Genome-wide association study of maize resistance to Pythium aristosporum stalk rot

Genome-wide association study for resistance to Macrophomina phaseolina in maize (Zea mays L.)

Maize (Zea mays L.) is a frequently used food source in human and animal nutrition. Macrophomina phaseolina is a fungal pathogen causing charcoal rot disease in many plants, especially maize. This pathogen causes high yield losses in maize. The development of resistant maize genotypes is of great importance in controlling this disease. In this study, the population structure of 120 different maize genotypes with varying levels of disease resistance was determined and genome-wide association studies were performed. Each genotype was subjected to the pathogen under controlled conditions and their phenotypic responses to the disease were analyzed. Afterwards, single nucleotide polymorphisms were determined by DArT-seq sequencing. After filtering the SNP data, 37,470 clean SNPs were obtained. The population structure was analyzed with STRUCTURE software, and it was determined that the population was divided into two subgroups. The relationship between phenotypic and genotypic data was analyzed using the MLM (Q + K) model in TASSEL software. As a result, seven SNPs markers located on four different chromosomes were associated with disease resistance. The related markers can be used in the future for the development of maize varieties resistant to M. phaseolina by marker-assisted selection.

An assessment of the species diversity and disease potential of Pythium communities in Europe

Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.

Transcriptomic and Metabolomic Analyses Reveal the Role of Phenylalanine Metabolism in the Maize Response to Stalk Rot Caused by Fusarium proliferatum

Stalk rot is a prevalent disease of maize (Zea mays L.) that severely affects maize yield and quality worldwide. The ascomycete fungus Fusarium spp. is the most common pathogen of maize stalk rot. At present, the molecular mechanism of Fusarium proliferation during the maize stalk infection that causes maize stalk rot has rarely been reported. In this study, we investigated the response of maize to F. proliferatum infestation by analyzing the phenotypic, transcriptomic, and metabolomic data of inbred lines ZC17 (resistant) and CH72 (susceptible) with different levels of resistance to stalk rot. Physiological and phenotypic results showed that the infection CH72 was significantly more severe than ZC17 after inoculation. Transcriptome analysis showed that after inoculation, the number of differentially expressed genes (DEGs) was higher in CH72 than in ZC17. Nearly half of these DEGs showed the same expression trend in the two inbred lines. Functional annotation and enrichment analyses indicated that the major pathways enriched for DEGs and DEMs included the biosynthesis of plant secondary metabolites, phenylalanine metabolism, biosynthesis of plant hormones, and plant-pathogen interactions. The comprehensive analysis of transcriptome and metabolome data indicated that phenylalanine metabolism and the phenylalanine, tyrosine, and tryptophan biosynthesis pathways played a crucial role in maize resistance to F. proliferatum infection. In addition, a transcription factor (TF) analysis of the DEGs showed that several TF families, including MYB, bHLH, NAC, and WRKY, were significantly activated after inoculation, suggesting that these TFs play important roles in the molecular regulatory network of maize disease resistance. The findings of this study provide valuable insights into the molecular basis of the response of maize to Fusarium proliferatum infection and highlight the importance of combining multiple approaches, such as phenotyping, transcriptomics, and metabolomics, to gain a comprehensive understanding of plant-pathogen interactions.