Isolation and characterization of microsatellite loci for Bixa orellana, an important source of natural dyes

Abstract

ABSTRACT. Annatto (Bixa orellana) is a plant native from the American continental tropical zone. The seeds are used to produce a carotenoid-based yellow to orange food coloring. Microsatellite markers were developed for the Brazilian native species Bixa orellana to describe its genetic diversity and structure as well as to support conservation studies. Twenty-five microsatellite loci were isolated and characterized using an enriched genomic library. Ten loci were polymorphic in the 50 accessions sampled in this study, while 15 were considered monomorphic. The mean number of alleles per locus was 3.8, ranging from 2 to 6 alleles per locus. Mean values for the observed and expected heterozygosities were 0.541 (ranging from 0 to 0.658) and 0.639 (ranging from 0.422 to 0.787), respectively. All markers described in this study will be useful in further studies evaluating the genetic diversity, population dynamics, and conservation genetics of Bixa orellana.

New microsatellite loci for annatto (Bixa orellana), a source of natural dyes from Brazilian Amazonia

“…As a result, local inbreeding coefficients were high in all populations (Table 2). Similar results for cultivated accessions were reported by Dequigiovanni et al (2014) Higher levels of genetic diversity in wild than cultivated crops were also found in other crops, due to genetic bottleneck effects during domestication, such as in tepary beans (Phaseolus acutifolius) (Blair et al 2012, Gujaria-Verma et al 2016 (Bitocchi et al 2013), apricot (Prunus armeniaca) (Bourguiba et al 2012), and sunflower (Helianthus annuus) (Mandel et al 2011). However, this is not always the case, since in some crops, e.g., in carrot (Daucus carota subsp.…”

“…Deviations from HWE may occur because B. orellana has a mixed mating system and can tolerate both autogamy and allogamy (Rivera-Madrid et al 2006, Valdez-Ojeda et al 2010, Joseph et al 2012)changes in botanical composition could cause variable (unstable. Similarly, Dequigiovanni et al (2014) found deviations from HWE in eight out of ten loci analyzed. No significant linkage disequilibrium was detected for any pair of loci tested after Bonferroni correction.…”

“…This level of polymorphism (35%) was also observed in other studies with Bixa orellana. Ten polymorphic in 25 evaluated loci were detected by Dequigiovanni et al (2014). Software Micro-Checker detected no genotyping errors due to stuttering and large allele dropout.…”

Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia

“…Sixteen SSR markers developed for B . orellana [ 17 , 23 ] were used in this study ( Table 2 ; S1 Table ). Three fluorescent dyes (NED, FAM and HEX) were attached to the 5' end of the M13 universal primer sequence ( ) following Schuelke [ 24 ].…”

“…Hence, SSR markers are important tools to assess genetic diversity and genetic structure of populations, especially for wild species [ 14 ]. There are very few genetic studies in annatto [ 15 – 17 ] and no studies have yet evaluated population structure and genetic diversity of wild populations of annatto ( B . orellana var.…”