Structural and nucleotide diversity at the Avr3a locus among 31 isolates of Phytophthora sojae reveal distinct haplotypes associated with virulence phenotypes. a Variants in the coding region of the Phytophthora sojae Avr3a region. Yellow box represents the coding region of the gene and gray bars, 5′ and 3′ UTR. Asterisk (*) indicate approximate positions of the SNPs and small indel. Those variants are representative of a cluster of variants defining a haplotype. b Schematic graph of the position of the variants for each isolate, regrouped by haplotypes. Variants in gray background are different from the reference genome (isolate P6497). Phenotype results were confirmed by re-testing a number of isolates with the hydroponic assay (Additional file 3). CNV of Avr3a gene for the reference genome (P6497) is based on data from Qutob et al.