The genetics of pathogen and microbiome control in the switchgrass leaf
Authors: Acer VanWallendael 1; Gian M. N. Benucci 1; Pedro B. da Costa 1; Linnea Fraser 1; Avinash Sreedasyam 2; Felix Fritschi 4; Thomas Juenger 3; John Lovell 2; Gregory Bonito 1; David Lowry 1
Affiliations: 1) Michigan State University, East Lansing, MI; 2) HudsonAlpha Institute of Biotechnology, Huntsville, AL; 3) University of Texas, Austin, TX; 4) University of Missouri, Columbia, MO
Keywords: Complex traits
Leaf fungal microbes can be fundamental drivers of host plant success, as they consist of pathogens that devastate crop plants as well as taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. In a replicated diversity panel of biofuel switchgrass, we quantified genetic and environmental variation in leaf fungal relationships, both for the whole microbiome and for a specific pathogen, leaf rust. While fungal colonization of the leaf varies over space and time, we uncovered genome-wide associations (GWAs) with several informative loci. In particular, three cysteine-rich receptor-like kinase genes (crRLKs) were linked to a genetic locus associated with microbiome structure. Since each of these genes is consistently upregulated in switchgrass genotypes typically more susceptible to fungal disease, we conclude that they may play a central role in the plant’s response to pathogens. Response to leaf rust is polygenic and environmentally sensitive, but resistance alleles are associated with higher biomass, indicating that breeding for rust-resistant plants will benefit growth without trade-offs in the absence of rust. Switchgrass response to fungal colonists is complex and variable, but an experimental design that accounts for variation over space and time allows for greater definition on genetic loci underlying fungal interactions.