The role of tree breeding in an IPM programme

 By Dr Marius du Plessis, Mondi: Tree breeding programme manager

Pest and pathogens are widely recognized as one of the greatest threats to plantation forestry in South Africa and across the globe. Forestry in South Africa is largely cultivated on the eastern seaboard and escarpment where exotic tree species perform well under conditions of high rainfall and deep, well weathered soils. The success of exotic plantation forestry is based on the principle that the natural enemies, such as pathogens and insects, are absent from its new environment. This frequently results in the net production of above ground biomass to be higher than at the specie’s origin.

Pressure from pests and diseases on the industry escalated due to easier and more frequent movement of business and trade, the demise of international quarantine controls and the adaptation of local pests and disease organisms, to plantation species.

Historically selection-breeding methods were suitable to stay ahead of the increased pest and disease incidence, that scenario has now changed, and tree breeding had to adapt its strategy and methodology. This necessitated tree breeding to become a partner in a much broader approach of Integrated Pest Management (IPM) to effectively manage the risk to its growing stock.


IPM is an approach to manage pests and diseases and based on a number of management strategies.

These strategies should typically be:

  • repeatable
  • affordable
  • address the core pest or disease
  • improve the resistance of the host
  • should not be harmful to the environment
  • use modern technology
  • excludes chemicals as far as possible; or as a last resort only.

Typical aspects of IPM in a forestry environment would include:

  • tree breeding to improve resistant genotypes,
  • molecular identification of separate pest or disease genotypes or to study defense mechanisms of the host trees,
  • monitoring of pests and diseases dynamics
  • bio-control release as a management strategy, to name a few.

Bio-control is an essential part of the suite of tools required to deal with pests and disease in plantation forestry. An example of a successful bio-control intervention in the Forest industry is the control Leptocybe invasa. Much effort is placed on the release and monitoring of the spread of the bio-control agent Selitrichodes neseri, with the National Leptocybe Monitoring Project, a combined initiative between all players in the sector, managed by the Tree Protection Cooperative Program (TPCP) at the University of Pretoria.

Tree Improvement

The goal of tree improvement is to increase the economic value of forest products derived from plantations.

Classical tree breeding, which is based on repeated selection within a breeding population, has for the past five to six decades sufficed to ensure a yield improvement of between 10 and 15 percent per breeding cycle. Due to the long-term nature of forestry, in which one breeding cycle can take anything from 10 – 15 years, most tree breeding programs on the specie level, are only in their 3rd and 4th generation of improvement. Fortunately, both Eucalyptus and Pinus genera have a large natural genetic variability from which breeding selection is done. It is important to maintain this variability within its genetic base through efforts of infusion with new provenances and families to ensure selection potential. Within this wide genetic variability lies the opportunity to select for disease resistance.

In the mid 80’s, with the first attack of serious pathogenic diseases on E. grandis plantations in Zululand, breeding programs moved quickly towards hybrid breeding. Hybrid vigour (heterosis) was employed as a potential management tool to overcome the disease e.g. Coniothyrium zuluense. C zuluense causes a very serious stem canker disease on Eucalyptus in South Africa, from where it was originally described. This technique to hybridise pure bred lines of two homozygous individual species e.g. E. grandis x E. urophylla was successful not only to show resistance to most pathogenic diseases but it also extended site adaptability. This also resulted in higher yields from the same land and more favorable wood properties for pulp and paper making. Soon it became the norm to select for multiple traits in a breeding program and to deploy genetics as interspecific hybrids. Various techniques of screening for pests and diseases resistance were employed, until recently only on the phenotype basis. Field inoculation was initially done but soon the inoculum pressures in the environment were high enough to merely observe disease status in hybrid trials, where after suitable candidates were selected for commercialization.

Pests and diseases all have an evolutionary potential and changes its biology in conditions of strong selection pressure e.g. to capture resistance in the tree populations; climate changes also drive behavioral changes in these organisms. Examples exist of pests that evolve faster than what tree genetics can be improved and hence species and its hybrids became hosts to these evolved pests and diseases e.g. Leptocybe invasa in 2007 which showed great affinity to E. grandis x E. camaldulensis. Clearly a new approach was required, the principles of IPM were well suited to step up the fight to keep trees healthy.

A modern approach

Apart from bio-control, a number of new technologies also emerged. One such technology is the field of chemical ecology which studies the communication between the pathogens or agents, associates and the host. The purpose is to identify the chemical signals that are communicated and find possible ways to interrupt that. Recent research confirms sugar signaling of eucalypt seedlings when inoculated with the Myrtle rust (Austropuccinia psidii) pathogen, which could shed some light on resistant seedling’s defense mechanisms. Some of these emerging technologies could be established in trees through gene editing of pests and diseases or the hosts but are sensitive to exploration due to certification requirements.

Genetic research in tree breeding indicated a higher heritability of wood product traits such as density and cellulose content, than for growth traits e.g. diameter and height. It was suggested that genes control a large proportion of phenotypic variation of eucalypt trees. In view of the long breeding cycles as mentioned before, there has been considerable interest to develop molecular markers to identify superior genotypes while they are still seedlings. Forest trees are unique in that they have a long history of recombination and a short history of domestication, resulting in trees having large stores of genetic variation for tree breeding. Although the potential for marker assisted selection (MAS) breeding has been recognized by scientists, the implementation thereof has been slow due to a lack of reliable markers. Earlier technology making use of quantitative trait locus (QTL) mapping, proved useful to understand the levels of genetic control of traits however, they were not suitable for the prediction of traits of a future population from a calibration population. More recently, association genetics was used in the eucalypt genome to identify markers useful for prediction of future qualities from young seedlings. Association genetics uses new marker technology known as single nucleotide polymorphism (SNP) and are currently used to identify alleles that effect a phenotypic trait and remains linked across populations of trees for a long time. These SNP-markers are used more frequently in tree breeding programs to correlate molecular breeding values (GEBV) with estimated breeding values (EBV).

Concomitant to identifying SNP-markers on a genome wide selection basis for breeding values (explained above), researchers are now also identifying SNP – markers for the identification of defense mechanisms of trees that shows a natural (genetically programmed) resistance to pests and diseases. These SNP-markers can then be used in selection criteria of for example the commercialisation of clones, to only release genetic material with this programmed resistance, with high growth potential, with good wood, pulp and paper properties. This concept is widely known as Marker Assisted Selection (MAS) breeding.


IPM principles are relying heavily on strong collaboration amongst all parties which forms an essential information channel providing early warning for emerging pests and diseases, information sharing about its biology e.g. spread and virulence and collaborative research on control.

Selection breeding is still practiced in most tree breeding programs due to the wide genetic variation in breeding populations, relatively high gains and ease of implementation. However, as our knowledge of DNA markers (SNP) associated with biomass productivity and disease resistance improve, so will the implementation thereof improve the selection potential for trees that are less effected by pests and disease.

Good forestry practice, depicted by good sites, high quality genetics, good plants and well planned and executed silviculture are all key components to ensure successful and sustainable forestry.

Literature cited

  • Naidoo, S in Coutinho, TA (Ed.). (2017).Eucalyptus and Pine Pathogen Interactions. Forestry and Agricultural Biotechnology Institute Biennial Report May 2015-May 2017. FABI, University of Pretoria, South Africa: pp 17-18.
  • Slippers, B and Wingfield MJ (Eds.). (2017). Tree Pathology Co-operative Programme (TPCP). Report for year ending 2017. Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa: pp 25-28.
  • Thavamanikumar S, Southerton S, Southerton R, Brawner J and Thumma, B. (2018). Eucalypt MAS: Implementation of marker-assisted selection in Australia’s major plantation eucalypts Project Report No: PNC378-1516. Forest and Wood Products Australia. Melbourne, VIC Australia.
/ Pesticide interest piece