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 Protocol | Type | Description | Potential / Known IP | Reference | Contact |
|---|---|---|---|---|---|
| A method to screen for Energy Use Efficiency | Field Phenotyping | Hyperspectral signatures can be used as a proxy to predict leaf respiration and an opportunity to screen for energy use efficiency (EUE) | None | metabolome-express | barry.pogson@anu.edu.au |
| 12Mb Capture Design for wheat genotyping and allele mining | Genotyping | 90% 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. | None | anthony.hall@earlham.ac.uk | |
| Biomass prediction | Field Phenotyping | A multiple linear model combining NDVI, Canopy Temperature and Phenology to predict biomass | None | g.molero@cgiar.org |
|
| Parbars | Field Phenotyping | High throughput low cost light measurement | None | Salter 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 Experiments | andrew.merchant@sydney.edu.au |
| Octoflux | Field Phenotyping | High throughput low cost gas exchange system | None | andrew.merchant@sydney.edu.au |
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| HT Chlorophyll Flourescence screen | Lab Phenotyping | Rapid screening of germplasm for photosynthesis and photoprotection | None | erik.murchie@nottingham.ac.uk |
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| Whole plant gas exchange system | Lab Phenotyping | Rapidly and accurately measures water use efficiency | None | Jauregui 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 screen | Field Phenotyping | High throughput phenotyping in field trials | None | richard.richards@csiro.au | |
| Wheat Expression Browser | Expression analysis | Wheat Expression Browser with over 1,000 RNA-Seq datasets mapped to the RefSeqv1.1 gene models | None | Expression Browser | cristobal.uauy@jic.ac.uk |
| Wheat eFP Expression Browser | Expression analysis | Visualisation of 210 RNA-Seq datasets in spring cultivar Azhurnaya | None | eFP Expression Browser | cristobal.uauy@jic.ac.uk |
| Wheat Training | Website | Wheat traning website to help researchers interested in wheat navigate the different datasets and repositories available. | None | Wheat Training | cristobal.uauy@jic.ac.uk |
| Wheat co-expression networks | Co-expression networks | Co-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. | None | knetminer | cristobal.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 | None | eakhunov@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 genome | eakhunov@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 | MTA | eakhunov@ksu.edu | |
| Stomatal conductance screen | Lab Phenotyping | Methodology for screening dynamic shifts in stomatal conductance | None | Silvere 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/erz068 | tlawson@essex.ac.uk |
| Photosynthetic induction in the Field | Field Phenotyping | High-throughput protocol to screen for photosynthetic induction in the field using PhotosynQ | None | e.carmosilva@lancaster.ac.uk | |
| GRF4-GIF1 transformation technology | Lab transformation | New transformation technology using a chimeric protein including the wheat (GRF4) and its cofactor (GIF1) | Likely | Debernardi, J.M., Tricoli, D.M., Ercoli, M.F. et al. A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nat Biotechnol 38, 12741279 (2020). https://doi.org/10.1038/s41587-020-0703-0 | jdubcovsky@ucdavis.edu |