Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates

Authors: ARSENAULT-LABRECQUE, GENEVIÈVE - University Of Laval; SONAH, HUMIRA - University Of Laval; LEBRETON, AMANDINE - University Of Laval; LABBÉ, CAROLINE - University Of Laval; MARCHAND, GENEVIÈVE - Agriculture And Agri-Food Canada; XUE, ALLEN - Agriculture And Agri-Food Canada; BELZILE, FRANÇOIS - University Of Laval; Knaus, Brian; Grunwald, Niklaus - Nik; BÉLANGER, RICHARD - University Of Laval

Submitted to: BMC Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/19/2018
Publication Date: 7/26/2018
Citation: Arsenault-Labrecque, G., Sonah, H., Lebreton, A., Labbé, C., Marchand, G., Xue, A., Belzile, F., Knaus, B.J., Grunwald, N.J., Bélanger, R.R. 2018. Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates. BMC Biology. 16:80. https://doi.org/10.1186/s12915-018-0549-9.
DOI: https://doi.org/10.1186/s12915-018-0549-9

Interpretive Summary: The interaction between the plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence genes (Avr genes) in P. sojae and corresponding resistance genes (Rps) in soybean. As soybean has become the third most important crop in Canada, a recent survey has highlighted a rapid shift in the diversification of P. sojae Avr genes in soybean fields, and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates in Canada remains poorly defined and is mostly characterized on the basis of phenotypic associations with soybean differentials. We sequenced genomes of 31 isolates of P. sojae, representing the spectrum of the pathotypes found in Canada and determined Avr gene content. Our results discovered several new variants within the genes studied and more importantly. This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic analysis can be used as an accurate assessment of interactions between hosts and pathogens soybean.

Technical Abstract: The interaction between Phytophthora sojae and soybean is characterized by the presence of avirulence genes (Avr genes) in P. sojae and corresponding resistance genes (Rps) in soybean. As soybean has become the third most important crop in Canada, a recent survey has highlighted a rapid shift in the diversification of P. sojae Avr genes in soybean fields, and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates in Canada remains poorly defined and is mostly characterized on the basis of phenotypic associations with soybean differentials. We sequenced genomes of 31 isolates of P. sojae, representing the spectrum of the pathotypes found in Canada and compared all the structural variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. Our results discovered several new variants within the genes studied and more importantly, some discrepancies with previously described Avr genes, notably with Avr1b and Avr1c. In addition, we identified nearly 11% (26/217) potentially erroneous phenotypes on the basis of genomic signatures, with a strong bias for false positive virulence. When these interactions were re-phenotyped using a more robust hydroponic assay, all but one displayed the expected pattern of virulence, indicating that genomic signatures alone accurately predicted 99.5% of the interactions. This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. This precise phenotyping also highlights some inconsistencies with regards to the virulence model previously reported for genes Avr1b and Avr1c and proposes a new definition for both genes.