Abstract
BackgroundPhytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae.ResultsResistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes.ConclusionsQTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial resistance to P. sojae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2918-5) contains supplementary material, which is available to authorized users.
Highlights
Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae
Phenotypic data were collected for inoculated root rot score (IRRS; 1, no rot, to 9, completely rotted) as well as for root weight (RW), shoot weight (SW) and plant height (PH) from inoculated (I) and non-inoculated (N) assays
There was no observable root rot in 306 plant introduction (PI) (IRRS ≤ 1.5) following inoculation with one or both isolates of P. sojae and these were excluded from analysis in order to eliminate any possible Rps-mediated resistance response
Summary
Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Phytophthora root and stem rot was the second most yield-limiting disease of soybean [Glycine max (L.) Merr] between 1996 and 2009 [1, 2] This disease, caused by the soil-borne oomycete pathogen Phytophthora sojae [3], is prevalent when soil conditions become saturated [4], allowing the asexual, motile zoospores to chemotactically travel to soybean roots [5, 6]. Deployment of Rps genes places high selection pressures on the P. sojae populations causing the population to adapt and potentially gain virulence such that the Rps gene is no longer effective. Pathogen diversity and adaptation limits the efficacy of an Rps gene to eight to twenty years [8, 25] breeders cannot rely solely on Rps genes
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