Forest Trees

Research Summary

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 which 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 projects include:

  • Tea tree (Melaleuca alternifolia) root systems Melaleuca alternifolia is a small tree native to the north coast of New South Wales and highlands of South East Queensland, were it is found along water courses and the margins of swamps. Geographically distinct upland and coastal races have been resolved genetically and are associated with distinct plant architectural and chemical ecotypes. Plantations for the production of essential oil are largely located in the more productive coastal regions of Northern NSW and the Atherton region in North Qld and utilise coastal sources of M. alternifolia because of their favourable biomass and chemical composition. Currently, study is being undertaken to revisit adaptive variation in plants from across diverse regions that might influence crop productivity and resilience. Field and glasshouse experiments are underway to determine the genetic basis of shoot and root system architecture attributes that may influence abiotic stress tolerances, biomass, and propagation characteristics (Shepherd et al. 2013a). Other current projects with tea tree include the evaluation of its potential as a model woody Myrtaceous species for developing mutant populations and for reverse genetics of terpene biogensis.

  • Population structure and species delineation of Blackbutts

    Study of the distribution and relationship of genetic variation between and among taxonomic entities, and the impact of natural and artificial modification processes can inform policy and management of forest resources.

    One project examined the genetic structure and species delineation in the Blackbutts which includes a major solid wood plantation taxon for the subtropics, Eucalyptus pilularis.

    The study used microsatellite markers (Shepherd et al. 2013b) to characterise the distribution of genetic variation across the natural range of E. pilularis along the east coast of Australia from Fraser Island in Queensland to Bega on the NSW/Victorian boarder and that of its sister taxon, large fruited Blackbutt (Eucalyptus pyrocarpa).

    The study found there were two geographic races within E. pilularis coincident with its span of two biogeographic regions (Shepherd et al. 2010). The sister taxon E. pyrocarpa was indistinguishable genetically from the northern race of E. pilularis and was therefore thought to be best considered as an ecotype (Shepherd and Raymond 2010).

  • Gene pool management of Corymbia

    Rapid expansion of the hardwood plantation estate in Australia over the past few decades has given rise to concern over the potential for gene flow between planted and native eucalypt forests.In the subtropics this has been mainly with Corymbia spp (spotted gums) and their hybrid with C. torelliana.Our research has been to underpin the development of risk management strategies, defining the taxonomic entities at risk and their relationship with planted taxa (Shepherd et al. 2008a; Shepherd et al. 2012; Ochieng et al. 2007b; Ochieng et al. 2007a; Ochieng et al. 2010), the potential for hybridisation and how to detect and monitor hybridisation (Abasolo et al. 2012, 2013, 2014), as well as the ecological and evolutionary consequences of hybridisation and introgression.

  • Genetics of adaptive traits and pre-breeding of tree crops

    Pre-breeding concerns the provision of knowledge of genetics to underpin breeding programs. The use of experimental hybrid populations and population genomics are powerful approaches in the search for genome segments and genes that traits of economic significance that are also adapt tree populations to variation in their environment. Recent projects have focused on genetics of propagation traits in Corymbia spp. (Shepherd et al. 2007; Shepherd et al. 2008b; Shepherd et al. 2009) and Melaleuca alternifolia, and wood quality attributes in Eucalyptus pilularis (Sexton et al. 2009; Sexton et al. 2010; Sexton et al. 2011). The generation of a Corymbia genome sequence is a key resource supporting pre-breeding research on abiotic and biotic stress tolerances in this group.


  • CRC for Forestry
  • Forests NSW
  • ARC
  • USC
  • U. of Tasmania

Research outcomes

  • Genetic maps for Corymbia and Pinus hybrids
  • Identification of genomic segments influencing foliar oil chemistry, branching architecture, wood quality, propagation and productivity in Corymbia spp, Pinus, or Araucaria spp.
  • Identification of allelic variation underlying solid wood quality attributes in Eucalyptus pilularis
  • DNA fingerprint analysis for quality control and parental analysis of forest trees
  • Descriptions of the population structuring and genetic relationships among taxonomic entities in a range of eucalypt species complexes including, the Blackbutts, the Red Mahoganies, and the spotted gum complex.

Delivery of research

  • Molecular genetic analysis of forest trees
  • Quantitative genetics
  • Genome and DNA sequencing of forest tree species
  • DNA fingerprinting for quality control and paternal analysis
  • Analysis of species delineation and population structure


Dr Merv Shepherd:


Abasolo M, Lee D, Shepherd M (2012) Identification of intersectional Corymbia hybrids based on seedling morphology improves with paternal divergence. Forest Ecology and Management 279 189-202.

Abasolo M, Lee DJ, Raymond C, Medar R, Shepherd M (2013) Deviant near-infrared spectra identifies Corymbia hybrids. Forest Ecological Management 304, 121-131.

Abasolo M, Lee DJ, Raymond C, Brooks L, Shepherd M (2014) Genetics of flowering in spotted gum, Corymbia citriodora subspecies variegata and C. maculata. Australian Journal of Botany in press

Ochieng J, Shepherd M, Baverstock P, Nikles G, Lee DJ, Henry RJ (2010) Two sympatric spotted gum species are molecularly homogeneous. Conservation Genetics 11:45-56. doi:DOI 10.1007/s10592-009-0001-3

Ochieng J, Steane DA, Ladiges PY, Baverstock PR, Henry RJ, Shepherd M (2007a) Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae). Genet Mol Biol 30 (4):1125-1134

Ochieng JW, Steane DA, Baverstock P, Henry RJ, Shepherd M (2007b) Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs. Molecular Phylogenetics & Evolution 44:752-764

Sexton T, Henry R, Harwood C, Thomas A, McManus LJ, Raymond CA, Henson M, Shepherd M (2011) Pectin methylesterase genes influence solid wood properties of Eucalyptus pilularis. Plant Physiology 158:531-541. doi:10.1104/pp.111.181602

Sexton T, Henry RJ, McManus LJ, Bowen S, Shepherd M (2010) Capture of assay template by multiplex PCR of long amplicons for genotyping SNPs and InDels with MALDI-TOF mass spectrometry. Molecular Breeding 25:471-480. doi:10.1007/s11032-009-9345-0

Sexton T, Henry RJ, McManus LJ, Henson M, Thomas D, Shepherd M (2009) A first glimpse of wood property associations in Eucalyptus pilularis (Blackbutt). Paper presented at the Australian Forest Genetics Conference, Freemantle, Perth, WA, 20 April 2009

Shepherd M, Dieters MJ, Baltunis BS (2009) Genetic control and architecture of adventitious rooting in forest trees. In: Niemi K, Scagel C (eds) Adventitious root formation of forest trees and horticultural woody plant - from genes to applications. Research Signpost, Kerala, India, Kerala, India, pp 51-84

Shepherd M, Henson M, Lee DJ (2012) Revisiting genetic structuring in spotted gums (Genus Corymbia Section Politaria) focusing on C. maculata, an early diverged, insular lineage. Tree Genet Genomes 8 (1):137-147. doi:DOI: 10.1007/s11295-011-0428-9

Shepherd M, Kasam S, Ablett G, Ochieng JW, Crawford A (2008a) Genetic structuring of the spotted gum complex (Genus Corymbia Section Politaria). Aust J Sys Bot 21:15-25

Shepherd M, Kasem S, Lee D, Henry R (2008b) Mapping species differences for adventitious rooting in a Corymbia torelliana x C. citriodora subspecies variegata hybrid. Tree Genetics and Genomes 4:715-725. doi:DOI10.1007/s11295-008-0145-1

Shepherd M, Pomroy P, Dieters MJ, Lee DJ (2007) Genetic control of propagation traits in a single Corymbia torelliana x C. citriodora spp variegata family. Can J For Res 37 (12):2563-2574. doi:doi:10.1139/X07-111

Shepherd M, Raymond CA (2010) Species delineation and gene flow in the Blackbutts (Genus Eucalyptus Subgenus Eucalyptus Section Pseudophloius). Conservation Genetics 11 (5):1965-1978. doi:DOI 10.1007/s10592-010-0086-8

Shepherd M, Sexton TR, Thomas D, Henson M, Henry RJ (2010) Geographical and historical determinants of microsatellite variation in Eucalyptus pilularis. Can J For Res 40 (6 ):1051-1063

Shepherd M, Rose T, Raymond C (2013a) Rejuvenation of mature native Tea Tree (Melaleuca alternifolia) for vegetative propagation. Propagation of Ornamental Plants 13(3), 103-111.

Shepherd M, Bihua C, Henry R (2013b) Microsatellite markers for Eucalyptus pilularis (Subgenus Eucalyptus); sourcing genetic markers outside the subgenus. Silvae Genetica 62(4-5), 246-256.