Genetic diversity and population structure of a Peruvian Coffea arabica collection

Roberto Mansilla-Samaniego1*, Rosa Espejo-Joya1, Giovanni Bernacchia2, Javier Wither-Villavicencio1, Cinthia Quispe-Apaza1, and César López-Bonilla1
Peru is an important producer of specialty coffee beans in the world, however the genetic of their coffee plant populations is unknown. Therefore, the genetic diversity and population structure of a Peruvian germplasm collection of plant coffee was analyzed to ascertain its potential use in plant breeding and conservation. In this work 54 DNA genotypes from 17 Coffea arabica L. and one C. canephora Pierre ex A. Froehner accessions were analyzed by microsatellite and sequence-related amplified polymorphism (SRAP) markers. In the assessment of molecular markers both systems were adequate to perform C. arabica germplasm collection genetic analysis. The obtained genetic diversity estimators were similar to germplasm assessments from other plant breeding programs. In the population structure analysis, the genetic differentiation (GST = 0.6584) and genetic flow (Nm = 0.2594) estimators were high. In analysis of molecular variance (AMOVA), total variation was divided 43.05% between accessions and 56.95% within accessions. In the Bayesian analysis with STRUCTURE software using admixed model for K = 2, the C. arabica and C. canephora accessions were separated, while for K = 7, the C. arabica accessions were grouped similarly to what obtained by the unweighted pair group method with arithmetic mean (UPGMA) dendrogram. The high genetic differentiation and genetic structuring of the accessions would indicate that the cultivars, from which the accessions were originated, have been preserved over time. The genetic diversity of Peruvian coffee might be the consequence of a long history of introductions of cultivars from different origins.
Keywords: Coffee, genetic diversity, microsatellites, molecular markers, Peruvian coffee, SRAP.
1Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, 15024 Lima, Perú.
*Corresponding author (rmansilla@lamolina.edu.pe).
2Università degli Studi di Ferrara, Dip Scienze della Vita e Biotecnologie, Via Borsari 46, 44121 Ferrara, Italia.