Annatto (Bixa orellana L.) is a tropical crop indigenous to the Americas, probably Amazonia. Annatto is commercially valuable in the food and cosmetics industries as a natural dye used instead of synthetic dyes. In addition, annatto contains other important substances for human health, such as geranylgeraniol, tocotrienols and other carotenoids. The aim of the present study was to evaluate the genetic diversity of 63 accessions from the annatto germplasm bank at the Agronomic Institute (IAC), São Paulo, Brazil, using four phytochemical compounds and 16 microsatellite markers. Significant variation was observed for the phytochemical compounds, ranging from 2 to 7.31 g (100 g dry matter—DM)−1 for bixin, 2.14–7.11 g (100 g DM)−1 for lipids, 0.25–1.05 g (100 g DM)−1 for tocotrienols, and 0.49–2.61 g (100 g DM)−1 for geranylgeraniol content. A total of 73 alleles was observed in the molecular characterization with 16 microsatellite loci. We found higher expected heterozygosity than observed heterozygosity for all loci, indicating strong deficits of heterozygotes. For both molecular and phytochemical compounds, cluster and PCoA analyses tended to separate the accessions from Rondônia, northern Brazil, with only a few exceptions, from the Southwestern accessions. The same two groups were found in the Bayesian analysis with molecular data. Rondônia accessions showed higher values for all the phytochemical compounds and higher levels of genetic diversity. Some accessions presented bixin levels well above the average and are promising materials to be used in genetic improvement programs. © 2017, Springer Science+Business Media B.V.
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