The high cost of biotechnology will likely steer its primary use towards short-rotation plantations as opposed to less intensively managed forests, but some applications are suitable for all forest types and can guide forest conservation activities (see Tables 1 and 2) (Sedjo 1999; Yanchuk 2001). An attempt indicating the status and trends of each tool will be made in the following section.
Biotechnology has progressed from phenotype to genotype, and has been trying to quantify relationships between the two ever since. Early work focused on biochemistry (e.g., terpene analysis), progressed to biosynthetic constitutive or induced protein expression (isoenzymes) and is now utilizing DNA-based tools (e.g., microsatellites, quantitative trait loci - QTL) since the advent of PCR technology.
Molecular markers can either be dominant - only the dominant allele is expressed if both parents are genetically different at a given locus, or codominant – the genotypes of both parents are quantifiable at a locus. Dominant markers (amplified fragment length polymorphism – AFLP, randomly amplified polymorphic DNA – RAPD) require larger sample sizes for statistical analysis than codominant markers (isoenzymes, microsatellites/simple sequence repeats – SSR, restricted fragment length polymorphism – RFLP, sequence-tagged sites – STS, expressed sequence tags – EST, single nucleotide polymorphisms – SNP).
The different markers all have varying benefits, drawbacks, costs and ease of development, and all can be applied to a limited range of optimal applications, generally focused on neutral or non-adaptive genetic variation (see Table 1, Ritland and Ritland 2000; Krutovskii and Neale 2001, and others for reviews). Molecular tools have been widely used to measure gene flow and genetic diversity of natural and artificial populations of forest trees and associated species, and the impacts of anthropogenic disturbance on their evolutionary potential (Haines 1994; Ritland and Ritland 2000; Yanchuk 2001). The long-term viability of species and endemics subject to influences like pollution or climate change can be modeled using genetic data. There are still no highly repeatable, easily assayed markers directly linked to quantitative traits.
Although progress has been made identifying QTLs for some adaptive traits in some species, a good genomic linkage map is essential, as are breeding and identification and sequencing of candidate genes for quantitative traits of interest. The application of markers technology in forestry is by far the most extensive among other tools. It is not restricted to neither developed nor developing countries, however, the type of markers, the speed of its use, and frequency of utilization differed due to the status of markers development and the biometrical methods needed for data analyses (Table 1 and 2).
Clonal forestry using both hardwoods and conifers is gaining popularity due to the resulting uniformity and ease of silviculture, harvesting and processing. More importantly, it allows the capture of level of genetic gains that can not be attained through sexual reproduction. This technology is restricted to organogenesis and somatic embryogenesis, which require extremely detailed understanding of cell biology, multiplication, biochemical signaling, differentiation and the production of copies or clones in a laboratory setting. Both of the above methods capitalize on plant species’ ability to regenerate an entire genetically identical individual from a single cell or group of differentiated or undifferentiated cells via in vitro tissue culture. Individuals with selected traits or the highest performers from testing trials or breeding programs can be replicated at a large scale, capturing both additive and non-additive genetic variation from traditional breeding. The advantage of these methods is the ability to indefinitely store regenerated tissues in liquid nitrogen or under laboratory conditions (i.e., hold the genotype constant) while field testing is underway to identify elite lines. This allows selected lines with desirable attributes to be further multiplied for operational deployment. Currently some operational scale productions are underway in both developed and developing countries, however, it should be stated that the scale of production in hardwoods is larger than that of softwoods.
Our understanding of fundamental biology and evolution is also being enriched through collaborative efforts using model species in genomics research around the world (Krutovskii and Neale 2001). Evolutionary synteny among taxa, even those as distantly related as algae and angiosperms, can be quantified and candidate genes or groups of proteins (microarrays) involved in biochemical pathways of interest can be identified easily: this process of identifying putative genes controlling certain traits is called gene discovery.
Expression of key gene families or microarrays and their relative up- or down-regulation following stress or environmental changes can be gauged, possibly leading to identification of compounds of significant importance, and their interactions with genotype and environment. Characterization of genetic components of disease or pest resistance is a rapidly expanding field (Ellis et al. 2001; Gartland et al. 2002). Genomics is a fairly new field with many sub-disciplines (Krutovskii and Neale 2001), which requires substantial investment for start-up and maintenance: high-technology automata, costly supplies and chemicals, PCR and other machines, highly trained laboratory staff, marker (EST, SNP) development, as well as vast bioinformatics and associated statistical capacity are necessary. At present, the majority of activity in this area is at the research level and is restricted to developing countries.
While the phenotype is the desired end result of breeding, variation associated with differences in expression, genotype-by-environment interaction and non-additive or epistatic genetic variability necessitates large, costly and time-consuming and field trials for trees with traits of interest (Haines 1999; Yanchuk 2001). Mendelian inheritance and our increasing ability to understand and target specific genes have enabled the development of marker-aided selection to complement traditional breeding (Haines 1994; Campbell et al. 2003).
This technique has been used with tremendous success in agricultural crop breeding for various genes and traits over the past two decades, and is increasing in importance as more comprehensive genetic maps, and the locations of QTLs on those maps, are developed for each species. If marker-assisted selection can be used to characterize and select tree genotypes, substantial cost savings may be realized by a much shorter breeding cycle (i.e., more rapid turnover between generations) (Haines 1994; Sedjo 1999). Although based on tools developed using markers, it requires the use of material of known pedigree and integrates the study of specific structural, functional and morphological attributes of species’ genomes. Although this work is experimental at this stage, several studies in both developed and developing on hardwoods and softwoods are underway. Exact account of these studies and their state-of-the-art are sketchy due to their mixed funding nature (i.e., public and private).
Research and the potential for deployment of genetically modified trees have caused widespread public concern. Regulatory agencies have called for more research on gene flow, likelihood of horizontal and vertical gene transfer via escapes, hybridization and introgression, and a range of ecological impacts of transgenic material in the field (Owusu 1999; Johnson and Kirby 2001; Pew Initiative 2001; Gartland et al. 2002; Anonymous 2003). Concerns around transgenic trees share similarities with agricultural crops, but while the latter are grown and used for research and consumer products throughout many developed and developing nations, transforming trees has only recently begun, and is currently only at the experimental stage. In the laboratory, transformation has been achieved using ballistics and Agrobacterium species for three conifer and ten hardwood genera of commercial importance. Specific genes and regions, primarily conferring insect or disease resistance, sterility, and wood quality attributes, have been the focus of nearly all of the research (Pilate et al. 2002; Campbell et al. 2003). Some promoter and marker genes have also been tested. In some regions, pulp and paper processing has achieved dramatic reductions in the amount of highly toxic chlorine and other chemicals by employing enzymes genetically modified to digest lignin (Ellis et al. 2001; Pilate et al 2002; Campbell et al. 2003). The use of genetic engineering during industrial processing does not currently appear to cause public concern, especially when the outcome includes substantial environmental benefits. Accurate account of this type of work is very difficult to document since the majority of work is being conducted by the private sector and its associated growing negative publicity.