High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection

Abstract

We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee-H. vastatrix interaction over a time course in susceptible and resistant coffee plants.

Structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: a functional marker based approach

“…To identify the candidate R genes activated against H. vastatrix incursion, two contigs (contigs 3 and 9) were mapped against the transcriptome of C. arabica - H. vastatrix interaction [25]. Genes 9, 10, 11 and 12 were mapped to transcripts differentially-expressed during incompatible interactions at 12 and 24 hai with H. vastatrix (race XXXIII) as illustrated in S5 Fig.…”

“…DNA was stored at -20 °C until further use. RNA-Seq libraries (hereafter, referred to as transcriptome) were constructed at 12 and 24 h after infection (hai) during the C. arabica CIFC 832/2 – H. vastatrix (race XXXIII) incompatible interaction [25] and were used as the reference in the search for novel candidate resistance genes.…”

Cambios bioquímicos en respuesta al ataque de roya en plantaciones de café

“…El café (Coffea arabica) es una de las plantas más cultivadas y comercializadas en México, siendo Chiapas el principal estado productor de café orgánico (Temis, Lópes & Sosa, 2011). Uno de los principales problemas en la producción de café es la enfermedad de la roya, la cual puede causar pérdidas de rendimiento de hasta el 50% (Florez et al, 2017). Actualmente, es el principal problema al que se enfrenta el sector cafetalero en México.…”

“…Actualmente, es el principal problema al que se enfrenta el sector cafetalero en México. El agente causal es Hemileia vastatrix, el cual es un hongo biótrofo que depende completamente de las células vivas de la planta para su reproducción (Florez et al, 2017), por lo que afecta principalmente el follaje de C. arabica, provocando una defoliación total de las plantas hasta ocasionar su muerte, originando así, pérdidas de hasta un 40% de los cultivos (Fernandez et al, 2012). Para el control de éste hongo, se han empleado fungicidas a base de cobre, triazoles y estroburilinas, microorganismos antagónicos, defoliaciones, por mencionar algunos (Fernandez et al, 2012;Haddad, Saraiva, Mizubuti, Romeiro & Maffia, 2013).…”

“…La enfermedad de la roya del café, causada por el hongo H. vastatrix, es una de las principales enfermedades del café en todo el mundo. El uso de cultivares resistentes es considerada una de las estrategias de control más efectiva para esta enfermedad (Florez et al, 2017). En ocasiones, en los cultivos de café infectados con H. vastatrix se pueden observar plantas con ausencia de síntomas.…”