Phytophthora root and stem rot (PRSR) disease results in substantial losses in soybean production worldwide. The occurrence of PRSR caused by Phytophthora sojae Kaufmann & Gerdemann has become increasingly important for soybean production in the Republic of Korea, but domestic soybean–P. sojae interaction has been less studied. The disease has been managed by developing varieties harboring resistance to the Phytophthora sojae (Rps) gene. The present study aimed to identify a major gene locus conferring resistance to new P. sojae isolate 2858 in the recombinant inbred line population derived from a cross between parental lines ‘Daepung’ (susceptible) and ‘Saedanbaek’ (resistant). Seventy-three recombination inbred lines (RILs) were evaluated for resistance to P. sojae isolate 2858. A resistance locus was identified in the approximate 3.3–4.3 megabase pair region on chromosome 3 using both single-marker and linkage analyses. The Rps of Saedanbaek (RpsSDB) was located on the well-known Rps gene/allele cluster region, which also partially overlapped with a locus previously identified in the Korean soybean variety, ‘Daewon’, resistant to another P. sojae isolate 2457 (RpsDW). Approximately 402 kilobase pairs of the interval region overlapped, including six nucleotide-binding site-leucine-rich repeat (NBS-LRR)-coding genes. Additional phenotypic assays revealed that Saedanbaek was susceptible to isolate 2457 and that Daewon was susceptible to isolate 2858, indicating that RpsSDB and RpsDW are different genes or alleles that confer race-specific resistance to the two P. sojae isolates. These results provide information that will be helpful for breeders developing P. sojae-resistant cultivars.

Phytophthora sojae (Kauffman and Gerdemann) is an oomycete pathogen that threatens soybean (Glycine max L.) production worldwide. The development of soybean cultivars with resistance to this pathogen is of paramount importance for the sustainable management of the disease. The objective of this study was to identify genomic regions associated with resistance to P. sojae isolate 40468 through genome-wide association analyses of 983 soybean germplasms. To elucidate the genetic basis of resistance, three statistical models were employed: the compressed mixed linear model (CMLM), Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK), and fixed and random model circulating probability unification (FarmCPU). The three models consistently identified a genomic region (3.8–5.3 Mbp) on chromosome 3, which has been previously identified as an Rps cluster. A total of 18 single nucleotide polymorphisms demonstrated high statistical significance across all three models, which were distributed in eight linkage disequilibrium (LD) blocks within the aforementioned interval. Of the eight, LD3-2 exhibited the discernible segregation of phenotypic reactions by haplotype. Specifically, over 93% of accessions with haplotypes LD3-2-F or LD3-2-G displayed resistance, whereas over 91% with LD3-2-A, LD3-2-C, or LD3-2-D exhibited susceptibility. Furthermore, the BLINK and FarmCPU models identified new genomic variations significantly associated with the resistance on several other chromosomes, indicating that the resistance observed in this panel was due to the presence of different alleles of multiple Rps genes. These findings underscore the necessity for robust statistical models to accurately detect true marker–trait associations and provide valuable insights into soybean genetics and breeding.

Phytophthora sojae is the causal agent of the Phytophthora root and stem rot in soybean, which has resulted in a significant increase in the incidence of the disease and substantial yield losses on a global scale. The proliferation of Phytophthora sojae can be mitigated through the development of Phytophthora-resistant soybean cultivars. A fundamental understanding of the genetic diversity and dynamic changes within the P. sojae population is essential for disease management and the development of new P. sojae-resistant varieties. Although a large number of pathogen samples can lead to more comprehensive interpretations and better conclusions, only six indigenous P. sojae isolates were available in the Republic of Korea at the time of the experiments. Due to the limited availability, this study preliminarily aimed to assess the pathotypes and genetic variation of the six P. sojae isolates collected in the Republic of Korea. The virulence patterns of all the six P. sojae isolates differed based on the 15 soybean differentials known for P. sojae resistance. The six isolates displayed high levels of pathotype complexities, ranging from 8 to 15, which is notably higher than those observed in other countries. Furthermore, 18 of the 21 simple sequence repeat markers used exhibited polymorphisms. The mean allele number (3.8) shows higher genetic variability compared to that (2.5) of isolates from the USA. The gene diversity (0.624) and the mean polymorphic information content (0.579) also displayed high levels of variation among the six isolates. A low mean heterozygosity (0.019) indicated a rare but possible outcrossing between the isolates, which was detected by the SSR marker PS07. Genetic dissimilarity assessments were employed to categorize the six P. sojae isolates into three groups using a neighbor-joining phylogenetic tree and principal component analysis. Although on a small scale, the phenotypic and genotypic assay results obtained indicated a significant variability in the pathotypes and genetic variation within the P. sojae isolates in the Republic of Korea. Though limited in scope, these results will be a cornerstone for elucidating the virulence pathotype and genetic diversity of the P. sojae population in future analyses. These findings also have the potential to improve the soybean breeding strategies aimed at enhancing resistance to P. sojae in the Republic of Korea.