Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

Authors: VANWALLENDAEL, ACER - Michigan State University; BONNETE, JASON - University Of Texas At Austin; JUENGER, THOMAS - University Of Texas At Austin; FRITSCHI, FELIX - University Of Missouri; Fay, Philip; Mitchell, Robert - Rob; LLOYD-REILLEY, JOHN - Natural Resources Conservation Service (NRCS, USDA); ROUQUETTE JR, FRANCIS - Texas Agrilife Research; BERGSTROM, GARY - Cornell University; LOWRY, DAVID - Michigan State University

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2020
Publication Date: 8/18/2020
Citation: VanWallendael, A., Bonnete, J., Juenger, T.E., Fritschi, F.B., Fay, P.A., Mitchell, R.B., Lloyd-Reilley, J., Rouquette Jr., F.M., Bergstrom, G.C., Lowry, D.B. 2020. Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum). New Phytologist. 227(6):1696-1708. https://doi.org/10.1111/nph.16555.
DOI: https://doi.org/10.1111/nph.16555

Interpretive Summary: Pathogens play an important role in the evolution of plant populations and in agricultural yield, but genetic mechanisms underlying plant resistance to pathogens varies greatly across space and time. This study examined locally adapted forms of the widespread native perennial grass, switchgrass (Panicum virgatum), to identify genes conferring resistance to rust fungi in switchgrass in eight experimental plantings from Michigan to south Texas. Our results show that different genes may provide rust resistance in northern plantings compared to southern plantings. Fundamentally, this result highlights the role of plant pathogens the evolution of local switchgrass populations. Practically, it provides a first step that identifies important locations on the switchgrass genome that may allow for more effective breeding strategies for rust resistance. Further work should attempt to identify if rust resistance in switchgrass comes with trade-offs in other traits, such as cold tolerance.

Technical Abstract: Pathogens play an important role in the evolution of plant populations, but genetic mechanisms underlying disease resistance may differ greatly between geographic areas as well as over time. Local adaptation is thought to be an important step in plant evolution, and may be impacted by differential pathogen pressures in concert with abiotic factors. This study uses locally adapted ecotypes of the native perennial switchgrass (Panicum virgatum) to examine the temporal and spatial variation in the genetic architecture of resistance to fungal pathogens, namely switchgrass leaf rust (Puccinia novopanici). To identify loci underlying variation in pathogen resistance in switchgrass, we scored rust damage across an outcrossed mapping population at eight locations across the central United States from southern Texas to Michigan. We followed rust progression at these sites for three years and mapped quantitative trait loci (QTLs) using function-valued transformations of rust progression curves. Overall, we mapped 51 QTLs that varied in presence and strength over the three-year period. Two large-effect QTLs were consistently associated with variation in rust progression in multiple sites and years, and are therefore potentially the result of the same underlying resistance genes. Interestingly, these two large-effect QTLs were almost exclusively detected in northern sites. This pattern could be caused by geographic difference in genetic architecture is due to variation in the distribution of rust strains or variation in climatic conditions across the field sites could result in genotype-by-environment interactions in efficacy of rust resistance loci. Beyond reducing rust damage by 34%, the beneficial alleles at the two loci also increased biomass by 44%, suggesting a direct benefit by pleiotropy or indirect benefit through genetic linkage. Our results suggest an important role for fungal pathogens in the local adaptation of switchgrass and illustrate an influential geographic component of the genetic architecture of plant disease resistance.