Characterization of the genetic diversity of native cacao varieties using SSR molecular markers
Keywords:
cacao, genetic diversity, germplasm, microsatellites, molecular markers, SSR.Abstract
The conservation and characterization of cacao (Theobroma cacao L.) genetic diversity are fundamental for the sustainable use of plant genetic resources, the identification of materials with differentiated agronomic characteristics, and the strengthening of breeding programs. Simple sequence repeat (SSR) molecular markers are widely used to determine variability levels, genetic relationships, and population structure due to their high polymorphism, codominance, and reproducibility. The objective of this research was to characterize the genetic diversity of native cacao varieties using SSR molecular markers and to determine the similarity and differentiation relationships among the evaluated materials. Seventy-two native cacao accessions from six production areas were analyzed using a panel of 15 microsatellite loci. Genomic DNA was extracted from young leaves using a modified CTAB protocol, followed by polymerase chain reaction amplification and separation of amplified products. The number of alleles, polymorphic information content, observed and expected heterozygosity, genetic diversity index, and inbreeding coefficient were determined. Genetic structure was assessed through principal coordinate analysis, genetic distance-based clustering, and Bayesian analysis. The 15 SSR loci generated 142 alleles, with an average of 9.47 alleles per locus. Mean observed heterozygosity was 0.63, whereas expected heterozygosity reached 0.71. Polymorphic information content averaged 0.68, demonstrating the high discriminatory capacity of the selected markers. Analysis of molecular variance indicated that 76% of genetic variability was concentrated within populations and 24% among them. Structure analysis identified four major genetic groups with different levels of ancestral admixture. It is concluded that the evaluated native varieties maintain high genetic diversity and constitute strategic resources for conservation, genotype selection, and the development of cacao breeding programs.
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