Breeding, Genetics and Genomics
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:
Bambara groundnut is an underutilized pulse that can make a positive contribution to food and nutritional security at the regional and global level, particularly in tropical developing countries where the crop is currently grown. Improvement of the crop is constrained by limited understanding of variation in its nutritional composition compared with other pulses.
Our research with this underutilised crop involves linking genetics to nutritional composition of a set of Bambara groundnut cultivars and land races, representing a portion of available global genepool. At the same time we are developing a multi-disciplinary pipeline that can then be translated to other underutilised crops. We are using Bambara groundnut as an exemplar underutilised crop as it is known for its drought tolerance and ability to grow on marginal soils with little input. This crop, like many underutilised legume species, play a vital role in subsistence farming for rural poor, and is a potential source for vegetable protein.
- Halimi RA, Barkla B, Mayes S, King GJ (2019) The potential of the underutilised pulse bambara groundnut (Vigna subterranea (L.) Verdc.) for nutritional food security. J Food Composition & Analysis. 77:47-59
Brassica crops are of worldwide importance for trade and human diet, providing a wide range of vegetables such as cabbage, cauliflower, broccoli, Chinese cabbage and pak choi as well as the major oilseed crop canola and condiment mustards. Graham King has developed and characterised a range of Brassica genetic and genomic resources underpinning crop improvement traits. These have including reference mapping populations, linkage maps and detailed analysis of QTL for physiological and developmental traits, and resistance to diseases.
Key experimental platforms include genome sequences, as part of the Multinational Brassica rapa Sequencing Consortium, and initiating (with colleagues in the UK) development of Diversity Fixed Foundation Sets (DFFS). Advances in understanding the genetic basis of crop traits requires detailed knowledge of the complex genome structure of Brassica species. Ongoing work includes integration of information to allow navigation via comparative genomics from genetics loci to chromosome, and development of crop genetics databases.
Current research interests include:
• Understanding the domestication events and progenitors of the polyploid canola (B. napus)
• Genomic distribution and modulation of epigenetic marks affecting agronomic traits
• Epigenetic regulation of reproductive organs
• Genotype x Environment interactions, with focus on mineral nutrition
• Modulation and metabolic pathway engineering of health-beneficial glucosinolates
Funding / collaborators
• Dr Martin Broadley, U. Nottingham, UK
• Professor Mike Wilkinson, U. Adelaide
• Dr John Hammond, U. Western Australia
• Dr Sue Armstrong, U. Birmingham, UK
• Dr Smita Kurup, Rothamsted Research, UK
• Professor Jinling Meng, Dr Jing Wang, Huazhong Agricultural University, Wuhan, China
• Brassica rapa genome sequence
• Epigenetic map of canola genome
• Genetic resolution of seed oil fatty acid pathways
• Genetic regulatory networks associated with mineral nutrition
• Insights into developmental timeline of seed embryo
Delivery of research
Professor Graham King: firstname.lastname@example.org
- Yi L, Chen C, Yin S, Li H, Li Z, Wang B, King GJ, Wang J, Liu K (2018) Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus. BMC Plant Biology (2018) 18:32
- Gover J, Kendall T, Baten A, Burgess D, Freeling M, King GJ Mosher R (2018) Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa. The Plant Journal doi: 10.1111/tpj.13910
- Wang B, Wu Z, Li Z, Zhang Q, Hu J, Xiao Y, Cai D, Wu J, King GJ, Li H, Liu K (2018) Dissection of the genetic architecture of three seed-quality traits and consequences for breeding in Brassica napus. Plant Biotech. J. DOI:10.1111/pbi.12873
- Bayer PE, Hurgobin B, Golicz AA, Chan CK, Yuan Y, Lee H, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King GJ, Batley J, Edwards D. (2017) Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnol J. doi: 10.1111/pbi.12742.
- Eckes AH, Gubala T, Nowakowski P, Szymczyszyn, Wells R, Irwin JA, Horro C, Hancock JM, King GJ, Dyer SC, Jurkowski W (2017) Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data. F1000Research 6:465 (doi: 10.12688/f1000research.11301.2).
- Hurgobin B, Golicz A, Bayer P, Chan K, Tirnaz S, Dolatabadian A, Schiessl S, Samans B, Montenegro J, Parkin I, Pires C, Chalhoub B, King G, Snowdon R, Batley J, Edwards D. (2017) Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotech. J. doi: 10.1111/pbi.12867
- Yuan D, Li W, Hua Y, King, GJ, Xu F, Shi L. (2017) Genome-wide identification and characterization of the aquaporin gene family and their transcriptional responses to boron deficiency in Brassica napus. Frontiers in Plant Science. doi: 10.3389/fpls.2017.01336
- Bennett EJ, Brignell CJ, Carion PWC, Cook SM, Eastmond PJ, Teakle G, Hammond JP, Love C, King GJ, Roberts JA, Wagstaff C (2017). Development of a statistical crop model to explain the relationship between seed yield and phenotypic diversity within the Brassica napus genepool. Agronomy 7:31. doi:10.3390/agronomy7020031.
Cannabis is a key component of the SCPS high-value niche crop portfolio. For over a decade SCU has been investing and delivering into Cannabis research – evidenced by four recent publications, currently 3 active HDR students working in the area, and cannabinoid analytical services provided by the Analytical Research Lab (hyperlink this). The integration of the TGA-accredited analytical laboratory within SCPS ensures that Cannabinoid analyses for research purposes is carried out to the highest standards.
SCU is among the few academic leaders of Cannabis R&D in Australia, and is known globally in respect to Cannabis chemical analytics and genetics. Furthermore, SCU is establishing the National Cannabis Germplasm Resource to store and manage seed, tissues, DNA, herbarium voucher specimens, cannabinoid profiles and extracts and related data. SCU has approved facilities and permits necessary for Cannabis research in place and has invested significant time and money to prioritise this area of research. SCU has authority from the NSW Department of Primary Industries to supply and cultivate low THC-hemp for scientific purposes and authority from the NSW Department of Health under the NSW Drug Misuse & Trafficking Act to possess, produce, manufacture and supply Cannabis and derived products irrespective of the THC content for the purpose of scientific research and analysis. SCU holds import permits for low THC-hemp and high THC-cannabis (from the commonwealth Office of Drug Control) enabling sourcing of germplasm from international partners. SCU has established a number of Material transfer agreements (MTAs) with institutes and organisations in Australia and overseas to build their collection. In conjunction with the respective import permits, this will allow for complementing already existing germplasm at SCU providing a valuable diversity panel for research purposes.
To specifically enable Cannabis research, SCU has invested over $300,000 in establishing secure laboratory, controlled environment cultivation rooms and international standard genetic-resource seed conservation facilities, and over the past 6 years has developed protocols to meet regulatory requirements (NSW Health), along with associated data management experience.
- Welling MT, Liu L, Hazekamp A, Dowell A, King GJ (2019) Developing robust standardised analytical procedures for cannabinoid quantification: laying the foundations for an emerging Cannabis-based pharmaceutical industry. Medicinal Cannabis and Cannabinoids Journal. Medical Cannabis and Cannabinoids. DOI: 10.1159/000496868
- Welling M, Liu, L, Raymond, C Kretzschmar T, Ansari O, King GJ (2019) Complex Patterns of Cannabinoid Alkyl Side-Chain Inheritance in Cannabis. Scientific Reports 9: 11421.
- Welling MT, Liu L, Raymond CA, Ansari A, King GJ (2018) Developmental Plasticity of the Major Alkyl Cannabinoid Chemotypes in a Diverse Cannabis Genetic Resource Collection, Frontiers in Plant Science. DOI https://doi.org/10.3389/fpls.2018.01510
- Welling MT, Shapter T, Rose TJ, Liu L, Stanger R, King GJ (2016) A Belated Green Revolution for Cannabis: Virtual Genetic Resources to Fast-track Cultivar Development. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01113
- Welling MT, Liu L, Shapter T, Raymond CA, King GJ (2015) Characterisation of cannabinoid composition in a diverse Cannabis sativa L. germplasm collection. Euphytica. doi 10:1007/a10681-015-1585-y
Coffea arabica Coffee is the second most traded commodity in the world after oil, and economically an important commodity in most tropical and sub-tropical countries. Among the non-alcoholic beverages, it is one of the widely consumed. The two species most widely cultivated are: Coffea arabica, which is known to have better quality and more complex flavour profile; and C. robusta, which is mostly used in the production of instant coffee.
All Australian-grown coffee is from varieties of C. arabica, which is produced in the subtropical region of coastal northern New South Wales hinterland, south east Queensland and far north Queensland. Australia has the potential to produce a distinctive and high quality coffee suitable for the espresso and specialty coffee market but there is a shortfall in the supply, volume-wise and quality-wise. A premium is paid for high quality coffee and thus, the coffee industry will be better placed if they deliver a consistent supply of high quality product to the market.
This project, funded by AgriFutures Australia, will help the Australian coffee industry in achieving its goal to produce consistently high quality and distinctive tasting coffee by:
- Identifying any distinguishing chemical profile of the Australian coffee that can be associated with cupping quality that will provide the Australian coffee industry with well defined parameters to identify any significant distinctive characteristics present in Australian coffee
- Providing a definitive measurement of the levels of caffeine that exists in the analysed samples of coffee green bean, which will confirm present understandings that Australian coffee has a lower level of caffeine than coffees grown elsewhere.
- Correlating the results of the chemical analysis with traditional subjective methods (cupping) of assessing quality and identifying chemical components of the coffee that can be used as marker compounds
Current research interests include:
- Caffeine analysis of Australian-grown coffee beans to compare with imported coffee beans
- Identifying phytochemical diversity of Australian-grown coffee beans
- Determining chemical changes in the coffee bean at different stages of maturity
- Correlating cupping quality to metabolites in green coffee beans
Contact Professor Graham King
Macadamia is a tree nut crop derived from the Australian subtropical rainforest endemic species Macadamia integrifolia and M. tetraphylla and their hybrids. Belonging to the ancient Gondwanan family Proteaceae, macadamia is the first native Australian food plant to be cultivated and marketed worldwide. Commercial varieties developed primarily in Hawaii are the basis for the macadamia industry in Australia, Africa, Hawaii and Asia.
The domestication history of macadamia is short and most cultivated trees are only a few generations from their wild progenitors. Until recently, genomic sequence data for Macadamia and other Proteaceae species was limited. Genomic sequencing is providing new opportunities for understanding the genetic basis of traits that are of economic importance for the macadamia industry; and of adaptive importance for wild Macadamia populations.
Current interests include:
• Marker development
• Variety identification and pedigree analysis
• Genotype x Environment interactions
• Genome evolution in the Proteaceae Funding/Collaborators
• NSW Government Industry and Investment • Professor Robert Henry, QAAFI, University of Queensland
• Dr Craig Hardner, QAAFI, University of Queensland
• Mustard Seed Finance Trust
•Dr Wayne Hancock, Korora R & D Pty Ltd
Research outcomes Southern Cross Plant Science has generated the first genome-wide sequence data for Macadamia integrifolia and has used these data initially to develop markers for variety identification and population studies. A draft chloroplast genome sequence has been assembled and initial steps towards the characterisation of the genome of Macadamia are underway.
70% of the world's macadamia can be traced back to a single tree in Queensland, new research reveals
Contacts Dr Catherine Nock: email@example.com
Professor Graham King: firstname.lastname@example.org
Tea tree (Melaleuca alternifolia) oil is an iconic Australian essential oil product sold around the world for use in therapeutic agents and cosmetics.
In Australia, tea tree oil is produced from around 4000 hectares of plantations located between Ballina and Port Macquarie on the Nth Coast of NSW and near Atherton and Dimbulah in North Queensland.
Tea tree plantations at Ruthven in Northern Rivers region of NSW. Tea tree harvesting in the Dimbulah region in North Queensland
The industry is an important part of the economies in these regions and produced around 900 tonnes of oil with a total farm gate value of $35 million in 2016/17.
Breeding of tea tree commenced at NSW DPI Wollongbar Agricultural station in 1993 as an initiative between NSW DPI, CSIRO, the Australian Tea Tree Industry Association (ATTIA), and RIRDC. The inauguration of a breeding program paralleled the transition of tea tree oil production from a cottage industry based on “bush harvesting” in natural stands, to one based on the farming of tea tree grown in plantations. By generating new cultivars with increased yield and quality of oil over the past 25 years. This first breeding program was a major contributor to the growing of the industry into the mature, stable and internationally competitive industry that it is today.
A young tea tree crop growing in the Rappville region of northern NSW. (Photo S. Mirza).
During 2017, the tea tree breeding operations were transitioned to Southern Cross Plant Sciences (Southern Cross University). Southern Cross University’s involvement in tea tree research, however, extends back to the late 1990’s, when researchers at the then Centre for Plant Conservation Genetics undertook a population study of the geographical and genetic variation across the natural distribution of M. alternifolia in Queensland and NSW. At that time, an institute was also established at SCU for chemical analysis and formulation of tea tree products, the legacy of which today is the Analytical Research Laboratory, a major provider of natural products testing to the tea tree industry, and other food, herb and essential oils industries.
Further major forays into tea tree genetics and pre-breeding research at SCU was marked by the establishment of a living collection of diverse tea tree populations at SCPS’s Brookside field site at the Lismore Campus in 2010. This germplasm resource collection has been a key resource underpinning studies into the genetics of a range of traits affecting the agronomic and chemical properties of tea tree, including various pest and disease tolerances, root and shoot architecture, and terpene and methyl eugenol composition, since that time.
Collecting tea tree seed in the Southern Downs region of Queensland in 2010 for the establishment of a germplasm resource collection of tea tree.
Today, tea tree breeding activities at SCU are focused on a 4th generation breeding population. Breeding tea tree is a protracted process requiring about 8 years to carry out one full breeding cycle, from the formation of a breeding populations to making selections for the next generation.
Tea tree flowering in a living collection of diverse tea tree growing at SCU’s campus at Lismore, NSW.
Dr Merv Shepherd and his team have been preparing the ground and infrastructure for a new seed orchard for tea tree at Rifle Range Rd. They have been cultivating the ground, setting up irrigation lines and weed matting the mounds.
Contact: Dr Mervyn Shepherd email@example.com
The National Passionfruit Breeding program is run by Southern Cross University and aims to breed new varieties of passionfruit vines suitable for commercial fruit production. The program is funded through a levy paid by growers on each carton of fruit sold with an additional contribution from the Australian Government and is administered by Horticulture Innovations Australia (HIA).
NSW DPI is making a considerable contribution to the National Passionfruit Breeding Program by providing facilities at Alstonville (NSW Centre for Tropical Horticulture) and Wollongbar. DPI staff also contribute to the management of the sites. The contribution of valuable land, water, human resources and equipment enable this project to happen.
‘Crossing’ involves removing pollen (a yellow powder) from the anthers of the flower of one variety and transferring to the stigmas on the flower of another variety.
Breeding scheme for passionfruit. New selections are crossed with vines from inside or outside the program. Seedling vines are propagated, grown, fruit measurements made and the best vines selected for breeding. A passionfruit breeding cycle with full assessment is 4 yrs.
The breeding scheme aims to produce vines with improved performance as the breeding cycle continues. New commercial varieties should result from the best selections from the breeding program in due course.
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.
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.
- Epigenetic marks in the Brassica genome
- Epigenetic intervention as a crop improvement strategy
- King GJ (2015) Crop epigenetics and the molecular hardware of genotype x environment interactions. Frontiers in Plant Science.
- Chen X, Ge X, Wang J,Tan C, King GJ, Liu K. (2015) Genome-wide DNA Methylation Profiling by Modified Reduced Representation Bisulfite Sequencing in Brassica rapa Suggests that Epigenetic Modifications Play a Key Role in Polyploid Genome Evolution. Frontiers in Plant Science. doi: 10.3389/fpls.2015.00836
- Bloomfield JA, Rose TJ, King GJ (2014) Sustainable harvest: managing plasticity for resilient crops. Plant Biotechnology Journal 12: 517-533 (pdf).
- Parkin IAP, Koh C, Tang H, Robinson SJ....King GJ et al.(2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology 15:R77 doi:10.1186/gb-2014-15-6-r77 (pdf)
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.
- 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