Genetic identification of Theobroma cacao

Abstract

ABSTRACT. Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations Genetic identification of high Criollo ancestry cacao trees (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (F ST = 0.123, P < 0.0001). Sampled demes sites (1-7) in the Soconusco region did not show any evidence of clustering by geographic location, and this was supported by the Mantel test (R xy = 0.54, P = 0.120). Individuals with high Criollo lineage planted in Soconusco farms could be an important reservoir of genes for future breeding programs searching for fine, taste, flavor, and aroma cocoa.

Unique haplotypes of cacao trees as revealed bytrnH-psbAchloroplast DNA

“…The seeds had white or slightly pigmented cotyledons that were enveloped in sweet pulp. In agreement with the report by Vázquez-Ovando et al (2014), the individuals were classified as 12 trees with high Criollo ancestry, 11 Non-Criollo group trees and five admixtures (Table 1). Additionally, 10 accessions were sequenced and included as references: two Forastero variety (Catongo and EET 399), one Trinitario variety (RIM 24) and seven wild Criollo (one collected in the Lacandon rainforest (SL01) and six obtained from the germplasm of the Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, México (Yaxcabá, Xocen, Lacandón 06, Lacandón 28, Lagarto and Carmelo); Table 1).…”

“…*Classification based on membership (>90%) to Criollo type, see Table 1 (Vázquez-Ovando et al, 2014). …”

“…Thirty-eight trees were sequenced for the trnH-psbA spacer and analyzed, and seven sequence accessions were downloaded from GenBank as references. A total of 28 of the 38 sequenced trees were selected from plantations in Soconusco (Chiapas, Mexico) based on a previous characterization (Vázquez-Ovando et al, 2014) using 10 SSR molecular markers. The individuals were selected based on fruit (pod) and seed traits that resembled those of the Criollo variety.…”

“…Conversely, the genetic diversity of cacaos in southern Mexico was reported to be moderate to low in natural populations (Whitkus et al, 1998 using RAPD markers) and cultivated forms (Vázquez-Ovando et al, 2014 using microsatellite markers), although a wide diversity in cacao pod (fruit smooth, rugose, very rugose; apex blunt, apex point; cylindrical and oblate form; basal constriction slight/absent to very pronounced; colours green, red), and seed (elliptics and oblate forms; colour white, slightly pigment and purple intense) morphologies was observed and reported by Avendaño-Arrazate et al (2010). In the Soconusco farms (Chiapas, Mexico), Vázquez-Ovando et al (2014) found moderate to high allelic richness and high levels of homozygosity.…”

“…In the Soconusco farms (Chiapas, Mexico), Vázquez-Ovando et al (2014) found moderate to high allelic richness and high levels of homozygosity. The authors reported the presence of trees sharing genetic identity with those considered “Ancient Criollo” but also reported the presence of private alleles.…”