687 · Cited by 208 · see citing works
Jain, S., Jain, R. K., & McCouch, S. R. (2004) · Theoretical and Applied Genetics · doi:10.1007/s00122-004-1700-2 · Cited by 198 · see citing works
Nucleic acid and protein sequence analysis: a practical approach
(1988) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(88)90034-5 · Cited by 185 · see citing works
Sampling strategy for a core collection of Peruvian quinoa germplasm
Ortiz, R. O., Ruiz-Tapia, E. N., & Mújica, A. (1998) · Theoretical and Applied Genetics · doi:10.1007/s001220050764 · Cited by 146 · see citing works
Tang, S., Kishore, V. K., & Knapp, S. J. (2003) · Theoretical and Applied Genetics · doi:10.1007/s00122-003-1233-0 · Cited by 145 · see citing works
Dean, R. E., Dahlberg, J., Hopkins, M. S., et al. (1999) · Crop Science · doi:10.2135/cropsci1999.0011183x003900040043x · Cited by 114 · see citing works
Tommasini, L., Batley, J., Arnold, G. M., et al. (2003) · Theoretical and Applied Genetics · doi:10.1007/s00122-002-1125-8 · Cited by 113 · see citing works
Amaranthus rudis and A. tuberculatus, One Species or Two?
Pratt, D. B., & Clark, L. G. (2001) · The Journal of the Torrey Botanical Society · doi:10.2307/3088718 · Cited by 86 · see citing works
Self-citationRuales, J., de Grijalva, Y., López-Jaramillo, P. A., & Nair, B. M. (2002) · International Journal of Food Sciences and Nutrition · doi:10.1080/09637480220132157 · Cited by 85 · see citing works
Mason, S., Stevens, M. R., Jellen, E. N., et al. (2005) · Crop Science · doi:10.2135/cropsci2004.0295 · Cited by 83 · see citing works
Self-citationQuinua biosystematics I: Domesticated populations
Wilson, H. D. (1988) · Economic Botany · doi:10.1007/bf02862791 · Cited by 80 · see citing works
The grain chenopods of the tropical American highlands
Simmonds, N. W. (1965) · Economic Botany · doi:10.1007/bf02914309 · Cited by 76 · see citing works
McGregor, C., van Treuren, R., Hoekstra, R., et al. (2002) · Theoretical and Applied Genetics · doi:10.1007/s001220200018 · Cited by 74 · see citing works
Multivariate Analysis of Genetic Diversity of Bolivian Quinoa Germplasm
Rojas, W. (2003) · Food Reviews International · doi:10.1081/fri-120018864 · Cited by 72 · see citing works
Todd, J. J., & Vodkin, L. O. (1996) · The Plant Cell · doi:10.2307/3870344 · Cited by 68 · see citing works
The breeding system of Chenopodium quinoa I. Male sterility
Simmonds, N. W. (1971) · Heredity · doi:10.1038/hdy.1971.72 · Cited by 62 · see citing works
Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta)
Mace, E., & Godwin, I. D. (2002) · Genome · doi:10.1139/g02-045 · Cited by 60 · see citing works
Ward, S. (2000) · Euphytica · doi:10.1023/a:1004070517808 · Cited by 50 · see citing works
Quinua biosystematics II: Free-living populations
Wilson, H. D. (1988) · Economic Botany · doi:10.1007/bf02862792 · Cited by 38 · see citing works
Aellen, P. (1929) · Repertorium novarum specierum regni vegetabilis · doi:10.1002/fedr.19290260108 · Cited by 20 · see citing works
Multivariate analysis of the genetic diversity of Bolivian quinua germplasm.
Rojas, W., Barriga, P., & Figueroa, H. (2000) · Plant Genetic Resources Newsletter · Cited by 18 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Vega‐Gálvez, A., Miranda, M., Vergara, J., Uribe, E., Puente, L., & Martínez, E. A. (2010) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.4158 · Cited by 985 · see citing works
Fuentes, F. F., Martinez, E. A., Hinrichsen, P. V., Jellen, E. N., & Maughan, P. J. (2009) · Conservation Genetics · doi:10.1007/s10592-008-9604-3 · Cited by 128 · see citing works
Self-citationBotany, Nutritional Value, Phytochemical Composition and Biological Activities of Quinoa
Hussain, M. I., Farooq, M., Syed, Q. A., Ishaq, A., Al-Ghamdi, A. A., & Hatamleh, A. A. (2021) · Plants · doi:10.3390/plants10112258 · Cited by 96 · see citing works
Graf, B. L., Rojo, L. E., Delatorre‐Herrera, J., Poulev, A., Calfio, C., & Raskin, I. (2016) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.7134 · Cited by 46 · see citing works
- Authors
- Christensen, S. A., Pratt, D. B., Pratt, C., Nelson, P. T., Stevens, M. R., Jellen, E. N., Coleman, C. E., Fairbanks, D. J., Bonifacio, A., & Maughan, P. J.
- Affiliations
- Brigham Young University (US)
- Stephen F. Austin State University (US)
- Fundación PROINPA (BO)
- Corresponding author
- Maughan, P. J.
- Venue
- Plant Genetic Resources
- Publisher
- Cambridge University Press (CUP)
- Published
- 2007-08
- Volume
- 5
- Issue
- 2
- Pages
- 82-95
- ISSN
- 1479-2621 (ISSN-L)
- 1479-263X
- OpenAlex
- W1985481873
- Cited by
- 125
- References
- 30
- Citations by year
- 2026: 5 · 2025: 9 · 2024: 20 · 2023: 12 · 2022: 5 · 2021: 20 · 2020: 9 · 2019: 6 · 2018: 1 · 2017: 5 · 2016: 5 · 2015: 5 · 2014: 4 · 2013: 3 · 2012: 3
- FWCI
- 1.43
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Plant Genetic Resources (publishedVersion)
- ScholarsArchive (Brigham Young University) (submittedVersion)
- Funders
- U.S. Department of Agriculture
- McKnight Foundation
- Centro Internacional de la Papa
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Food Science › Seed and Plant Biochemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- quinoa, genetic diversity, germplasm collection, microsatellite markers, landraces, center of origin, domestication origin, Andean highlands, quinoa breeding, genetic mapping population
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
