Tools and protocols

Tools and protocols developed as part of the IWYP Science Program fall into several categories. These include tools for field phenotyping, phenotyping under controlled conditions such as laboratory and glasshouse, tools to facilitate large-scale genotyping studies and online tools for computationally intensive analyses or interrogating databases. The listing in the table below provides the name of the tool or protocol, what category it is, followed by a brief description of the tool itself. In addition, and where possible, a link to an article is provided where more information can be found with also the contact details of the developer where requestors can direct their queries.



Tool or ProtocolTypeDescriptionPotential / Known IPReferenceContact
A method to screen for Energy Use EfficiencyField PhenotypingHyperspectral signatures can be used as a proxy to predict leaf respiration and an opportunity to screen for energy use efficiency (EUE)Nonemetabolome-expressbarry.pogson@anu.edu.au
12Mb Capture Design for wheat genotyping and allele miningGenotyping90% of probes distributed evenly across the wheat genome (including the Breeders' 35K Axiom Array to maintain legacy). The remaining 10% of probes tiled across key genes in photosynthesis and biomass accumulation, including promoter regions. In collaboration with Arbor Bioscience.Noneanthony.hall@earlham.ac.uk
Biomass predictionField PhenotypingA multiple linear model combining NDVI, Canopy Temperature and Phenology to predict biomassNoneg.molero@cgiar.org
ParbarsField PhenotypingHigh throughput low cost light measurementNoneSalter W. T, Merchant A, Gilbert M. E, Buckley T. N., (2018) PARbars: cheap, easy to build ceptometers for continuous measurement of light interception in plant canopies. Journal of Visualized Experimentsandrew.merchant@sydney.edu.au
OctofluxField PhenotypingHigh throughput low cost gas exchange systemNoneandrew.merchant@sydney.edu.au
HT Chlorophyll Flourescence screenLab PhenotypingRapid screening of germplasm for photosynthesis and photoprotectionNoneerik.murchie@nottingham.ac.uk
Whole plant gas exchange systemLab PhenotypingRapidly and accurately measures water use efficiencyNoneJauregui I, Rothwell SA, Taylor SH, Parry MAJ, Carmo-Silva E, Dodd IC (2018) Whole plant chamber to examine sensitivity of cereal gas exchange to changes in evaporative demand. Plant Methods 14:97.i.dodd@lancaster.ac.uk
Canopy architecture screenField PhenotypingHigh throughput phenotyping in field trialsNonerichard.richards@csiro.au
Wheat Expression BrowserExpression analysisWheat Expression Browser with over 1,000 RNA-Seq datasets mapped to the RefSeqv1.1 gene modelsNoneExpression Browsercristobal.uauy@jic.ac.uk
Wheat eFP Expression BrowserExpression analysisVisualisation of 210 RNA-Seq datasets in spring cultivar AzhurnayaNoneeFP Expression Browsercristobal.uauy@jic.ac.uk
Wheat TrainingWebsiteWheat traning website to help researchers interested in wheat navigate the different datasets and repositories available. NoneWheat Trainingcristobal.uauy@jic.ac.uk
Wheat co-expression networksCo-expression networksCo-expression networks of over 850 RNA-Seq samples. This also includes Genie3 directed network of transcription factors to identify putative downstream targets for transcription factors.Noneknetminercristobal.uauy@jic.ac.uk
(KNetMiner developed by Keywan Hassani-Pak from Rothamsted Research)
Nimblegene regulatory capture assay
Genotyping
Designed to capture 2 kb upstream of most of the genes in wheat genome
Noneeakhunov@ksu.edu
1000 wheat exome genotyping data
Diverse collection of wheat lines and landraces
Lines selected to represent maximum diversity of wheat worldwide; genotypes usng 300 Mb capture assay (Jordan et al., 2015)
None
Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genomeeakhunov@ksu.edu
Bobwhite expressing gene editing constructs for yield component genes
Gene editing
Transgenic plant express gene editing constructs that can be used for editing other wheat lines
MTAeakhunov@ksu.edu
Stomatal conductance screenLab PhenotypingMethodology for screening dynamic shifts in stomatal conductanceNoneSilvere Vialet-Chabrand, Tracy Lawson, Dynamic leaf energy balance: deriving stomatal conductance from thermal imaging in a dynamic environment. Journal of Experimental Botany, erz068, https://doi.org/10.1093/jxb/erz068tlawson@essex.ac.uk