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Creating a searchable network of Australian

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Improving and protecting our agricultural crops is essential in the face of rising populations and changing climates.

Data are vital in this process, and the complexity of crop growth means there is a pressing need to collect, collate and integrate different types of data on crop composition, function and performance.

The compendium of Crop Proteins with Annotated Locations (cropPAL) is an important new data collation project that draws data from current genome assemblies and predictive computation and links it to experimental biology.

Wheat harvesting at Blyth SA (CSIRO CC-BY)

Using 15 years of crop research, cropPAL provides a leading data resource that defines the location of proteins within crop plant cells. Identifying where proteins function within a cell can play an important role in understanding and controlling plant growth, fruit and seed production and stress tolerance.

The project started in 2015 with the release of cropPAL1, which contained the four most economically important crops: wheat, barley, corn and rice. The compendium has since expanded to 11 plants, with cropPAL2 also including banana, canola, grape wine, potato, soybean, sorghum and tomato.

Users can search over 600 experimental data sets and millions of pre-computed predicted location data.

The AgriConnect collaboration

Building on the success of cropPAL - and with an aim to more broadly combine it with similar ventures in Australia – AgriConnect was born as an Australian-wide collaborative project.

Five major agricultural data-producing universities have come together to combine their agricultural findings and forge connections between previously siloed data collections. In addition to cropPAL, the data collections of the partner institutions include:

  • RNA-seq (tissue specific and time series) for rice and barley experimentation from La Trobe University (expression.latrobe.edu.au)
  • collated experimental data describing membrane transporters and signalling systems in plants from the University of Adelaide (croptips.org)
  • high resolution growth trial images from a variety of plants from the Australian Plant Phenomics Facility (APPF) based at the Australian National University (traitcapture.org)
  • genotyping and yield/growth trait quantification data for Pulses from the Queensland University of Technology (research.qut.edu.au/ngmungbean).

In total, the AgriConnect search platform generates links between genomic, proteomic and phenomic data from more than 14 plant species. Users can access five data collections, beyond descriptive metadata, to enable discovery-based research and draw novel links between genotype and phenotype.

Instant multi-database access presents a novel and cutting edge way to pursue understanding of complex factors involved in plant growth, crop yield and targeted breeding success.

The result is a unique data advantage for Australia and world leading resources for modernising agricultural breeding.

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