Abstract
Sclerotinia stem rot is a major disease in Brassica napus that causes yield losses of 10–20% and reaching 80% in severely infected fields. SSR not only causes yield reduction but also causes low oil quality by reducing fatty acid content. There is a need to identify resistant genetic sources with functional significance for the breeding of SSR-resistant cultivars. In this study, we identified 17 QTLs involved in SSR resistance in three different seasons using SNP markers and disease lesion development after artificial inoculation. There were no common QTLs in all 3 years, but there were three QTLs that appeared in two seasons covering all seasons with a shared QTL. The QTLs identified in the 2 years were SRA9a, SRC2a and SRC3a with phenotypic effect variances of 14.75 and 11.57% for SRA9a, 7.49 and 10.38% for SRC3a and 7.73 and 6.81% for SRC2a in their 2 years, respectively. The flowering time was also found to have a negative correlation with disease resistance, i.e., early-maturing lines were more susceptible to disease. The stem width has shown a notably weak effect on disease development, causing researchers to ignore its effect. Given that flowering time is an important factor in disease resistance, we used comparative RNA-sequencing analysis of resistant and susceptible lines with consistent performance in 3 years with almost the same flowering time to identify the resistance genes directly involved in resistance within the QTL regions. Overall, there were more genes differentially expressed in resistant lines 19,970 than in susceptible lines 3936 compared to their mock-inoculated lines, demonstrating their tendency to cope with disease. We identified 36 putative candidate genes from the resistant lines that were upregulated in resistant lines compared to resistant mock and susceptible lines that might be involved in resistance to SSR.
Highlights
Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic and non-host-specific fungal pathogen that infects more than 400 plant species, including several valuable oil crops, such as oilseed rape, soybean, and sunflower (Purdy, 1979; Boland and Hall, 1994)
The heritability for Sclerotinia stem rot (SSR) resistance is as high as 68.36% (Table 2), indicating that the phenotype is primarily attributable to genetic factors with less environmental effects
One of the TIR-NBS-LRR class genes, BnaC03g05380D, present in the quantitative trait loci (QTL) region of SRC3a, was differentially expressed in R plants compared to R-mock plants at 48 hpi with a log2 foldchange of more than 1, and its expression was entirely absent in S plants at all time points with a log2FC of almost 10 at each time point
Summary
Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic and non-host-specific fungal pathogen that infects more than 400 plant species, including several valuable oil crops, such as oilseed rape, soybean, and sunflower (Purdy, 1979; Boland and Hall, 1994). Many techniques have been developed to identify the genes, genetic networks, and genome regions contributing for the traits Some of these techniques have been applied for the identification of resistant genetic resources against Sclerotinia stem rot (SSR) in Brassica napus. Comparative transcriptomic studies revealed a network of genes involved in resistance to SSR when differential gene expression was studied (Wu et al, 2016b) Despite all these efforts to identify sources of resistance, there is still a gap for having a firm genetic source of resistance against SSR, and more studies are needed to achieve complete genetic control over the disease
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