Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis

Abstract

Sclerotinia head rot (SHR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating sunflower crop diseases. Despite its worldwide occurrence, the genetic determinants of plant resistance are still largely unknown. Here, we investigated the Sclerotiniasunflower pathosystem by analysing temporal changes in gene expression in one susceptible and two tolerant inbred lines (IL) inoculated with the pathogen under field conditions. Differential expression analysis showed little overlapping among ILs, suggesting genotype-specific control of cell defense responses possibly related to differences in disease resistance strategies. Functional enrichment assessments yielded a similar pattern. However, all three ILs altered the expression of genes involved in the cellular redox state and cell wall remodeling, in agreement with current knowledge about the initiation of plant immune responses. Remarkably, the over-representation of long non-coding RNAs (lncRNA) was another common feature among ILs. Our findings highlight the diversity of transcriptional responses to SHR within sunflower breeding lines and provide evidence of lncRNAs playing a significant role at early stages of defense. Sunflower is one of the most important crops for the production of high-quality oil and seeds consumed by both humans and livestock. In recent years, sunflower production showed a steady increase driven by a boost in sunflower oil consumption (FAO, 2017). However, the projected expansion of the sunflower oil market requires appropriate agronomic management and improved genetic resources to cope with abiotic and biotic stresses. Among the latter, special attention should be paid to fungal diseases, as they have the greatest impact on yield and seed quality 1. The necrotrophic fungus Sclerotinia sclerotiorum is the causal agent of Sclerotinia head (SHR) and stalk (SSR) rots in sunflower. In particular, SHR is a recurrent disease in sunflower-growing areas worldwide. It affects oil quality and, under favourable conditions, may lead to total production loss 1,2. Chemical fungicides proved to be ineffective and breeding of resistant genotypes has emerged as the most promising control strategy 3. So far, there is no evidence of any major gene controlling the resistance to SHR in sunflower. Instead, inbred lines (ILs) show a broad range of responses in accordance with quantitative disease resistance (QDR) patterns depending on the genotype 4-8. During the last 20 years, QTL mapping techniques have been used to unravel the complexity of the defense response to both SHR and SSR in sunflower. Biparental mapping has led to the discovery of several main effect loci and epistatic interactions 9-11 , whereas association mapping has served to identify candidate genes

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

“…Changes in calcium concentration are sensed by proteins, such as calmodulin, which affects the plant’s ability to respond to pathogens [ 77 ]. Interestingly, LOC110926044 was reported as differentially expressed in sunflower after artificial inoculation with S. sclerotiorum [ 78 ], in the partially resistant inbred line RK416. In addition, a gene encoding a putative Rho-associated protein was also identified (LOC110920635, near SNP X1907, associated with PSC-DS).…”

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“…By comparing the gene expression patterns of plants that are resistant or susceptible to a particular pathogen, researchers can identify key players in plant defense responses and study their functions. RNA-seq is a powerful tool for exploring the genetics of plant-pathogen interactions and identifying genes involved in plant defense responses (Fass et al 2020). It provides valuable insights into the mechanisms by which plants resist or succumb to diseases.…”

Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview

“…This is helpful in organisms with a limited genome and some non-model lacking reference genes (Strickler et al, 2012 ). RNA-seq has been used in many oilseeds like in canola (Jiang et al, 2013 ), soybean (Kim et al, 2011 ; Ding et al, 2020 ), oil palm (Shearman et al, 2013 ), sunflower (Fass et al, 2020 ), and groundnut (Chen et al, 2013 ). Phylogenetic, collinearity, and multi-plesynteny analyses exhibited dispersed, segmental, proximal, and tandem gene duplication events in the HSF gene family.…”