Key Genes and Genetic Interactions of Plant-Pathogen Functional Modules in Poplar Infected by Marssonina brunnea

Abstract

Marssonina brunnea, the causative pathogen of Marssonina leaf spot of poplars (MLSP), devastates poplar plantations by forming black spots on leaves and defoliating trees. Although MLSP has been studied for over 30 years, the key genes that function during M. brunnea infection and their effects on plant growth are poorly understood. Here, we used multigene association studies to investigate the effects of key genes in the plant-pathogen interaction pathway, as revealed by transcriptome analysis, on photosynthesis and growth in a natural population of 435 Populus tomentosa individuals. By analyzing transcriptomic changes during three stages of infection, we detected 628 transcription factor genes among the 7,611 differentially expressed genes that might be associated with basal defense responses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that transcriptomic changes across different stages of infection lead to the reprogramming of metabolic processes possibly related to defense activation. We identified 29,399 common single-nucleotide polymorphisms (SNPs) within 221 full-length genes in plant-pathogen interaction pathways that were significantly associated with photosynthetic and growth traits. We also detected 4,460 significant epistatic pairs associated with stomatal conductance, tree diameter, and tree height. Epistasis analysis uncovered significant interactions between 2,561 SNP-SNP pairs from different functional modules in the plant-pathogen interaction pathway, revealing possible genetic interactions. This analysis revealed many key genes that function during M. brunnea infection and their potential roles in mediating photosynthesis and plant growth, shedding light on genetic interactions between functional modules in the plant-pathogen interaction pathway.

High-Throughput Sequencing Reveals the Regulatory Networks of Transcriptome and Small RNAs During the Defense Against Marssonina brunnea in Poplar

“…Genes associated with the phenylpropanoid pathway responsible for producing the three lignin monomers called monolignols, such as PAL (Podel.10G229600) and CAD (Podel.16G069500), were induced by M. brunnea at 6 hpi, and HCT (Podel.19G001400), F5H (Podel.07G018500), and POD11 (Podel.10G135900), were significantly upregulated at 24 hpi; and bGL (Podel.01G233500) consuming the intermediate cinnamic acid was downregulated at 24 hpi ( Figure 3 ). Our results were supported by previous studies (Chen et al, 2020 ; von Tiedemann et al, 2021 ). Thus, lignin biosynthesis is intensively accelerated in the poplar defense against a fungal pathogen.…”

Genome-Wide Analysis of Coding and Non-coding RNA Reveals a Conserved miR164–NAC–mRNA Regulatory Pathway for Disease Defense in Populus

“…In the present study, we combined transcriptome and genomic analyses to explore the origin, evolution, functional innovation, and plant defense effects of the poplar miRNAs during the three essential stages of MLSP fungus (M. brunnea) infection, including conidia germinated stage [12 h post-inoculation (hpi)], infective vesicle stage (24 hpi), and intercellular infective hyphae stage (48 hpi), as described in Chen et al (2020). By exploring the origin and evolutionary patterns of poplar miRNAs, our study provides new insight into the feedback regulation mechanism of miRNAs.…”

Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in four Ipomoea species

“…In wheat, a set of differentially expressed transcripts (e.g., TaGLI1 , TaACT1 , and TaSSI2 ) were identified to be involved in glycerol and fatty acid metabolism that were upregulated in response to powdery mildew fungal infection and might contribute to glycerol-3-phosphate (G3P) and oleic acid (OA18:1) accumulation ( Li et al, 2020 ). In poplar, 18 R -genes were significantly upregulated during Marssonina brunnea infection ( Chen S. et al, 2020 ). Therefore, I. batatas stem nematodes and C. fimbriata -responsive NBS-encoding genes identified in the present study may be useful in studying the downstream signal transducers of pathogen sensing proteins in Ipomoea and other related plant species.…”