RESEARCH
Assessment of Genetic Diversity in Peruvian Amaranth (Amaranthus caudatus and A. hybridus) Germplasm using Single Nucleotide Polymorphism Markers Felix R. Jimenez, P. Jefrey Maughan, Aquilino Alvarez, Kiel D. Kietlinski, Scott M. Smith, Donald B. Pratt, David B. Elzinga, and Eric N. Jellen*
ABSTRACT Amaranth (Amaranthus caudatus L.) is an important seed crop in the Andes. It has excellent nutritional value and ample capacity for growth under drought, heat, and soil nutrient deiciency. The objective of this study was to characterize and quantify genetic diversity among a series of 178 mostly peruvian amaranth individuals genotyped from among 48 accessions using 96 biallelic single nucleotide polymorphism (SNp) markers in KASpar assays on a 96.96 Fluidigm Ep1 platform. The 178 seed genotypes included the predominant white-opaque (waxy), white-vitreous (nonwaxy), black, and brown types, all from within the Centro de Investigacion de Cultivos AndinosUniversidad Nacional de San Antonio Abad del Cusco collection. The samples separated into two groups based on the seed color parameter (black, brown, and white-vitreous versus whiteopaque) with STrUCTUrE analysis but did not form distinct genotypic groups based on geographic origin. When analyzed as seed-color subgroups—black vs. brown vs. white-vitreous vs. white-opaque—83.46% of the genetic variation was explained by genetic differences within subgroup. The highest average observed heterozygosity (Ho) within color-based subgroups was 0.2612 in the vitreous-seeded subgroup, and within-group expected heterozygosity (He) was highest in the brown-seeded subgroup (0.398). Cluster analysis and principal component analysis partitioned the amaranth accessions into two clusters with four distinct subclusters. Analyses also revealed evidence for selection of nonwaxy, vitreous-seeded amaranth in the Andes.
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F.R. Jimenez, P.J. Maughan, S.M. Smith, D.B. Elzinga, and E.N. Jellen, Dep. of Plant and Wildlife Sciences, 275 WIDB, Brigham Young Univ., Provo, UT, 84602; A. Alvarez, Centro de Investigaciones de Cultivos Andinos, Universidad Nacional San Antonio Abad del Cusco, Cusco, Peru; K.D. Kietlinski and D.B. Pratt, Dep. of Biology, P.O. Box 13003, Stephen F. Austin State Univ., Nacogdoches, TX, 75962. Joint contribution of Brigham Young University, Stephen F. Austin State University, and the National University of San Antonio Abad of Cuzco. Received 6 July 2012. *Corresponding author (
[email protected]). Abbreviations: AMOVA, analysis of molecular variance; CICA, Centro de Investigacion de Cultivos Andinos; PCA, principal component analysis; RAPD, random ampliied polymorphic DNA; SNP, single nucleotide polymorphism; SSR, simple sequence repeat; UNSAAC, Universidad Nacional de San Antonio Abad del Cusco.
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he South American Andes is a major center of origin, domestication, and dispersion of high-protein pseudocereal crops. This group includes one of the amaranths known as “kiwicha” (Amaranthus caudatus L.), quinoa (Chenopodium quinoa Willd.), and kanihua (Chenopodium pallidicaule Aellen) (Vavilov, 1926; Hawkes, 1999). Kiwicha is an annual diploid (putative paleotetraploid; 2n = 2x = 32) of nutritional importance for intermediate-altitude (
