Fingerprinting Amazonian coffees: assessing diversity through molecular markers

Characterization of genetic resources is a prerequisite for plant breeding and germplasm management. In this context, the use of molecular markers for validation of genetic passports based on DNA analyses is crucial for identification of cultivars and traceability in coffee breeding programs. A total of 96 Coffea canephora genotypes cultivated in the Western Amazonia were evaluated, including plants of the botanical varieties Conilon, Robusta, and hybrids from the germplasm bank of the Brazilian Agricultural Research Corporation (Embrapa), as well as clones in the public domain coming from growers in the state. The germplasm was evaluated with 12 simple sequence repeat (SSR) marker to quantify the genetic diversity also considering the discrimination power of these markers. Were identified 96 unique fingerprint profiles and a set of primers of higher efficiency for discrimination C. canephora genotypes. The genetic relationships illustrated by hierarchical clusterings and discriminant analyses showed distinction between the botanical varieties Conilon and Robusta and higher diversity in the Robusta variety. The set of molecular markers allowed to identify hybrid genotypes that were misclassified in populations of Conilon and Robusta botanical varieties as well as genealogy mistakes. Unique genetic profiles were detected for each clone in the public domain of the state. Previously unknown, these genotypes were classified according to their phenotypic similarities with each other and with the Conilon, Robusta, and hybrid accessions. These results are valuable for future management of the Amazonian coffee and useful to assist and accelerate the selection and crosses in the genetic breeding program.