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

Abstract

<jats:title>Summary</jats:title><jats:p>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 (<jats:italic>Triticum aestivum</jats:italic>) 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 <jats:italic>TPS1</jats:italic> 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 <jats:italic>TPS1</jats:italic> gene on chromosome 1D substantially increased plant height and peduncle length which was inversely related to grains per m<jats:sup>2</jats:sup>. 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 <jats:italic>TPS1</jats:italic> 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.</jats:p>

Trehalose 6-phosphate signalling and impact on crop yield

“…OsTPP1 overexpression in maize improves grain numbers and yield under drought at flowering [13]. Wheat TPSs and TPPs have been linked to several traits [45]. Those listed here are significantly linked to yield related traits in [45].…”

“…Wheat TPSs and TPPs have been linked to several traits [45]. Those listed here are significantly linked to yield related traits in [45]. GM2 is grains per m 2 ; PH is plant height; GFR is grain filling rate; SM2 is spikes per m 2 ; GWSP is grain weight per spike; SpS is spikelets per spike; InfSpS is infertile spikelets per spike.…”

“…SWEET transporters may be important downstream targets for the regulation of sucrose allocation [19]. Wide ranging traits in four food security cereals are associated with T6P as seen through transgenic modification in maize and rice [13,24], natural genetic variation in wheat [43,45], rice [26] and sorghum [40] and chemical intervention with T6P precursors in wheat [42].…”

“…Up until now a comprehensive evaluation of genetic variation in TPS and TPP genes and link to traits had yet to be performed for a major crop. Lyra et al [45] used exome-capture sequencing on TPS and TPP genes from [46] to estimate and partition the genetic variation of yield-related traits in a spring wheat high biomass associated breeding panel (HiBAP [47]). Two analyses were carried out with the sequences of TPS and TPP genes to look for associations with several traits measured on the same population at the gene-level and at the level of SNPs within these genes.…”

“…• Importance of T6P signalling in crops: For the improvement of crop yields there are likely to be few individual genes that can be targeted, yet for T6P signalling there are examples of several TPS and TPP genes that underlie yield traits [13,25,43,45]. Further confirmation of T6P as a major regulator of yield was shown where increasing T6P chemically in wheat improved grain size and growth recovery from drought [42].…”