Breeding, Genetics and Genomics

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Global Niche Crops

Australia is exceptionally well-placed to address the growing global demand for high quality, naturally safe, novel food and other agricultural products. This provides new opportunities for an agile and regionally-based agribusiness economy, able to adapt rapidly to new market opportunities.

Global niche plant products have provenance traceable to a ‘clean-green’ production and processing environment, have definable quality defensible by standards, and/or are novel and have high levels of perceived ‘nutraceutical’ benefit.  

SCPS engage in a range of R&D activities in support of Global Niche Crops. This includes:

Crop Genetics and Genomics

Crop genomics research at Southern Cross Plant Science provides a window into the genetic factors and variation underpinning plant cultivation and utlisation.

We have experience in a wide range of genetic analysis including use of segregating populations to generate genetic linkage maps and resolve loci and genes underpinning agronomic characteristics. This includes resolution of quantitative trait loci (QTL) and the ability to navigate between such genetic information and the underlying genome structure and gene regulatory networks. As well as characterising natural genetic variation, we have also used the generation of mutant populations to explore a wider range of genetic diversity.

SCPS has excellent facilities for genomic analysis, including Illumina next generation DNA sequencing.

Genetic Diversity

Southern Cross Plant Science has an deep interest in understanding the sources and extent of natural genetic variation that underpins adaption and utilisation of cultivated plants. In addition, this knowledge is being applied to a number of projects aimed at providing information for conservation of natural plant populations.

We make extensive use of DNA markers, and increasingly of whole-genome sequence information to provide insights into the relationships between different plants.

SCPS Plant Genetic Resources and Characterisation

Southern Cross Plant Science has developed facilities for the extraction, processing, analysis and storage of DNA. In addition to existing collections of plant material assembled for DNA analysis, we are sourcing and generating material that represents genetic diversity, particularly focused on cultivated plants and their wild relatives.


  • Crop genetic diversity collections
  • Allele mining in mutant populations


Epigenetics may be defined to include mechanisms that involve heritable changes other than those in DNA nucleotide sequence.

Genetic improvement of crops underpinned massive increases in yield and food production over the past century. This was based on breeding programs carried out within a framework and understanding of Mendelian and quantitative genetics. However, despite whole-genome DNA sequencing and precision genetics, the rates of increase have now slowed.

Sequencing of the human genome did not provide the anticipated answers about the causative mutations for common diseases and cancers. However, over the past decade understanding the role for epigenetic modifications has advanced rapidly, and revealed the complex interactions underlying these phenotypes. The study and appreciation of epigenetics has thus rapidly become mainstream in human and animal genetics.

Although it is now apparent from many studies that epigenetic regulation, mediated through marks that affect chromatin structure, play a major role in the control of development and response of plants to environment, there has not yet been a corresponding paradigm shift, particularly in crop breeding and agronomy. However, an increasing range of agronomic traits are being shown to be affected to some extent by stably inherited epigenetic modifications. The molecular basis of the innate plasticity that plants possess in terms of phenotype and development, is gradually being unravelled.

Many of the fundamental molecular insights into regulation of epigenetic processes have originated in plants (transposons, miRNA), but relatively little in relation to crop phenotype and quality. Compared with animal genomes, there are important differences in the prevalence and pattern of DNA methylation marks in plant genomes, where epiallelic variation in methylation is also often stably inherited through meiosis.

Current Research

  • Epigenetic marks in the Brassica genome
  • Epigenetic intervention as a crop improvement strategy



Natural Products

Our research on natural products is centred on their chemistry and biological activity. We work primarily on secondary metabolites from plants but also on compounds from algae and fungi.

The around 400,000 known plant species produce an astonishingly diverse array of chemical compounds. These are broadly divided into primary metabolites, which are essential for the short-term survival of the plant, such as carbohydrates, proteins, fatty acids and nucleotides, and secondary metabolites, which may not be essential for the primary biochemical activities in the plant, but in many cases confers some kind of evolutionary advantage. For example, many secondary metabolites serve as chemical defence compounds against herbivores or infection, or they are involved in other types of interactions with different organisms (such as attraction of pollinators or allelopathy).

Secondary metabolites display great chemical diversity and are represented by many different classes of compounds, such as alkaloids, terpenes, flavonoids and a range of glycosides with different aglycone (non-sugar) moieties, such as cyanogenic glycosides, mustard oil glycosides (glucosinolates) and salicylate glycosides.Humans have a long and intimate relationship with natural products, not least in the form of medicinal agents, and more than 90% of therapeutic classes of drugs are derived from a natural product prototype. Microorganisms have yielded many important antibiotics, and fish and other marine organisms are the source of fatty acids with important health benefits. Plants have provided humans with medicines for millennia, and many modern drugs are still plant derived, such as opioids (incl. morphine and codeine), anti-cancer agents such as paclitaxel (Taxol®) and vincristine, and galanthamine, which is used for the treatment of Alzheimer's disease.

Forest Research and Genetics

Forest research at SCPS encompasses aspects of environmental, ecological and evolutionary genetics, of economically important subtropical forest trees.

A unifying feature of this research has been the characterisation of patterns of neutral and adaptive genetic variation in natural and planted tree populations, and the identification of influential natural and anthropogenic factors to inform natural resource management and tree improvement. Research has a strong pre-breeding emphasis, aimed at providing an understanding of genetics of adaptive traits that may be of economic significance in the establishment, propagation, and resilience of forest trees, and the quality of their products.

Located at Lismore, at the confluence of several major bioregions, and with its world class genomics and plant chemistry facilities, SCPS is ideally placed for the study of genetic and chemical diversity of a number of the subtropical eucalypts and other native trees of Australian and international significance, including, Eucalyptus grandis, Eucalyptus pilularis, and spotted gum (Corymbia citriodora). Our research has also included other natives, E. cloeziana, the Red Mahogany group, Tea Tree (Melaleuca alternifolia), native pine (Araucaria cunninghamii), as well as exotic Pinus hybrids.

Current Research

  • Tea Tree (Melaleuca alternifolia) root systems
  • Corymbia genome project
  • Population structure and species delineation of Blackbutts
  • Gene pool management of Corymbia
  • Genetics of adaptive traits and pre-breeding of tree crops