Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel

Trehalose 6-phosphate (T6P) signalling regulates carbon use and allocation and is a target to improve crop yields. However, the specific contributions of trehalose phosphate synthase (TPS) and trehalose phosphate phosphatase (TPP) genes to source- and sink-related traits remain largely unknown. We used exome-capture sequencing on TPS and TPP genes to estimate and partition the genetic variation of yield-related traits in a spring wheat (Triticum aestivum) breeding panel with diverse genetic heritage. Twelve phenotypes were directly correlated to TPS and TPP genes including final biomass (source) and spikes and grain numbers and grain filling traits (sink) showing indications of both positive and negative gene selection. Additionally, individual genes explained a substantial proportion of heritability (e.g. 3, 12, and 18% of the variance in gene homeologues most closely related to Arabidopsis TPS1 for final biomass), indicating a considerable contribution of this regulatory pathway to the phenotypic variation. Most importantly, two significant missense point mutations in the exon 6 of the TPS1 gene on chromosome 1D substantially increased plant height and peduncle length which was inversely related to grains per m2. Gene-based prediction resulted in significant gains of predictive ability (6% improvement) for grain weight when gene effects were combined with the whole genome markers, potentially helping breeding programs in designing strategic crosses. Three TPS1 homeologues were particularly significant in trait variation. Our study has generated a wealth of information on the role of natural variation of TPS and TPP genes related to yield potential.