Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.)

Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.)

Quinoa (Chenopodium quinoa Willd.) is a widely consumed food crop and a primary protein source for many of the indigenous inhabitants of the Andean region of South America. The objective of this study was to develop a collection of reproducible and highly informative microsatellite markers for quino...

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Bibliographic Details
Published in:Crop science Vol. 45; no. 4; pp. 1618 - 1630
Main Authors: Mason, S.L, Stevens, M.R, Jellen, E.N, Bonifacio, A, Fairbanks, D.J, Coleman, C.E, McCarty, R.R, Rasmussen, A.G, Maughan, P.J
Format: Journal Article
Language:English
Published: Madison, WI The Crop Science Society of America, Inc 01-07-2005
Crop Science Society of America
American Society of Agronomy
Subjects:
Agronomy. Soil science and plant productions
alleles
Biological and medical sciences
Chenopodium berlandieri
Chenopodium quinoa
clones
Computer software industry
Crop science
Cultivars
Deoxyribonucleic acid
DNA
Fundamental and applied biological sciences. Psychology
Generalities. Genetics. Plant material
genetic markers
genetic polymorphism
Genetic resources, diversity
genetic variation
Genetics and breeding of economic plants
germplasm
grain crops
heterozygosity
loci
microsatellite repeats
plant genetic resources
Plant material
Plant reproduction
Proteins
Quinoa
small grains
wild relatives
South America
America
United States
Food crop
Germplasm
Genetic resource
Dicotyledones
Microsatellite DNA
Angiospermae
Spermatophyta
Molecular marker
Cereal crop
Chenopodiaceae
Chenopodium quinoa
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Summary:Quinoa (Chenopodium quinoa Willd.) is a widely consumed food crop and a primary protein source for many of the indigenous inhabitants of the Andean region of South America. The objective of this study was to develop a collection of reproducible and highly informative microsatellite markers for quinoa. A total of 1276 clones were sequenced from three microsatellite-enriched (CA, ATT, ATG) libraries. Four hundred fifty-seven (36%) of the clones contained unique microsatellites. The most common repeated motifs, other than CA, AAT, and ATG, were GA and CAA. Flanking primers were designed for 397 microsatellite loci and screened using a panel of diverse quinoa accessions and one accession of C. berlandieri Moq., a wild relative of quinoa. Two hundred eight (52%) of the microsatellite markers were polymorphic among the quinoa accessions. An additional 25 of the microsatellite markers (6%) were polymorphic when the C. berlandieri accession was included in the analysis. Only in rare instances (nine) did a microsatellite amplify in quinoa and not in C. berlandieri. The number of observed alleles ranged from 2 to 13, with an average of four alleles detected per locus. Heterozygosity values ranged from 0.20 to 0.90 with a mean value of 0.57. Sixty-seven markers (32%) were highly polymorphic (H greater than or equal to 0.70). These microsatellites markers are an ideal resource for use in managing quinoa germplasm, trait mapping and marker-assisted breeding strategies. The wide cross-species transportability of these markers may extend their value to research involving other Chenopodium species.
ISSN:0011-183X
1435-0653
DOI:10.2135/cropsci2004.0295