Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding

Abstract

Diseases caused by necrotrophic fungi, such as the cosmopolitan Sclerotinia sclerotiorum and the Diaporthe/Phomopsis complex, are among the most destructive diseases of sunflower worldwide. The lack of complete resistance combined with the inefficiency of chemical control makes assisted breeding the best strategy for disease control. In this work, we present an integrated genome-wide association (GWA) study investigating the response of a diverse panel of sunflower inbred lines to both pathogens. Phenotypic data for Sclerotinia head rot (SHR) consisted of five disease descriptors (disease incidence, DI; disease severity, DS; area under the disease progress curve for DI, AUDPCI, and DS, AUDPCS; and incubation period, IP). Two disease descriptors (DI and DS) were evaluated for two manifestations of Diaporthe/Phomopsis: Phomopsis stem canker (PSC) and Phomopsis head rot (PHR). In addition, a principal component (PC) analysis was used to derive transformed phenotypes as inputs to a univariate GWA (PC-GWA). Genotypic data comprised a panel of 4269 single nucleotide polymorphisms (SNP), generated via genotyping-by-sequencing. The GWA analysis revealed 24 unique marker-trait associations for SHR, 19 unique marker-trait associations for Diaporthe/Phomopsis diseases, and 7 markers associated with PC1 and PC2. No common markers were found for the response to the two pathogens. Nevertheless, epistatic interactions were identified between markers significantly associated with the response to S. sclerotiorum and Diaporthe/Phomopsis. This suggests that, while the main determinants of resistance may differ for the two pathogens, there could be an underlying common genetic basis. The exploration of regions physically close to the associated markers yielded 364 genes, of which 19 were predicted as putative disease resistance genes. This work presents the first simultaneous evaluation of two manifestations of Diaporthe/Phomopsis in sunflower, and undertakes a comprehensive GWA study by integrating PSC, PHR, and SHR data. The multiple regions identified, and their exploration to identify candidate genes, contribute not only to the understanding of the genetic basis of resistance, but also to the development of tools for assisted breeding.

Keywords: Diaporthe/Phomopsis; GWAS; Sclerotinia sclerotiorum; sunflower.

Figure 1

Histograms of standardized adjusted means. Upper panel: (a) Sclerotinia head rot (SHR) disease incidence (DI); (b) SHR area under the disease curve for DI (AUDPCI); (c) SHR disease severity (DS); (d) SHR AUDPC for DS (AUDPCS); (e) SHR incubation period (IP). Lower panel: (f) Phomopsis head rot (PHR) DI; (g) PHR DS; (h) Phomopsis stem canker (PSC) DI; (i) PSC DS.

Figure 2

Boxplots of disease response of AMP inbred lines, discriminated by their k-means grouping (three groups): (a) Sclerotinia head rot (SHR) disease incidence (DI); (b) SHR area under the disease curve for DI (AUDPCI); (c) SHR disease severity (DS); (d) SHR AUDPC for DS (AUDPCS); (e) SHR incubation period (IP); (f) Phomopsis head rot (PHR) DI; (g) PHR DS; (h) Phomopsis stem canker (PSC) DI; (i) PSC DS.

Figure 3

Plots of effect sizes for associated markers. Dot diameters are proportional to the effect size of the marker. (a) SNPs associated with phenotypic traits of SHR. DI, disease incidence; AUDPCI, area under the disease curve for DI; DS, disease severity; AUDPCS, AUDPC for DS; IP, incubation period. (b) SNPs associated with phenotypic traits of Diaporthe/Phomopsis. PHR, Phomopsis head rot; PSC, Phomopsis stem canker. (c) SNPs associated with principal components PC1 and PC2.

Figure 4

GO biological process terms enriched in the 364 genes physically close to the associated markers (only the first 15 major terms are shown).