Investment

GRDC Code: TRA2309-001SAX

Traitomic - mutant population acquisition

Background

Access to sources of genetic diversity for target traits is a core element of successful plant breeding programs. Sources of genetic diversity can be both natural and created. Natural diversity exists in the form of new genes and alternative alleles for target traits in either the cultivated germplasm pool or from wild relatives of cultivated crop species. Created forms of genetic diversity include mutation and targeted genetic modification such as genome editing. GRDC-supported breeding and pre-breeding programs currently use genetic diversity from all of these sources. Whilst natural diversity from the cultivated pool and wild relatives are the most common sources, there is increasing interest in the use of created diversity and its offering of unique higher value alleles not attainable through screening of natural populations.

Whilst gene editing technologies for created diversity are advancing, there are still technical and regulatory drawbacks and uncertainties that have so far precluded their wide-spread utilisation in commercial crop breeding. On the other hand, chemical mutagenesis is free from regulatory hurdles and has been employed by breeders as a source of created diversity for crop genetic improvement for almost 100 years; most notably underpinning the genetic improvements that drove the high-yielding traits of the green-revolution. Over the past 20 years, phenotypic screening of mutant populations has largely been replaced by genome-targeted molecular screening methods that enable rapid interrogation of larger population sizes (i.e. more individual mutagenized plants), thus increasing the likelihood of finding desired mutants. In grain crops, the TILLING (Targeting Induced Local Lesions IN Genomes) method has been extensively used to generate diversity and screen for desirable agronomic traits (e.g. herbicide tolerance, disease resistance). However, library sizes of conventional TILLING approaches are still restricted technically and financially, which constrains the assortment of gene variants available to isolate and deploy into breeding programs. Therefore, conventional TILLING approaches no longer meet the cost-effective, high-throughput, and precise genomic surveying, demanded by modern pre-breeding and breeding programs.

A new commercial service by 'Traitomic' (a subsidiary of Carlsberg Research Laboratories - Denmark) has arisen that uses proprietary new technology called FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR) that enables rapid and efficient processing of unprecedently large mutant libraries, two orders of magnitude larger than Tilling Projects (Knudsen et al., 2022). At this scale, FIND-IT offers a high probability of finding desired mutants down to specific base-pair level of a gene, something unimaginable in conventional TILLING. Essentially, this new non-GM approach for screening mutant populations, provides targeted identification of desired traits at single-nucleotide resolution, and at speeds (8-weeks from mutant order to receival) that meet the demands for rapid development of new crop varieties with improved industrial performance.

GRDC - Traitomic Partnership
The Traitomic mutation platform technology is of interest to GRDC as a cost-effective alternative to Gene Editing for some traits given that there are currently no regulatory impediments to the use of crops developed using mutation library resources globally. By contrast, various forms of Gene Editing are regulated differently in different destination markets for Australian grains with markets such as the EU currently regulating crops developed by any form of GE as GMOs'.

Traitomic presents an opportunity for GRDC to acquire mutant libraries of a range of grain crops and screen them for traits that are the focus of current and future pre-breeding investments at significantly lower cost, with higher likelihood of success, and with greater freedom to operate (FTO) than previously possible.

At the beginning of 2024, the GRDC-Traitomic partnership commenced, which will see Traitomic establish a tailored Australian-based (co-located) resource for Australian researchers to leverage and advance genetic gains for the Australian grains industry. Included is co-locating libraries between Copenhagen and Australia, with these proprietary libraries being developed in specific elite cultivars, with a negotiated sliding payment scale for the service, and clear royalty structure for any traits developed into commercially viable products.

The partnership is initially being established for mutant resources for Oats [Bannister & Bilby] and Lupins [Rosemont] in cultivars of relevance to Australia. Breeder and pre-breeders can access these genetic libraries in elite oat and lupin cultivars to generate and identify new versions of genes with bespoke enhanced functions of interest. Oats are an important export market for Australian grain growers, while lupins are the biggest pulse crop in the country. Using the Traitomic service, breeders and pre-breeders will be able to increase the pace that they can develop new oat and lupin varieties with improved performance and desirable traits. New gene targets can be identified and provided to breeders at significantly lower cost, with a higher likelihood of success, and with greater freedom to operate than previously possible.

In the future, GRDC may expand these libraries to include other crop species. However, for now the FIND-IT technology and its application to wheat and barley are held exclusively with Carlsberg and not available through Traitomic (except for a European durum wheat). The GRDC - Traitomic partnership also provides access to other 'public' libraries held by Traitomic in crops such as (but not necessarily in Australian adapted backgrounds): Faba bean, quinoa, rapeseed, rye, chickpea, green pea, lentils, linseed, peanut, and sunflower (https://www.traitsource.com/libraries).

Importantly, the GRDC-Traitomic assets are available to ALL Australian breeders and pre-breeders to help accelerate genetics research. Whether the project is GRDC-funded or another source, this service is available to any research group looking to improve genetic gains for the benefit of the Australian grains industry.

More information on pricing, terms, etc to follow.

Contact Michael Groszmann - GRDC Investment Manager (michael.groszmann@grdc.com.au) for more information.

Project start date:

02/11/2023

Project end date:

31/12/2033

Crop type: