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Background  Phytophthora root and stem rot (PRR) caused by  Phytophthora sojae  is one of the most serious diseases affecting soybean ( Glycine max  (L.) Merr.) production all over the world. The most economical and environmentally-friendly way to control the disease is the exploration and utilization of resistant varieties.    Results  We screened a soybean mini core collection composed of 224 germplasm accessions for resistance against eleven  P. sojae  isolates. Soybean accessions from the Southern and Huanghuai regions, especially the Hubei, Jiangsu, Sichuan and Fujian provinces, had the most varied and broadest spectrum of resistance. Based on gene postulation,  Rps 1b,  Rps 1c,  Rps 4,  Rps 7 and novel resistance genes were identified in resistant accessions. Consequently, association mapping of resistance to each isolate was performed with 1,645 single nucleotide polymorphism (SNP) markers. A total of 14 marker-trait associations for  Phytophthora  resistance were identified. Among them, four were located in known PRR resistance loci intervals, five were located in other disease resistance quantitative trait locus (QTL) regions, and five associations unmasked novel loci for PRR resistance. In addition, we also identified candidate genes related to resistance.    Conclusion  This is the first  P. sojae  resistance evaluation conducted using the Chinese soybean mini core collection, which is a representative sample of Chinese soybean cultivars. The resistance reaction analyses provided an excellent database of resistant resources and genetic variations for future breeding programs. The SNP markers associated with resistance will facilitate marker-assisted selection (MAS) in breeding programs for resistance to PRR, and the candidate genes may be useful for exploring the mechanism underlying  P. sojae  resistance.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-016-0383-4) contains supplementary material, which is available to authorized users.

Phenotypic evaluation and genetic dissection of resistance to Phytophthora sojae in the Chinese soybean mini core collection