Abstract
Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations) and genetic origin (based on a previous study). We identified six polymorphic sites, including five insertion/deletion (indels) types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038). Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80) with 10 and 12 haplotypes, respectively. The common haplotype (H1) for both networks included cacao trees from all geographic locations (geographic approach) and four genetic groups (genetic approach). This common haplotype (ancient) derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (FST = 0) and SAMOVA (FST = 0.04393) results. One population (Mazatán) showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding.
Highlights
The Neotropical cacao tree (Theobroma cacao L.) is widely cultivated in Central and South America, Africa, Indonesia and Malaysia
These polymorphisms resulted in 12 haplotypes over all samples, of which four were singletons represented by a unique sequence in the sample (Table 2)
Indels and one transversion located in the chloroplast DNA trnH-psbA spacer region of cacao trees can distinguish individuals that are indistinguishable in other marker systems or separated by only few simple sequence repeat (SSR) markers, and further support use of these cpDNA markers.The molecular analysis showed low nucleotide diversity but high haplotype diversity possibly due to population bottleneck events
Summary
The Neotropical cacao tree (Theobroma cacao L.) is widely cultivated in Central and South America, Africa, Indonesia and Malaysia. It is considered an economically important crop because its seeds are used in the chocolate industry (Wood, 2001). Trees can be traditionally classified based on agromorphological traits as Criollo, Forastero and Trinitario (Cheesman, 1944; Toxopeus, 1985). In Mesoamerica, the Criollo cacao has been widely used as food and other purposes as well for nearly 4,000 years (De la Cruz et al, 1995; Whitkus et al, 1998; Powis et al, 2011). How to cite this article Gutiérrez-López et al (2016), Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA.
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