- In 1996, Andrzej Kilian, then director of Genomics at CAMBIA, recognised that genotyping technologies developed to explore the human genome were not universally relevant or applicable to agriculture.
- Cost, technical constraints and excessive centralisation of control and capital prevented these technologies from having a significant impact on plant breeding and germplasm management. A concept of DArT technology was developed.
- New high-throughput technology platforms such as the Genetic Microsystems microarray system became available.
- The concept of diversity detection on low cost microarray was developed to circumvent the limitations of human-centred technologies and to make high-throughput genotyping available for the benefit of all genomes.
- Following the successful proof of concept work (Jaccoud et al. 2001, NAR), the DArT P/L company was established in 2001 by Andrzej Kilian and Eric Huttner.
- DArT received its initial assistance from CAMBIA, the Biotechnology Innovation Fund of the Australian Federal Government, and the ACT Government.
- One of the first truly automated microarray data extraction software tools, DArTSOFT (Cyril Cayla) was developed.
- Data extracted was linked to the DArTdb database and Laboratory Information Management System (LIMS) (Grzegorz Uszynski).
- Australia’s grains industry expressed continued interest in the technology and invested in DArT through its Research and Development body (GRDC), enabling the speedy development of DArT for barley and wheat.
- The formation of Triticarte Pty Ltd, a joint venture between the Cooperative Research Centre for Value Added Wheat (VAWCRC) and DArT P/L delivered commercially the DArT genotyping services for wheat and barley until 2009.
- After the termination of VAWCRC, DArT P/L assumed full control over Triticarte which then delivered the wheat and barley services.
- DArT commenced work on Sugarcane, arguably a crop with the most complicated genetics and difficult to genome profile, for the Bureau of Sugar Experimental Stations Limited (BSES Limited), the Cooperative Research Centre for Sugar Industry Innovation through Biotechnology (CRC SIIB) and International Consortium for Sugarcane Biotechnology (ICSB) (Heller-Uszynska et al. 2011, Mol Breed).
- Beginning of multinational consortia, often through participation of visiting scientists, supporting the development of DArT for Oats, Hops, Brassica, Triticale, Eucalyptus and many other species over several years.
- DArT enabled whole genome profiling using the DArT platform within the Generation Challenge Program of the CGIAR, CIRAD, (Montpellier, France) and ICRISAT (Hyderabad, India).
- DArT PL initiated the transfer of its Technology Package to a number of international partners in the context of building a DArT Network. Our first partners benefiting from accessing the DArT platform were ICRISAT and CIRAD after their scientists were trained in Canberra for a few months to transfer DArT technology to their home institution.
- DArT PL continued supporting genetic research and breeding activities of ICRISAT and CIRAD through provision of a DArTseq service for a number of important crops for international agriculture.
- Andrzej Kilian and DArT PL were finalists of the Ethnic Business Award, a national competition recognising contributions from migrants to Australian economy and society.
- Several years of collaboration with NICTA (National ICT Australia) resulted in development of genetic analysis software based on Statistical Machine Learning (SML). The paper describing this technology (Bedo et al, 2008) was published at BMC Genetics and still remains a very highly accessed paper.
- A paper in Science (Paux, E., P. Sourdille, J. Salse, C. Saintenac, F. Choulet, P. Leroy, A. Korol, M. Michalak, S. Kianian, W. Spielmeyer, E. Lagudah, D. Somers, A. Kilian, M. Alaux, S. Vautrin, H. Bergès, K. Eversole, R. Appels, J. Safar, H. Simkova, J. Dolezel, M. Bernard, and C. Feuillet. 2008. A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B. Science 322 (5898), 101.) reported construction of a physical map of the wheat chromosome which is much bigger than whole genomes of many organisms. DArT maps (out of over 500 generated by DArT PL for wheat) and DArT marker sequences were used in this research.
- Our collaborators from The Natural History Museum, London, UK published a paper in PloSOne (James et al., 2008, PLos One) demonstrating the power of DArT platform for populational and evolutionary analysis of non-model organisms.
- A two year collaboration with the Chinese Academy of Agricultural Sciences (CAAS) in Beijing, supported by the China Fund program of Australian Government resulted in the development of technology for several horticultural species and several papers, notably on the sequencing of the cucumber genome.
- DArT initiated work on a new data integration platform, later to be named KDDart, in collaboration with the Departments of Primary Industry of NSW and Queensland. Initial support was obtained for this work through Horticulture Australia grant.
- With support from GRDC DArT developed the first efficient genetic ID and purity testing assay and service, initially for barley and wheat.
- DArT PL received one of the first units of Polonator G007, the Next Generation Sequencer co-developed by Harvard Medical School and Danaher Motion and initiated work on DArTseq™, its genotyping by sequencing platform.
- DArT PL’s most significant partner at this time was another CGIAR organisation – CIMMYT. DArT PL provided genotyping services for CIMMYT for the last decade, initially on the array platform and more recently using DArTseq.
- DArT PL launches DArTseq platform as a regular service for an increasing number of organisms on Illumina sequencers. New version of DArTdb and analytical pipelines are released in support of this platform.
- Memorandum of Agreement executed with CIMMYT to transfer DArTseq platform to Mexico as a part of broader interaction between the organisations, focusing on the Seed of Discovery (SeeD) project.
- DArT PL trained seven of CIMMYT’s staff and students in genome profiling and data analysis with the aim of transferring the DArT technology package to Mexico. Almost all trainees were already using these technologies in Mexico in a new facility called SAGA, established and operated with support from the Mexican government.
- DArT also performed a major part of the wheat and maize genotyping for the SeeD project and worked with CIMMYT and the James Hutton Institute on the IT infrastructure for the project
- DArT worked with more than 100 organisms and added at least one organism every week to its DArTseq platform.
- DArTseq was rapidly taken up for work on a number of animal systems (and plants) in the context of “landscape genomics” which represented modern ecological/populational research areas.
- DArT delivered the first reliable, DNA-based data on the varietal adoption in Africa using DArTseq platform and its genetic ID and purity testing system.
- This work, initially on wheat and maize in Ethiopia, was supported by a pilot grant from Bill and Melinda Gates foundation (BMGF) and quickly expanded to other African countries and crops.
- The demand for DArTseq grew rapidly, the number of organisms in DArTdb nearly doubling in 12 months and a new pipeline for marker data extraction from sequencing of genomic representations was developed (DArTsoft14).
- The algorithm was successfully tested in hundreds of projects against the initial pipeline and was implemented into KDDart’s KDCompute software.
- The SAGA facility in Mexico started producing a high volume of DArTseq data on wheat and maize, proving a successful technology platform transfer.
- KDDart’s Data Access Layer (API) was released in January as Open Source.
- New field data capture software, KDSmart, was developed and offered for free on the Google PlayStore.
- Several organisations started using the complete KDDart platform as further useful user interfaces were developed (www.KDDart.org).
- DArT commenced offering low(er) plex SNP assays (Targeted Genotyping) on several platforms (DArTag, DArTcap and DArTmp).
- With further support from BMGF, DArT PL initiated training of future staff for the DArT platform operations on the BecA/ILRI campus in Nairobi.
- DArTseq was developed for new organisms at an increasing rate, rapidly expanding its range of applications, including for use in ecology and genetic testing of crops in Africa.
- The same applied to Targeted Genotyping assays.
- DArT PL also intensified the rollout of the KDDart platform in Australia and internationally.
- DArT technology platform commenced operations in Nairobi while training of additional staff for the platform continued at DArT PL headquarters.
- DArT completed the first million assays on our platforms and again managed to nearly double the volume of assays compared to previous year.
- New versions of all KDDart applications were released during the year with new features.
- DArT initiated collaboration with IAA program at University of Minnesota focusing on extending analysis of Genotype x Environment x Management space by adding Socioeconomics dimension.