Genome-wide association study for deoxynivalenol production and aggressiveness in wheat and rye head blight by resequencing 92 isolates of Fusarium culmorum

Abstract

Background Fusarium culmorum is an important pathogen causing head blight of cereals in Europe. This disease is of worldwide importance leading to reduced yield, grain quality, and contamination by mycotoxins. These mycotoxins are harmful for livestock and humans; therefore, many countries have strict regulatory limits for raw materials and processed food. Extensive genetic diversity is described among field populations of F. culmorum isolates for aggressiveness and production of the trichothecene mycotoxin deoxynivalenol (DON). However, the causes for this quantitative variation are not clear, yet. We analyzed 92 isolates sampled from different field populations in Germany, Russia, and Syria together with an international collection for aggressiveness and DON production in replicated field experiments at two locations in two years with two hosts, wheat and rye. The 30x coverage whole-genome resequencing of all isolates resulted in the identification of 130,389 high quality single nucleotide polymorphisms (SNPs) that were used for the first genome-wide association study in this phytopathogenic fungus. Results In wheat, 20 and 27 SNPs were detected for aggressiveness and DON content, respectively, of which 10 overlapped. Additionally, two different SNPs were significantly associated with aggressiveness in rye that were among those SNPs being associated with DON production in wheat. Most of the SNPs explained only a small proportion of genotypic variance (pG), however, four SNPs were associated with major quantitative trait loci (QTLs) with pG ranging from 12 to 48%. The QTL with the highest pG was involved in DON production and associated with a SNP most probably located within the Tri4 gene. Conclusions The diversity of 92 isolates of F. culmorum were captured using a heuristic approach. Key phenotypic traits, SNPs, and candidate genes underlying aggressiveness and DON production were identified. Clearly, many QTLs are responsible for aggressiveness and DON content in wheat, both traits following a quantitative inheritance. Several SNPs involved in DON metabolism, among them the Tri4 gene of the trichothecene pathway, were inferred as important source of variation in fungal aggressiveness. Using this information underlying the phenotypic variation will be of paramount importance in evaluating strategies for successful resistance breeding.

Pathogenicity and mycotoxin profile of Fusarium spp. inducing wheat head blight in Algeria

“…Similar analysis on F. culmorum strains collected from various cropping areas of North Algeria showed 75% of strains were able to produce a signi cant content of DON that reached 80000µg/kg, also exceeding EC limits. DON levels in F. culmorum detected in this work (62239µg/kg mean) were typically higher than the mean value for DON levels in wheat (12300µg/kg) (Miedaner et al, 2021). It's worth noting the potential threat that could jeopardize human safety.…”

The Genomic Variation and Differentially Expressed Genes on the 6P Chromosomes in Wheat–Agropyron cristatum Addition Lines 5113 and II-30-5 Confer Different Desirable Traits

“…Resequencing of 145 landmark cultivars revealed asymmetric subgenome selection and strong founder genotype effects on wheat breeding in China [ 67 ]. Whole-genome resequencing of 92 isolates of Fusarium culmorum resulted in the identification of 130,389 high-quality SNPs that were used for the first genome-wide association study in this phytopathogenic fungus [ 68 ]. Whole-genome resequencing of 968 bread wheat and its progenitors helped establish the Wheat Genome Variation Database (WGVD), an integrated web database including genomic variations and selective signatures [ 69 ].…”

Fusarium culmorum Produces NX-2 Toxin Simultaneously with Deoxynivalenol and 3-Acetyl-Deoxynivalenol or Nivalenol

“…For instance, an increase in the 3-ADON chemotype at locations where 15-ADON producers used to be predominant was reported in a study from North America [ 49 ]. Many studies of the population structure in F. graminearum elucidated the relationship between genotype, chemotype, and aggressiveness, aiming to explain how selection and gene flow shaped the populations (e.g., [ 17 , 20 , 35 , 41 , 46 , 49 , 50 , 51 , 52 ]). Field studies documented the success of the 3-ADON chemotype of F. graminearum, but they could not address its cause, which requires a biochemical approach.…”