Assessing European Wheat Sensitivities to Parastagonospora nodorum Necrotrophic Effectors and Fine-Mapping the Snn3-B1 Locus Conferring Sensitivity to the Effector SnTox3.

Rowena C Downie,Nick Gosman,Gemma A Rose,Keith A Gardner,Eiko Furuki,James Cockram,Richard P Oliver,Kar-Chun Tan,Huyen T T Phan,Greg Mellers,Laura Bouvet,Ian J Mackay,Camila Campos Mantello

doi:10.3389/fpls.2018.00881

Abstract

Parastagonospora nodorum is a necrotrophic fungal pathogen of wheat (Triticum aestivum L.), one of the world’s most important crops. P. nodorum mediates host cell death using proteinaceous necrotrophic effectors, presumably liberating nutrients that allow the infection process to continue. The identification of pathogen effectors has allowed host genetic resistance mechanisms to be separated into their constituent parts. In P. nodorum, three proteinaceous effectors have been cloned: SnToxA, SnTox1, and SnTox3. Here, we survey sensitivity to all three effectors in a panel of 480 European wheat varieties, and fine-map the wheat SnTox3 sensitivity locus Snn3-B1 using genome-wide association scans (GWAS) and an eight-founder wheat multi-parent advanced generation inter-cross (MAGIC) population. Using a Bonferroni corrected P ≤ 0.05 significance threshold, GWAS identified 10 significant markers defining a single locus, Snn3-B1, located on the short arm of chromosome 5B explaining 32% of the phenotypic variation [peak single nucleotide polymorphisms (SNPs), Excalibur_c47452_183 and GENE-3324_338, -log10P = 20.44]. Single marker analysis of SnTox3 sensitivity in the MAGIC population located Snn3-B1 via five significant SNPs, defining a 6.2-kb region that included the two peak SNPs identified in the association mapping panel. Accordingly, SNP Excalibur_c47452_183 was converted to the KASP genotyping system, and validated by screening a subset of 95 wheat varieties, providing a valuable resource for marker assisted breeding and for further genetic investigation. In addition, composite interval mapping in the MAGIC population identified six minor SnTox3 sensitivity quantitative trait loci, on chromosomes 2A (QTox3.niab-2A.1, P-value = 9.17-7), 2B (QTox3.niab-2B.1, P = 0.018), 3B (QTox3.niab-3B.1, P = 48.51-4), 4D (QTox3.niab-4D.1, P = 0.028), 6A (QTox3.niab-6A.1, P = 8.51-4), and 7B (QTox3.niab-7B.1, P = 0.020), each accounting for between 3.1 and 6.0 % of the phenotypic variance. Collectively, the outcomes of this study provides breeders with knowledge and resources regarding the sensitivity of European wheat germplasm to P. nodorum effectors, as well as simple diagnostic markers for determining allelic state at Snn3-B1.

Highlights

The necrotrophic pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley, and Crous is the causal agent of the disease septoria nodorum blotch (SNB) and glume blotch in wheat (Triticum aestivum L.), a disease of significant economic importance in Australia, Europe, North America, and Northern Africa (Friesen et al, 2005; Oliver et al, 2012; Quaedvlieg et al, 2013)
To investigate gene content at the Snn3-B1 locus on chromosome 5B, the sequences containing the most significant single nucleotide polymorphism (SNP) identified in the association mapping (AM) panel (−log10P > 16, seven SNPs) and the multi-parent advanced generation inter-cross (MAGIC) population by SAM (−log10P > 16, effect > 1, five SNPs) were aligned to the IWGSC RefSeq v1.0 wheat reference genome
The seven SNPs from the AM panel delineated a physical region of 326 kb (∼6.648–6.975 Mb), while the five MAGIC SNPs delineated physical regions of 6.2 kb (6.648–6.654 Mb), located within the physical interval as defined in the AM panel

Summary

Introduction

The necrotrophic pathogen Parastagonospora (synonyms: Septoria, Stagonospora, Phaeosphaeria) nodorum (Berk.) Quaedvlieg, Verkley, and Crous is the causal agent of the disease SNB and glume blotch in wheat (Triticum aestivum L.), a disease of significant economic importance in Australia, Europe, North America, and Northern Africa (Friesen et al, 2005; Oliver et al, 2012; Quaedvlieg et al, 2013). The visual symptoms of SNB are chlorosis and necrosis of the leaf tissue, as well as discoloration of the glumes, often in the form of lesions (Solomon et al, 2006). The necrotic response in the sensitive host is hypothesized to facilitate pathogen colonization, promoting infection and providing a rich nutrient source, via cell death (Oliver and Solomon, 2010; Vincent et al, 2012). This is known as effector-triggered susceptibility and is genetically induced via an “inverse gene for gene system” (Friesen et al, 2007). Targeted breeding could be used to eliminate host sensitivity on an effector by effector basis

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Results

Conclusion