The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)

Authors: ZHANG, LI - University Of Texas At Austin; MACQUEEN, ALICE - University Of Texas At Austin; WENG, XIAOYU - University Of Texas At Austin; BEHRMAN, KATHRINE - University Of Texas At Austin; BONNETTE, JASON - University Of Texas At Austin; REILLEY, JOHN - Natural Resources Conservation Service (NRCS, USDA); ROUGUETTE, FRANCIS - Texas Agrilife Research; Fay, Philip; WU, YANQI - Oklahoma State University; FRITSCI, FELIX - University Of Missouri; Mitchell, Robert - Rob; LOWRY, DAVID - Michigan State University; BOE, ARVID - South Dakota State University; JUENGER, THOMAS - University Of Texas At Austin

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2022
Publication Date: 7/2/2022
Citation: Zhang, L., MacQueen, A., Weng, X., Behrman, K.D., Bonnette, J., Reilley, J.L., Rouguette, F.M., Fay, P.A., Wu, Y., Fritsci, F.B., Mitchell, R., Lowry, D.B., Boe, A.R., Juenger, T.E. 2022. The genetic basis for panicle trait variation in switchgrass (Panicum virgatum). Theoretical and Applied Genetics. 135:2577-2592. https://doi.org/10.1007/s00122-022-04096-x.
DOI: https://doi.org/10.1007/s00122-022-04096-x

Interpretive Summary: The ability of grasses to produce seeds depends in part on the way they arrange their flowers into aggregate structures termed panicles. Seed production is critical in native and domesticated plants because seeds are the harvestable commodity for many crops and they determine the evolutionary fitness and population success in native species. Previous research indicates that both genes and environmental factors contribute to panicle structure, but how these combine to determine panicle structure is not well understood, particularly for switchgrass (Panicum virgatum), a native grass widespread throughout North America and a promising species for bioenergy feedstock production. In this study we analyzed gene expression and panicle structure in switchgrass at ten field sites spanning the north-to-south climatic range of the central U.S. We identified 18 locations in the switchgrass genome that predicted various features of switchgrass seed production, including the number and length of branches in the panicle. Further, we found that these locations were related to flowering time, suggesting joint control of when and how many seeds are produced. These findings can aid breeding to develop switchgrass cultivars with improved seed productivity.

Technical Abstract: Panicle architecture plays a decisive role in determining seed productivity across wild and domesticated grass species. Panicle related traits are known to exhibit quantitative variation controlled by genes (G), the environment (E), and their interaction (G x E). In switchgrass, a potential perennial biofuel crop, identification of quantitative trait loci (QTL) and QTL x E interactions controlling panicle architecture could aid breeding efforts and cultivar development by impacting seed productivity. In this study, we evaluate the genetic architecture of panicle traits including panicle length (PL), primary branching number (PBN), and secondary branching number (SBN) in an outcrossing switchgrass population across ten field sites in the central US. We explored pleiotropic relationships between panicle traits and flowering time, tiller production and biomass. We identified environmental factors correlated with QTL x E interactions and potential candidate genes underlying panicle trait QTL in switchgrass. Our multi-environment mixed QTL model detected 18 QTL for panicle traits. QTL for PL and PBN had more QTL x E than QTL affecting SBN. Twelve of the QTL exhibited consistent effects (i.e., no QTL x E), and over half (4 of 6) of the effects with QTL x E exhibited condition-specific effects. Many of the QTL x E effects were associated with yearly mean temperature, while a limited number of interactions were associated with rainfall or solar radiation. Panicle QTL co-localized with previously identified flowering time QTL and candidate genes associated with flowering, supporting a pleiotropic model of panicle development based on shared developmental genetics and responses to environmental signals.