Discriminant haplotypes of avirulence genes of Phytophthora sojae lead to a molecular assay to predict phenotypes

Abstract

The soybean–Phytophthora sojae interaction operates on a gene‐for‐gene relationship, where the product of a resistance gene (Rps) in the host recognizes that of an avirulence gene (Avr) in the pathogen to generate an incompatible reaction. To exploit this form of resistance, one must match with precision the appropriate Rps gene with the corresponding Avr gene. Currently, this association is evaluated by phenotyping assays that are labour‐intensive and often imprecise. To circumvent this limitation, we sought to develop a molecular assay that would reveal the avirulence allele of the seven main Avr genes (Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a, and Avr6) in order to diagnose with precision the pathotypes of P. sojae isolates. For this purpose, we analysed the genomic regions of these Avr genes in 31 recently sequenced isolates with different virulence profiles and identified discriminant mutations between avirulence and virulence alleles. Specific primers were designed to generate amplicons of a distinct size, and polymerase chain reaction conditions were optimized in a final assay of two parallel runs. When tested on the 31 isolates of known virulence, the assay accurately revealed all avirulence alleles. The test was further assessed and compared to a phenotyping assay on 25 isolates of unknown virulence. The two assays matched in 97% (170/175) of the interactions studied. Interestingly, the sole cases of discrepancy were obtained with Avr3a, which suggests a possible imperfect interaction with Rps3a. This molecular assay offers a powerful and reliable tool to exploit and study with greater precision soybean resistance against P. sojae.

The Histological, Effectoromic, and Transcriptomic Analyses of Solanum pinnatisectum Reveal an Upregulation of Multiple NBS-LRR Genes Suppressing Phytophthora infestans Infection

“…Thus, the detection of mutations in cloned Avr probe genes may not be sufficient for a virulent profile prediction of filed isolates. This is different from the scenario of P. sojae, in which the presence of functional Avr genes in selected isolates is highly consistent with their avirulent phenotype [30]. Moreover, co-expression of Avrvnt1 and Rpi-vnt1 or single Avrvnt1 failed to induce HR in S. pinnatisectum, suggesting that specific interacting proteins are needed for Avrvnt1-Rpi-vnt1 recognition.…”

Mutations in the Promoter and Coding Regions of Avr3a Cause Gain of Virulence of Phytophthora sojae to Rps3a in Soybean

“…Interestingly, all five cases of discrepancy were present in the Avr3a gene. The PCR amplification for the avirulent alleles of Avr3a was achieved in the five cases, but the compatible interactions with Rps3a were observed in the phenotyping assay (Dussault-Benoit et al, 2020). Avr3a is a RXLR effector gene and encodes a predicted protein of 111 amino acids that includes a signal peptide, a RXLR motif and a carboxyterminal effector domain (Qutob et al, 2009;Dong et al, 2011b).…”

“…Hence, the development of simple and rapid molecular diagnostic methods is the main tendency for pathotype identification. More recently, Dussault-Benoit et al (2020) developed a molecular assay that could define P. sojae pathotypes using seven Avr genes ( Avr1a , Avr1b , Avr1c , Avr1d , Avr1k , Avr3a , and Avr6 ). The matching rate between the molecular assay and the phenotyping assay was as high as 97% (170/175).…”

Table_1.DOCX

“…Polymorphism analysis indicated that there were five Virulence structure of P. sojae should be constantly monitored to determine and deploy effective Rps genes (Dorrance et al, 2016;Stewart et al, 2016). Conventional virulence tests are labor-intensive and time-consuming, thus a rapid and simple PCR assay for pathotype identification of P. sojae was developed (Dussault-Benoit et al, 2020). However, when the PCR assay was used to detect the virulence of isolate Ps0903 with Avr3a(IV) to Rps3a in this study, a false positive result occurred.…”