ArticleBMC biology2018
Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates.
Article in BMC biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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15 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
- A global-temporal analysis on Phytophthora sojae resistance-gene efficacy.Nature communications · 2023Pooled it
- A Rare Recombination in the Phytophthora sojae Genome Allows the Redefinition of a Major Avirulence Gene.Molecular plant pathology · 2026Article
- Targeted capture and cloning of Rps6 reveal redundancy in soybean resistance genes.BMC plant biology · 2026Article
- Genetic diversity and evolution of nine avirulence genes in South KoreanFrontiers in microbiology · 2026Article
- Allelism of Rps3b and Rps11 revealed by NLR gene capture of resistance genes to Phytophthora sojae in soybean.The plant genome · 2025Article
- Pathotypes and Simple Sequence Repeat (SSR)-Based Genetic Diversity ofMicroorganisms · 2025Article
- Progress and Challenges in Elucidating the Functional Role of Effectors in the Soybean-Journal of fungi (Basel, Switzerland) · 2022Review
- RXLR effector gene Avr3a from Phytophthora sojae is recognized by Rps8 in soybean.Molecular plant pathology · 2022Article
- The SoyaGen Project: Putting Genomics to Work for Soybean Breeders.Frontiers in plant science · 2022Review
- Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean.The plant genome · 2021Article
- Mutations in the Promoter and Coding Regions ofFrontiers in microbiology · 2021Article
- Discriminant haplotypes of avirulence genes of Phytophthora sojae lead to a molecular assay to predict phenotypes.Molecular plant pathology · 2020Article
- Review
- Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes.The New phytologist · 2019Article
- Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution ofFrontiers in microbiology · 2019Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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