H2 Statements on Progress of ARC-Funded Projects
Project ID: LP140100572
First Named Investigator: Justin Borevitz
Scheme Name: Linkage Projects
Project Title: TraitCapture: Genomic modelling for plant phenomics under environmental stress
- Identification of composite phenotypes that constitute heritable genetic traits;
- Determination of the genetic architecture allowing phenotypic prediction;
- Modelling of the interaction with the environment to select optimal genotypes.
Progress: Project start was delayed until April 2015 due to contract negotiations.
- Riyan Cheng - Statistical Geneticist (Level B, Employed 04/2015-04/2016); Developing software to integrate hi-resolution phenotyping data into standard GWAS and QTL pipelines and visualize results
- Computer Vision Specialist (Level A): In collaboration with the ANU Centre of Excellence for Robotic Vision. Sarah Namin (4/2016-4/2018) is working on recursive neural network based machine learning genotype classification of time lapse images.
- Tim Brown - Project management and oversight (Level B, Employed 04/2015-1/2016)
- Contract arabidopdis experiments with ANU plant phenomics to generate data.
- PhD student: Tepsuda (Keng) Rungrat. Genetic basis of natural variation in photoprotection in Arbidopsis.
- Undergrads and support staff (part time):
- Gareth Dunstone: Website, camera control, point cloud visualization
- Jordan Braiuka: Data management and image processing tools for high throughput ingest of terrabytes of image data (supported automated ingest of >150,000 images from multiple projects and varied camera types)
- Zac HatfieldDodds: Automation of 3D reconstruction; automating point cloud creation, analysis & visualization
- Contractors: Joel Granados (Kamay Consultants; part time, 04/2015 ) - provide ongoing support and development for the image processing pipeline while we hire the CV post doc.
- Visiting Sabbatical Scientist: Professor Olivier Loudet (INRA, France) 4 months.
- Partner Organization Scientist has made two 3-month visits for collaboration and upgrades to PlantScreen
Equipment, hardware and software
- Development (ongoing) of web services, data management and project website supporting both the TraitCapture project and providing an open platform for other phenomics projects in Australia including the Supersites network.
- Phenocam website currently supports dynamic visualization of any time-series image data, basic project management and scheduling, and realtime monitoring and remote management of all phenotyping cameras. Realtime visualization of time-series images from all current and historic experiments will be implemented by late December.
- Arabidopsis 1) Two Global Diversity experiments were performed in simulated Autumn inland and coastal conditions (300 genotype each). Plants were grown/imaged for 8 weeks in the Spectral Pheno Climatron and scanned weekly in PlantScreen. Non-Photochemical Quenching was analyzed in a Genome Wide Association Study (GWAS) and NPQ4 was identified as a major QTL. Growth analysis is under way. 2) Pilot experiment (Olivier Loudet) used PlantScan to continuously grow and scan plants for 5 weeks across 5 levels of calibrated drought treatments to calculate GxE on water use efficient growth.
- Brachypodium 1) Subset of 75 diverse diploid genotypes were grown & imaged in simulated autumn conditions in 2015 and 2050 in the Spectral Pheno Climatron for the full life cycle of 7 months. PlantScreen was also used to measure photosynthetic traits at early developmental stages. GWAS is in progress. 2) A heritability study of early vigour traits and their relationship with photosynthetic traits was undertaken in a set of 8 highly replicated lines using PlantScreen and manual measurements. 3) Pilot study of drought tolerance and high light stress tolerance in 4 highly replicated genotypes was undertaken using PlantScreen for watering and weighing as well as monitoring photosynthetic traits. 4) Growth of 96 accessions in triplicate across spring and fall seasons simulated across Turkey for full life cycle of 7 months. Growth traits measured by hand and tissue harvested for GWAS and methylation studies.
- Brown, Tim B., et al. TraitCapture: genomic and environment modelling of plant phenomic data. (2014). Current opinion in plant biology 18 (2014): 73-79.
- Brown, Tim B. et al, (2016) Using phenocams to monitor our changing Earth: towards a global phenocam network. Frontiers in Ecology and the Environment
- PB Wilson, J Streich, J Borevitz, Genomic Diversity and Climate Adaptation in Brachypodium (Cold Spring Harbor Labs Journals (2016)
- Rungrat T, Awlia M, Brown T, Cheng R, Sirault X, Fajkus J, Trtilek M, Furbank B, Badger M, Tester M, Pogson B, Borevitz JO, Wilson P Using phenomic analysis of photosynthetic function for abiotic stress response gene discovery. The Arabidopsis Book (2016)
- we will focus on (1) automating the analysis pipeline to provide real-time phenotyping data for analysis, (2) automating and integrating the genomic analysis with the phenotyping data; (3) additional exploratory experiments to identify traits for further analysis with targeted experiments