Population genetic studies of Hemileia vastatrix have been conducted in order to describe the evolutionary dynamics of the pathogen and the disease epidemiology as consequence of changes in disease management and host distribution occurred in Peru after the 2013 epidemic. These analyses were performed by sequencing the internal transcribed spacers of the nuclear ribosomal DNA (rDNA-ITS) of H. vastatrix collected from two coffee growing areas in 2014 and 2018. H. vastatrix population showed high haplotype diversity ( Hd = 0.9373 ± 0.0115) with a low nucleotide diversity (π = 0.00322 ± 0.00018). Likewise, AMOVA indicated that fungus population has behaved as a large population without structuring by geographical origin and sampling years ( F ST = 0.00180, P = 0.20053 and F ST = 0.00241, P = 0.19693, respectively). Additionally, the haplotype network based on intraspecific phylogenetic analysis of H. vastatrix using Peruvian and NCBI sequences revealed that Peruvian ancestral haplotypes, which were maintained in time and space, would correspond to the reported sequences of the races II and XXII. This result suggests that no substantial changes have occurred through time in Peruvian Hemileia vastatrix population.

<p>Se analizó la diversidad genética del patógeno del café <em>Hemileia vastatrix</em>, a través de secuenciación de los espaciadores internos transcribibles del ADN ribosomal (ITS). El análisis se realizó en muestras de roya de 12 predios de dos zonas cafetaleras del Perú, Quillabamba (Cusco) y Villa Rica (Pasco). Se hallaron los índices de diversidad haplotípica y nucleotídica. Además, se determinaron las semejanzas entre las poblaciones analizadas por medio de una red de haplotipos. Del análisis, se determinó que ambas regiones productoras presentan valores altos de diversidad genética; sin embargo, la zona de Quillabamba albergó la mayor diversidad haplotípica de <em>H. vastatrix</em> (Hd = 0.977 +/- 0.012). Asimismo, la red de haplotipos permitió evidenciar la estructura de las poblaciones de <em>H. vastatrix</em> para cada zona, las que juntas se comportan como una gran población indiferenciada con presencia de haplotipos ancestrales a partir de los cuales se fueron generando nuevas variantes del hongo. También, se analizaron las secuencias de la región ITS de <em>H. vastatrix</em> peruanas y las almacenadas en el GenBank, no encontrándose distribución de las poblaciones por región geográfica; además, se determinó que las poblaciones de <em>H. vastatrix</em> peruanas presentan haplotipos similares a los de Colombia y a las razas II y XXII.</p>

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.