QTL x environment interactions for panicle traits in switchgrass (Panicum virgatum)

Panicle traits exhibit quantitative variation controlled by genes, the environment, and their interaction. In switchgrass, a 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, primary branching number, and secondary branching number in an outcrossing switchgrass population grown across ten field sites in the central United States. We evaluated pleiotropic relationships between panicle traits and flowering time, tiller production and biomass. We also identified environmental factors correlated with QTL x E interactions and potential candidate genes underlying panicle trait QTL in switchgrass. Overall, our multi-environment mixed QTL model detected 18 QTL for panicle traits. Twelve of the QTL exhibited consistent effects (i.e., no QTL x E), and most (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 and photoperiod. 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.