Soybean sudden death syndrome (SDS) is one of the most important soybean diseases in the Midwestern United States, leading to average losses of $396 million per year from 1996 to 2015. The causal agent of SDS, soilborne fungus Fusarium virguliforme (Fv), causes root rot symptoms and releases phytotoxins taken up by the plant to produce chlorosis and necrosis in the leaves. The main management practice used to reduce the impact of SDS is planting resistant soybean cultivars. Resistance to SDS is known to be quantitative with 88 known quantitative trait loci (QTL) based on Soybase.org. Many of these QTL were identified using germplasm from the southern United States. In an effort to identify QTL from germplasm from the northern U.S., a mapping population of F2:3 lines created by crossing the highly resistant cultivar ‘MN1606SP’ and the susceptible cultivar ‘Spencer’ was phenotyped in the greenhouse at three different planting times, each with three replications. Plants were artificially inoculated using SDS infested sorghum seed homogeneously mixed with the soil. Data were collected on three disease criteria, foliar disease incidence (DI), foliar leaf scorch disease severity (DS), and root rot severity. Disease index (DX) was calculated as DI x DS. Ten QTL were identified for the different disease assessment criteria, three for DI, four for DX, and three for root rot severity. Three QTL identified for root rot severity and one QTL for disease incidence are considered novel, since no previous reports related to these QTL are available. Among QTL, two interactions were detected between four different QTL. The interactions suggest that resistance to SDS is not only dependent on additive gene effects.

Building on the genomic data from the QTL mapping study, a gene expression study using the parents of the F2:3 mapping population was run. The two parents were screened again using the same Fv isolate, but with a different method to prevent expression differences due to inoculum load. Using a 106 spore suspension two time points, 1 day after inoculation (DAI) and 7 DAI were inspected for differences in gene expression in root and foliar tissue to SDS. Comparisons between inoculated and non-inoculated as well as comparisons between resistant, ‘MN1606SP’, and susceptible, ‘Spencer’, were made. The results showed the resistant and susceptible lines had different gene expression responses when infected with Fv and when compared to each other in the mock treatment. The resistant response included more genes significantly (P<0.05) overrepresented than the susceptible in root tissue and the susceptible had more than the resistant response in foliar tissue. Overlaying DE genes with previously identified QTL allowed us to identify candidates within these QTL contributing to resistance. These results will lead to insights into the mechanism soybean employs to defend itself against F. virguliforme and will allow breeders to develop markers to select for resistant lines.