Main and epistatic loci studies in soybean for Sclerotinia sclerotiorum resistance reveal multiple modes of resistance in multi-environments

Abstract

Genome-wide association (GWAS) and epistatic (GWES) studies along with expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of Sclerotinia stem rot (SSR) [caused by Sclerotinia sclerotiorum (Lib.) de Bary], a significant fungal disease causing yield and quality losses. A large association panel of 466 diverse plant introduction accessions were phenotyped in multiple field and controlled environments to: (1) discover sources of resistance, (2) identify SNPs associated with resistance, and (3) determine putative candidate genes to elucidate the mode of resistance. We report 58 significant main effect loci and 24 significant epistatic interactions associated with SSR resistance, with candidate genes involved in a wide range of processes including cell wall structure, hormone signaling, and sugar allocation related to plant immunity, revealing the complex nature of SSR resistance. Putative candidate genes [for example, PHYTOALEXIN DEFFICIENT 4 (PAD4), ETHYLENE-INSENSITIVE 3-LIKE 1 (EIL3), and ETHYLENE RESPONSE FACTOR 1 (ERF1)] clustered into salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways suggest the involvement of a complex hormonal network typically activated by both necrotrophic (ET/JA) and biotrophic (SA) pathogens supporting that S. sclerotiorum is a hemibiotrophic plant pathogen.

Figure 1

Contributions to the phenotypic variance of identified Sclerotinia stem rot loci via genome-wide association and epistatic analyses for each environment and trait. The number of loci and/or pair of loci used to estimate contributions are indicated above each bar. Blue bars represent contributions due to loci identified using GWAS and orange bars represent contributions of both loci identified using GWAS and loci interactions identified using GWES.

Figure 2

Regional association plot of ss715588567 associated with 14GHSE-DAI03 and expression of the putative candidate gene Glyma.04g209700. (a) The top panel shows the negative log10-transformed P values from a genome-wide scan by using a mixed linear model (MLM) for plant severity taken 3 DAI within the adjacent region of peak SNP ss715588567 plotted against base pair positions (Mb) on soybean chromosome 4. The significance threshold line is distinguished (gray dotted line), and each SNP depicts the extent of linkage disequilibrium in the region based on pairwise values with respect to the peak SNP. The values are indicated using the color intensity index shown. The bottom panel shows all putative genes in the region. The putative candidate gene indicated in green. (b) The expression of Glyma.04g209700, the putative candidate gene for ss715588567, in a modern resistant (blue) and susceptible (orange) cultivar. Error bars shown to indicate significance (p < 0.05).

Figure 3

Regional association plot of ss715630264 associated with 15GHSE-DAI03 and expression of the candidate gene Glyma.18g039900. (a) The top panel shows the negative log10-transformed P values from a genome-wide scan by using a mixed linear model (MLM) for plant severity taken 3 DAI within the adjacent region of peak SNP ss715630264 plotted against base pair positions (Mb) on soybean chromosome 18. The significance threshold line is distinguished (gray dotted line), and each SNP depicts the extent of linkage disequilibrium in the region based on pairwise values with respect to the peak SNP. The values are indicated using the color intensity index shown. The bottom panel shows all putative genes in the region. The putative candidate gene indicated in green. (b) The expression of Glyma.18g039900, the putative candidate gene for ss715630264, in a modern resistant (blue) and susceptible (orange) cultivar. Error bars shown to indicate significance (p < 0.05).

Figure 4

Proposed phytohormones-dependent disease defense model against Sclerotinia sclerotiorum in soybean. SA, salicylic acid; JA, jasmonic acid; ET, ethylene; LRR-RLKs, Leucine-rich repeat receptor-like protein kinases; PAD4, Phytoalexin-dependent4; SIZ1, small ubiquitin-related modifier E3 ligase; PRs, Pathogenesis-related proteins; EIL1, Ethylene-insensitive 3-like 1; ERF1, Ethylene response factor 1.