Abstract
Effectors, a group of small proteins secreted by pathogens, play a critical role in the antagonistic interaction between plant hosts and pathogens through their dual functions in regulating host immune systems and pathogen infection capability. In this study, evolution in effector genes was investigated through population genetic analysis of Avr3a sequences generated from 96 Phytophthora infestans isolates collected from six locations representing a range of thermal variation and cropping systems in China. We found high genetic variation in the Avr3a gene resulting from diverse mechanisms extending beyond point mutations, frameshift, and defeated start and stop codons to intragenic recombination. A total of 51 nucleotide haplotypes encoding 38 amino acid isoforms were detected in the 96 full sequences with nucleotide diversity in the pathogen populations ranging from 0.007 to 0.023 (mean = 0.017). Although haplotype and nucleotide diversity were high, the effector gene was dominated by only three haplotypes. Evidence for a selective sweep was provided by (i) the population genetic differentiation (G ST) of haplotypes being lower than the population differentiation (F ST ) of SSR marker loci; and (ii) negative values of Tajima's D and Fu's FS. Annual mean temperature in the collection sites was negatively correlated with the frequency of the virulent form (Avr3aEM), indicating Avr3a may be regulated by temperature. These results suggest that elevated air temperature due to global warming may hamper the development of pathogenicity traits in P. infestans and further study under confined thermal regimes may be required to confirm the hypothesis.
Highlights
Pathogens and their host plants are engaged in a never-ending battle, in which pathogens are continuously evolving invasive mechanisms to break plant defense systems and host plants responding with the constant development of new protection to prevent or mitigate damage (Zhan, Thrall, & Burdon, 2014; Zhan, Thrall, Papaïx, Xie, & Burdon, 2015)
Genetic diversity of Avr3a gene was found to be high in the current study, and nucleotide diversity (Table 1) was positively correlated
More than 50 nucleotide haplotypes were detected in 96 sequences, and the combined nucleotide diversity was 0.017 (Table 1)
Summary
Pathogens and their host plants are engaged in a never-ending battle, in which pathogens are continuously evolving invasive mechanisms to break plant defense systems and host plants responding with the constant development of new protection to prevent or mitigate damage (Zhan, Thrall, & Burdon, 2014; Zhan, Thrall, Papaïx, Xie, & Burdon, 2015). Virulent types of effector genes can emerge quickly from avirulent types in the plant pathogen populations, leading to the breakdown of many major gene-mediated plant resistances within a few years of their commercialization (Cooke et al, 2012; Pilet, Pellé, Ellisseche, & Andrivon, 2005) In addition to their genetic characters, other biological and ecological processes may influence genetic variation and the. Avr3a, recognized by the corresponding resistance gene R3a in the host plant, was the first effector gene characterized in P. infestans (Armstrong et al, 2005) It is a RXLR effector containing conserved W, Y, and L motifs in C-terminal domains. The specific objectives of this study were as follows: (i) to determine evolutionary mechanisms generating genetic variation of Avr3a; (ii) to infer the contribution of natural selection to the spatial population genetic dynamics of Avr3a; and (iii) to evaluate the potential impact of temperature on the spatial distribution and evolution of Avr3a
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