Amaranth (Amaranthus caudatus L.) is an important seed crop in the Andes. It has excel-lent nutritional value and ample capacity for growth under drought, heat, and soil nutri-ent deficiency. The objective of this study was to characterize and quantify genetic diversity among a series of 178 mostly Peruvian ama-ranth individuals genotyped from among 48 accessions using 96 biallelic single nucleo-tide 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 Andinos-Universidad 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 white-opaque) with STRUCTURE analysis but did not form distinct genotypic groups based on geo-graphic origin. When analyzed as seed-color subgroups—black vs. brown vs. white-vitreous vs. white-opaque—83.46% of the genetic varia-tion was explained by genetic differences within subgroup. The highest average observed het-erozygosity (Ho) within color-based subgroups was 0.2612 in the vitreous-seeded subgroup, erozygosity (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 and within-group expected heterozygosity (He) was highest in the brown-seeded subgroup (0.398). Cluster analysis and principal compo-nent analysis partitioned the amaranth acces-sions into two clusters with four distinct sub-clusters. Analyses also revealed evidence for selection of nonwaxy, vitreous-seeded ama-ranth in the Andes.
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