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

Abstract

BackgroundThe interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid 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 remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines.ResultsWe sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions.ConclusionsThis 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. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0549-9) contains supplementary material, which is available to authorized users.

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

“…Haplotype letters refer to those previously identified by Arsenault‐Labrecque et al . (). Scaffold positions refer to the position of the markers used as per the P. sojae reference genome v. 3.0…”

“…Sequence alignments with isolates P6497, P7064, P7074, and P7076 showed that the primers would accurately predict the phenotypes for the latter three isolates (Figure ), isolate P6497 being a rare outlier as reported by Arsenault‐Labrecque et al . ().…”

“…In some cases, markers defined by Arsenault‐Labrecque et al . () were used directly, and in cases where markers were not discriminant enough for polymerase chain reaction (PCR) (e.g., one single nucleotide polymorphism [SNP]), additional markers associated with the same alleles were used for the design of the primers. In other cases where the discriminant variants were located outside of the coding region, the primers were developed based on the specific haplotype linked to the avirulence allele.…”

“…Recently, Arsenault‐Labrecque et al . () provided an exhaustive description and comparison of haplotype diversity for seven Avr genes ( 1a , 1b , 1c , 1d , 1k , 3a , and 6 ) of P. sojae through whole‐genome sequencing of 31 isolates with different pathotypes. While all isolates for the study originated from Canada, their results showed that they had captured all the haplotype diversity previously reported (but for one rare allele in Avr1b [Shan et al ., ]) and even expanded it for a few Avr s. In this work, we further compared the allelic diversity of two avirulence genes ( Avr1k and Avr6 ) among isolates from China, the United States, and Canada and found that all alleles were well aligned with the predicted virulence, except for a single isolate phenotyped with the hypocotyl assay, indicating that the accuracy of the bioassay expands to most known P. sojae isolates, regardless of their origin (Figure ).…”

“…In a recent effort to associate phenotypes with genotypes, Arsenault‐Labrecque et al . () sequenced 31 P. sojae isolates collected from Canadian fields and analysed the sequences and variants of the seven most common Avr genes: 1a , 1b , 1c , 1d , 1k , 3a , and 6 . They were able to define specific haplotypes for each Avr gene and further show, through the use of the hydroponic assay, that each haplotype corresponded to a distinct virulence profile.…”