Genetic diversity and structure of Hemileia vastatrix populations on Coffea spp.

Abstract

Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms (AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity (h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance (r = −0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy.

Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust

“…One of the first and most striking findings of this work was the discovery of three well‐diverged evolutionary lineages within our sampling of a supposedly single species, which is in disagreement with previous studies (Cabral et al ., ; Maia et al ., ; Rozo et al ., ). Until now, disease management practices were heavily influenced by the idea that Hv represents a large unstructured population that is able to freely switch between coffee species (McCook and Vandermeer, ; Zambolim, ).…”

“…From the first epidemic report in Sri Lanka in 1869, Hv has spread to virtually every coffee-growing region in the world in about one and a half centuries (McCook and Vandermeer, 2015;Talhinhas et al, 2017). During this period, several major outbreaks have been registered in Asia and Africa and, more recently, since 2008, a cluster of outbreaks has been occurring across the Americas (Avelino et al, 2015;McCook and Vandermeer, 2015;Zambolim, 2016). Breeding for coffee resistance is considered to be the best long-term solution to control CLR (McCook and Vandermeer, 2015), but the introduction of resistant varieties in the field has inevitably resulted in the loss of resistance as a result of adaptation of the pathogen.…”

“…However, considerably less explored remains the evolutionary history of Hv populations, particularly at a global scale. Using random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers, population genetic studies of Hv populations have predominantly focused on restricted geographical areas, such as Brazil (Cabral et al, 2016;Maia et al, 2013;Nunes et al, 2009) and Colombia (Rozo et al, 2012), with the exception of Gouveia et al (2005) which included isolates from Asia, Africa and America. These studies have consistently found no evidence of population structure with respect to pathotype, host or geographical origin, but have reported mixed results regarding the level of genetic variability.…”

Diversidad genética de Hemileia vastatrix de dos Zonas productoras de café en el Perú

“…These results are similar to those obtained in Brazil by Cabral et al (2016) Al no observarse en la red haplotípica de la Figura 2, nodos exclusivos por región geográfica, se estaría evidenciando una población de H. vastatrix grande e indiferenciada, que pudo haberse generado por el flujo de las esporas entre ambas zonas, favorecido por el movimiento de personas, semillas y/o plantas infectadas. Estos resultados son similares a los obtenidos por Cabral et al (2016) en Brasil, quienes no observan una estructuración de la población de H. vastatrix respecto a su origen, hospedero ni razas fisiológicas; sin embargo, la diversidad genética fue relativamente menor a la hallada en el presente trabajo. No obstante, Maia et al (2013) también en Brasil, obtuvieron resultados similares al presente trabajo, a través del estudio de 91 aislados del hongo, proponiendo que H. vastatrix se comporta como una gran población populations were structured based on their origin, host or physiological race.…”

Assessment of genetic diversity of coffee leaf rust pathogen Hemileia vastatrix using SRAP markers

“…In another study, Maia, Maciel‐Zambolim, Caixeta, Mizubuti, and Zambolim () analysed the population structure of H. vastatrix from Brazil and observed high level of genotypic diversity using AFLP marker. In Brazil, Cabral, Zambolim, Oliveira, and Zambolim () studied the influence of host and geographic origin on the genetic diversity and population structure of H. vastatrix using AFLP markers and suggested that the fungal population revealed low levels of genotypic diversity. Recently, a new type of marker technology termed sequence‐related amplified polymorphism (SRAP) (Li & Quiros, ) was extensively used in the genetic diversity analysis of many fungal species such as Tricholoma matsutake (Ma, Yang, Mu, & Song, ), Puccinia striiformis (Pasquali, Komjati, Lee, & Bayles, ), Polyporous umbellatus (Zhang et al., ), Fusarium poae (Dinolfo, Castanares, & Stenglein, ) and Rhizoctonia solani (Tripathi & Dubey, ).…”