Unique haplotypes of cacao trees as revealed bytrnH-psbAchloroplast DNA

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.

Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacaoL.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential

“…High LD was characterized by many red squares in the heatmap generated. Many red blocks together would correspond to haplotype blocks [85,86].…”

Caracterización fenotípica y genotípica de cultivares de cacao (Theobroma cacao L.) de Dibulla, La Guajira, Colombia

“…La pequeña región nuclear escogida no representa todo el genoma y, por lo tanto, no cuenta toda la evolución genética de la especie. El análisis de marcadores de DNA de cloroplasto (cpDNA) se ha utilizado cada vez más en genética de poblacionales para determinar su estructura, ujo de genes, frecuencia de haplotipos y relaciones logenéticas (Gutiérrez-López et al, 2016). Por esta razón, se hizo una evaluación in silico de otros marcadores de secuencia del genoma de cloroplasto, que permitirán hacer en el futuro análisis más profundos y precisos entre cultivares de cacao.…”

Cacao biotechnology: current status and future prospects

“…In addition to markers based on nuclear genomic DNA, several loci of chloroplast DNA (cpDNA) such as matK , rbcL and trnH‐psbA can be used as markers in DNA barcoding (Bieniek et al ., ). Recently, sequence variation of the trnH‐psbA intergenic spacer has been analysed in 28 cacao accession obtained from different farms in southern Mexico (Gutiérrez‐López et al ., ). It was found that the indels located in this region could be considered as potential markers for development of a DNA barcoding system in cacao.…”

“…It was found that the indels located in this region could be considered as potential markers for development of a DNA barcoding system in cacao. These markers are useful in identification of accessions in situations when other marker systems can only discriminate between accessions on the basis of a very small number of SSR markers (Gutiérrez‐López et al ., ).…”