Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato

Abstract

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease in potato. For sustainable management of this economically important disease, resistance breeding relies on the availability of resistance (R) genes. Such R genes against P. infestans have evolved in wild tuber-bearing Solanum species from North, Central and South America, upon co-evolution with cognate avirulence (Avr) genes. Here, we report how effectoromics screens with Avr2 of P. infestans revealed defense responses in diverse Solanum species that are native to Mexico and Peru. We found that the response to AVR2 in the Mexican Solanum species is mediated by R genes of the R2 family that resides on a major late blight locus on chromosome IV. In contrast, the response to AVR2 in Peruvian Solanum species is mediated by Rpi-mcq1, which resides on chromosome IX and does not belong to the R2 family. The data indicate that AVR2 recognition has evolved independently on two genetic loci in Mexican and Peruvian Solanum species, respectively. Detached leaf tests on potato cultivar 'Désirée' transformed with R genes from either the R2 or the Rpi-mcq1 locus revealed an overlapping, but distinct resistance profile to a panel of 18 diverse P. infestans isolates. The achieved insights in the molecular R - Avr gene interaction can lead to more educated exploitation of R genes and maximize the potential of generating more broad-spectrum, and potentially more durable control of the late blight disease in potato.

Keywords: Avr gene; Co-evolution; Late blight; Phytophthora infestans; Potato; R gene; Resistance; Solanum.

Fig. 1

Solanum species that respond to AVR2 occur in Mexico and Peru. (A) Representative leaf panels of AVR2-recognizing Solanum species from Mexico (Hjt349-3) and Peru (Mcq717-3). Leaves were agro-infiltrated with pK7WG2:AVR2, with pK7WG2: empty and co-infiltrated R3a/AVR3a as negative and positive controls, respectively. Pictures were taken at 4 dpi. (B) Geographic map representing the origins of all tested Solanum genotypes (white circles) including those that respond to AVR2 (red circle), listed in Table 1.

Fig. 2

Classification of tested wild Solanum genotypes. Bayesian rooted tree of 80 screened Solanum genotypes and 6 Solanum etuberosum genotypes. The branch length represents expected changes per site and posterior probability values are shown near the respective nodes. Indicated clades are based on Spooner et al. (2014). The AVR2-responding Solanum genotypes are marked with red dots, and numbers correspond to their geographic location (Fig. 1). n.d. not determined.

Fig. 3

Classification of Rpi proteins. Phylogenetic tree derived from the full NB-ARC domains (range of amino acid sequences in Supplemental Table 1) obtained from 27 Rpi proteins. Rpi cloned from Mexican (red) and South American (blue) Solanum are highlighted. CNL clades are indicated. The nematode resistance protein Gro1.4 was used as outgroup in a Maximum-Likelihood analysis. The Bootstrap values of 60 % and higher are indicated in the nodes. Horizontal branches lengths and scale bar correspond to the evolutionary distances that are measured as the proportion of amino acid substitutions between sequences.

Fig. 4

Rpi-mcq1 and Rpi-blb3 confer response to AVR2. Leaves of potato cv. ‘Bintje’ were co-infiltrated with AVR2 and Rpi-mcq1 (A) and Rpi-blb3 (B) as a cell death control trigger by AVR2. Single infiltrations of AVR2, Rpi-mcq1, Rpi-blb3 and empty vector were included as negatives controls and co-infiltration of R3a/AVR3a was included as positive control. Each effector is tested twice on three leaves, over two plants and two biological replicates. Representative photographs of cell death symptoms were taken at 4 dpi.

Fig. 5

Disease index on ‘Désirée’, Désirée-Rpi-mcq1 and Désirée-Rpi-blb3 with isolates from group I–III. (A) Representative pictures of isolates from group I to III tested in ‘Désirée’ (WT), Désiree-Rpi-mcq1 (Rpi-mcq1) and Désirée-Rpi-blb3 (Rpi-blb3) are displayed. Pictures were taken after 6 dpi. (B) Disease symptoms were scored on a scale from 1 to 9: 1 represents intensive sporulation; 2–3, macroscopically visible sporulation, but to a less extend as 1. 4–5, represent sporulation only visible under the binocular; 6–7 represent necrotic lesion ≥ 10 mm of diameter and between 4–10 mm, respectively; 8, small necrotic lesion not exceeding 4 mm and 9 represents no symptoms. The percent of each category is shown with isolates of group I–III.