National tree genomics program (AS17000) - Hort Innovation

Completed project

National tree genomics program (AS17000)

Publication date: March 31, 2025

Delivery Partner: The University of Queensland, Queensland University of Technology, Department of Agriculture and Fisheries Queensland, Western Sydney University, Jain Irrigation, BGI, BioPlatforms Australia, Plant and Food Research, University of Adelaide

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What was it all about?

The National Tree Genomics Program delivered new genetic and molecular tools to support the future productivity, profitability and resilience of Australian horticultural tree crop industries. Across almond, avocado, citrus, macadamia and mango, the program improved understanding of how important crop traits are linked to genetics and plant biology.

Together, two programs of work delivered important foundations for the next generation of horticultural genetics and crop improvement in Australia. The Genomics Toolbox component provided the genomic resources needed to understand genetic variation across major tree crops, while the Molecular Physiology component linked that genetic knowledge to the biological processes that influence productivity in the orchard. Combined, these outcomes will support more efficient breeding, improved management practices and future innovation to help growers respond to production challenges and emerging industry needs.

Genomics Toolbox

The Genomics Toolbox component generated a major collection of genomic resources for Australia’s key horticultural tree crops. Improved reference genome sequences were produced for avocado, mango, citrus and macadamia, while important breeding material was sequenced across all five target crops, including almond. More than 300 macadamia genotypes, more than 400 mango genotypes and all available Australian avocado varieties were sequenced, alongside extensive work on Australian native citrus species. These datasets were made publicly available to support future research and breeding activities.

The project also developed and refined methods for generating high-quality genome sequences, helping to improve the speed and accuracy of genetic analysis in tree crops. The resulting resources will support plant breeding, variety identification, gene discovery and the protection of new varieties. Importantly, these tools provide a foundation for molecular breeding approaches that can help shorten breeding cycles and accelerate the development of improved cultivars. The methods and resources developed are also expected to benefit other horticultural crops beyond the program’s case-study species.

Molecular Physiology

The Molecular Physiology component investigated how key productivity traits are regulated within tree crops, focusing on avocado, macadamia and mango. The project combined field trials with molecular and genetic analysis to better understand precocity, flowering, fruit retention, tree vigour and the biological mechanisms that influence orchard productivity.

In avocado, the project identified promising approaches for increasing determinate flowering, which is associated with improved fruit retention. Girdling increased the proportion of determinate inflorescences, while paclobutrazol showed encouraging results in some trials and warrants further investigation. Researchers also began identifying genes associated with flowering determinacy.

In macadamia, the project identified candidate genes linked to precocious flowering and investigated how dwarfing rootstocks may influence tree vigour. Research into aquaporin genes revealed associations between gene activity and reduced tree vigour, providing new insights that could support future rootstock development and breeding programs.

The project also improved understanding of fruit retention in avocado and mango by examining the role of plant hormones and carbohydrate availability. New methods were developed to accurately measure plant hormones in tree crops, including hormones present at very low concentrations. These methods, together with improved techniques for RNA extraction and field sample collection, provide valuable tools for future horticultural research.