Forestry practices that maintain genetic diversity over the longer term will be required as an integral component of sustainable forest management

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Chapter 1. Overview of Forest Genetic Resources

Genetic diversity provides the fundamental basis for the evolution of forest tree species and for their adaptation to change. Conserving forest genetic resources (FGR) is therefore vital, as they constitute a unique and irreplaceable resource for the future, including for sustainable economic growth and progress, and environmental adaption. The sustainable management of forests and trees in agroforestry systems requires a better understanding of the specific features of forest trees and their genetic diversity and how this can be best conserved, managed and utilized using the scarce, available resources. Forest tree species are generally long lived and extremely diverse. One species can naturally occur in a broad range of ecological conditions. In addition, many forest species have evolved under several periods of major climatic change, and their genetic variability is needed for adaptation to climatic regimes different to those in which they are have evolved. FGR have provided the potential for adaptation in the past, and will continue to provide this vital role as we address the challenge of mitigating or adapting to further climate changes.

Forestry practices that maintain genetic diversity over the longer term will be required as an integral component of sustainable forest management. In future more proactive management of FGR may be needed to accelerate adaptation of forest trees to climate change including through breeding and deliberate movement and relocation of germplasm. Much remains to be discovered concerning how genes function and are regulated in different tree species and further research will likely yield findings of immense economic, social and environmental importance. As a precautionary principle, until there is an improved understanding of tree genetics, there is a need to conserve as much FGR as possible, viz. the heritable materials of important, including locally important, tree and woody plant species. There is also a need to ensure the survival of the vast majority, and preferably all, of tree and woody shrub species likely to have values hitherto unknown and/or novel products and services which may be required by future generations. Especially critical are those tree species in monotypic families or genera which are genetically more distinctive and irreplaceable.

This State of World Report on Forest Genetic Resources FGR (SoW – FGR) addresses the conservation, management and sustainable use of forest tree and shrub genetic resources of actual and potential value for human wellbeing in the broad range of management systems (see Table 1-Main types of forest and tree resources management)/ The definition of forest used in F!O’s global forest resource assessment 2010 is land spanning more than 0.5 hectares with trees higher than 5 metres and a canopy cover of more than 10% or trees able to reach these thresholds in situ. Palms and bamboo forests are included if these criteria are met, as tree-like monocotyledons such as palms, including climbing rattans, and bamboos, have generally been considered as FGR, and the responsibility of forestry agencies. Whilst the main focus of this SoW-FGR report, as reflected in national reports, is on tree and larger woody species present in forests, both natural and planted, this reports also deals with tree and woody shrub species outside forests which are arboreal components in more open situations, including agroforestry systems, woodlands and home gardens.

1.1 Attributes of FGR

1.1.1 Definitions of FGR, FGR conservation and related terms

Forest Genetic Resources (FGR) refers to the actual or potential economic, environmental, scientific and societal value of the heritable materials maintained within and among tree and other woody plant species. The country reports used several categories of values in nominating species for priority, with economic uses the most frequent (46%), conservation including threatened status values second (24%), and social and cultural values third (15%). Among 1451 cases of species used in plantations whose origin was identified, 1240 or 85% were used as exotic and only 211 or 15% were use as native, demonstrating the paramount importance of a small number of exotic, widely-planted, economically important ‘global’ forestry species. Some country reports included species which may be regarded as marginally FGR because they are woody shrubs which may often be of low stature when grown in difficult and arid environments. Country reports included fruit and nut trees and their wild ancestors, and these have been included in reporting as they are frequently multipurpose, providing timber, medicine and services and often being handled by Forestry agencies. The term FGR is also sometimes used incorrectly to more generally to cover the tree and forest resources and products themselves.

Table 1: Main types of forest and tree resources management

Naturally regenerated forests

Planted forests

Trees outside forests, and agroforestry systems


Modified natural



Assisted natural regeneration

Planted component



Forests of native species, where there are no clearly visible indications of human activities and the ecological processes are not directly disturbed by humans

Forests of naturally regenerated native species where there are clearly visible indications of significant human activities

Silvicultural practices in natural forest by intensive management:

  • weeding

  • fertilizing

  • thinning

  • selective logging

Forests of native species, established through planting or seeding intensively managed

Forests of introduced and/or native species established through planting or seeding mainly for production of wood or non wood goods

Forests of introduced and/or native species, established through planting or seeding mainly for provision of services

Stands smaller than 0.5 ha; tree cover in agricultural land (agroforestry systems, home gardens, orchards); trees in urban environments; and scattered along roads and in landscapes

Forest biodiversity has a broader connotation than FGR and denotes the variability among forest dwelling organisms and the ecological processes of which they are a part, and includes variation at forest ecosystem, species and molecular levels.

FGR comprise one subset of plant genetic resources for food and agriculture (PGRFA). PGFRA are defined as any genetic material of plant origin of actual or potential value for food and agriculture (which in the UN system is broadly circumscribed to include forestry). FGR are also included as a subset of agrobiodiversity which is defined as the variety and variability of animals, plants and micro-organisms that are used directly or indirectly for food and agriculture, including crops, livestock, forestry and fisheries. Agrobiodiversity includes the diversity of genetic resources (varieties, breeds) and species used for food, fodder, fibre, fuel and pharmaceuticals. It also includes the diversity of non-harvested species that support production (soil micro-organisms, predators, pollinators), and those in the wider environment that support agroecosystems (agricultural, pastoral, forest and aquatic) as well as the diversity of the agro-ecosystems (FAO, 1999). Increasingly traditional knowledge of biodiversity or ethnobiodiversity is being understood to be an integral component of agrobiodiversity (Thaman 2008) and its loss may proceed and threatens loss of diversity at different levels -agrobiodiversity systems, species and intraspecific diversity.

Intraspecific diversity, or the genetic variation within species, may be considered from several perspectives, ranging from formally recognised taxonomic categories of subspecies and varieties through to genetic differences between and within populations. Subspecies are usually morphologically or otherwise distinctive entities within a species which have evolved in geographic and reproductive isolation: if they continue to be separated for many generations, subspecies may become distinctive enough from each other, or have developed reproductive barriers, to develop into separate species. Ecotypes are an intraspecific group having distinctive characters which result from the selective pressures of the local environment. Genotypes can be considered as the sum of the total genetic information in an individual or the genetic constitution of an individual with respect to genetic loci under consideration. Individual long-lived trees of different species may develop into chimeras of many genotypes due to the accumulation of spontaneous mutations of neutral selective fitness in nuclear genes in bud meristems, but this topic has been little researched.

!n organism’s genome represents its total genetic material, and in plants is comprised of three separate genomes, viz. nuclear (c. 50-100,000 genes), chloroplast (c. 100-120 genes) and mitochondrial (c 40-50 genes) (Murray et al., 2000). Understanding of genetics and the nature of heritable materials in trees is rapidly evolving; informed by genomic studies in economically important forestry trees such as Eucalyptus and Populus (both angiosperms), woody fruit trees such as apple (Malus domestica) and sweet orange (Citrus sinensis), an ancestral flowering plant (Amborella trichopoda), in coniferous families through transcriptome (RNA) sequencing (e.g. Walter Lorenz et al. 2012) and by genetic research on other plants and other organisms. Advances in gene sequencing technologies, have made possible the sequencing of conifer giga-genomes and several such studies are now in progress or planned (see e.g. Mackay et al. 2012, Ch 2 and Ch6).

Genes, are a nuclear DNA sequence to which a specific function can be assigned, while allele are alternative forms of a gene located on the corresponding loci of homologous chromosomes. In plants, as well as other higher organisms, a variable proportion of the nuclear genome is composed of non-protein coding, repeat DNA sequences, which has several origins, and some of which has specific regulatory functions and/or may donate segments of DNA which can become incorporated into genes. Angiosperms possess genomes with considerable gene redundancy much of which is the result of ancient polyploidization events (Soltis et al. 2008).

DNA present in cellular organelles, notably chloroplasts and mitochondria, comprise vital components of a tree’s heritable materials/ While nuclear DN! is always inherited biparentally from the male and female parent, organellar DNA may have different modes of inheritance. Chloroplast DNA in usually maternally inherited in angiosperms (e.g. in poplars, Rajora and Dancik 1992; and in eucalypts Byrne et al. 1993), but may also be inherited from both parents (Birky 1995), or rarely paternally (Chat et al., 1999). In gymnosperms, chloroplast DNA is mainly inherited paternally or infrequently from both parents (e.g. Neale et al. 1989, Neale and Sederoff 1989, White 1990; Wagner 1992). The mitochondrial genome is most often maternally inherited in angiosperms (e.g. Reboud and Zeyl 1994, Vaillancourt et al., 2004), but may be maternally, paternally or biparentally inherited in gymnosperms (e.g. Neale et al. 1989, Neale and Sederoff 1989, Wagner 1992, Birky 1995). Chloroplast DNA is strongly conserved, and therefore useful for evolutionary studies (e.g. in Eucalyptus Freeman et al. 2001, and in Juglans Bai et al. 2010), while mitochondrial DNA is commonly used as a source of genetic markers in studies of gene flow and phylogeography. Heritable changes in gene expression or cellular phenotype may be caused by several mechanisms which do not involve any change in the underlying DNA sequence and these are the realm of the poorly understood science of epigenetics.

A population of a particular tree species comprises all of the individuals of that species in the same geographical area, and genetically isolated to some degree from other populations of the same species. In sexually reproducing species the population comprises a continuous group of interbreeding individuals. A metapopulation of a forest tree species comprises a set of spatially separated local or sub-populations, coexisting in time, and which interact infrequently via pollen and seed dispersal between them. The term provenance is particularly important in relation to forest tree germplasm and refers to the geographic origin of a particular germplasm source, although sometimes used synonymously and interchangeably with population. The field performance of a particular representatively sampled provenance seed source, if from a rather narrow geographic area (including same soil type and without much altitudinal variation) will generally be more consistent than for a population which may differ considerably due to clinal variation arising from gradients in selective pressures.

FGR conservation approaches

Practical approaches and best practices for conservation and management of forest and plant genetic resources have been extensively discussed in various practical guides and texts (Young et al. 2000; FAO, DFSC, IPGRI, 2001ab; FAO, FLD, IPGRI 2004; Heywood and Dulloo 2005). In situ conservation refers to the conservation of ecosystems and natural habitats and the maintenance and recovery of viable populations of species in their natural surroundings, and in the case of domesticated or cultivated in the surroundings in which they have developed their distinctive properties (CBD 1992). Circa situm conservation emphasises the role of regenerating saplings and linking vegetation remnants in heavily modified or fragmented landscapes such as those of traditional agroforestry and farming systems (Barrance 1999). The related term matrix management has been coined to refer to approaches to conserve and manage biodiversity in forests outside of protected areas (Lindenmayer and Franklin, 2002): dynamic conservation of FGR will mainly occur in the matrix and will involve management of trees on farms, in forest fragments and especially in sustainably managed production forests. Ex situ conservation refers to the conservation of components of biodiversity outside of their natural habitats, including FGR in plantations, tree breeding programs, ex situ gene conservation stands/field genebanks, seed and pollen banks, in vitro storage and through DNA storage (FAO, FLD, IPGRI 2004).

Evolutionary or dynamic conservation of FGR essentially involves a natural system in which the evolutionary forces, and natural selective processes, which gave rise to diversity are allowed to operate and which over time modify allelic frequencies. The recent past few decades, and the next century, represent an era of unprecedented change in selective pressures on almost all trees species. These altered selective forces include more extreme climatic events, gradual increases in temperature and altered rainfall regimes, changed fire regimes, increased air pollution and elevated atmospheric CO2 levels, habitat fragmentation, increases in and new pests and diseases, competition with invasive exotic plant species including transformer species capable of changing the ecology of entire ecosystems, and the loss of or changes in pollinators and dispersal agents. Dynamic in situ conservation allows species adaptation through continuous ‘selection of the fittest’ and co-adaptation of host-pathogen systems and other complex biological interactions (Kjær et al. 2001; Byrne 2000).

In situ conservation of the FGR associated with identified, superior provenances of economically important tree species is vital even when they may be relatively well conserved ex situ, e.g. through planting and breeding programs. This is because tree breeders may need to re-sample and infuse later breeding populations, and/ or identify new desired traits in already well-known and adapted populations. Selective forces may differ in the native and exotic/planted environments, and this is the basis of the, often remarkably swift evolution of land races which are much better adapted than the original introduction after just one or two generations of selection. Increasingly rapid climate change and associated extreme climatic events is altering the selective forces in both the native and exotic/planted environments and throwing up new challenges for FGR conservation.

Static conservation of FGR involves conserving individual genotypes, e.g. in the field as clonal archives and in vitro in tissue culture and cryo-preserved embryo culture, and groups of genotypes in long term seed storage for tree species with orthodox seed storage behaviour (Kjær et al. 2004). This approach has generally been viewed as a complementary approach to dynamic in situ conservation and more often as a short-term conservation strategy and for safety duplication in the case of cryopreservation. Given the unprecedented scale of threats to FGR and likely losses of diversity and changes in selective forces which will drive rapid changes in the genetic makeup of natural (and artificial) populations of tree species , it might be timely to reconsider the potential value and cost effectiveness of static conservation activities.

1.1.2 Characteristics of FGR

Forest tree species are generally long-lived and have developed natural mechanisms to maintain high levels of genetic variation within species. They include high rates of outcrossing and often long-distance dispersal of pollen and seed. These mechanisms, combined with native environments that are often variable have enabled forest tree species to evolve into some of the most genetically diverse organisms in existence. Forest community ecosystem processes, including evolution of biodiversity, have been found to be closely related to the genetic diversity in structurally dominant and keystone tree species (e.g. Whitham et al. 2006 and references contained therein).

Differences between trees and other organisms

Chromosomes and DNA

There are large and seemingly inexplicable differences and variations in chromosome number, ploidy level and genome size both within trees, and between trees and other organisms. The two major groups of trees, viz. gymnosperms (including conifers) and angiosperms, appear to have been separated by more than 290 million years of independent evolution. Conifers typically have very large genomes, or giga-genomes, with numerous highly repetitive, non-coding sequences (Ahuja and Neale 2005; Mackay et al. 2012). DNA sequencing studies of selected model plants species in these two groups are providing different perspectives and insights into plant genome biology and evolution. Whilst there are large overlapping sets of DNA sequences between conifers and angiosperms (e.g. Pozo et al.), about 30% of conifer genes have little or no sequence similarity to angiosperm plant genes of known function (Pavy et al. 2007; Parchma et al. 2010). Whilst polyploidization or whole genome duplication is rare in animals and conifers1, it is now considered ubiquitous in angiosperms and has occurred frequently through the evolution of angiosperms. Polyploidization is a mechanism of sympatric speciation because polyploids are usually unable to interbreed and produce fertile offspring with their diploid ancestors. Polyploidization may be involve autopolyploidy (spontaneous multiplication involving the chromosomes of a single species) or allopolyploidy (involving more than one genome or species). Whole genome duplication is considered likely have led to a dramatic increase in species richness in several angiosperm lineages including families with important FGR such as the legumes (Fabaceae) and provided a major diversifying force in angiosperms (Soltis et al., 2008). In animals, aneuploidy is usually lethal and so is rarely encountered, whereas in angiosperms the addition or elimination of a small number of individual chromosomes appears to be better tolerated; new research has indicated that aneuploidization may be a leading cause of genome duplication (Considine et al. 2012). These authors have found that auto-triploidization is important for speciation in apples (Malus spp.), and that the features of such polyploidization confer both genetic stability and diversity, and present heterozygosity, heterosis and adaptability for evolutionary selection. The monotypic small tree Strasburgeria robusta from New Caledonia has an extremely high ploidy level (20 n with n=25) and may have enabled it to adapt to an extreme edaphic environment, viz. ultramafic soil (Oginuma et al. 2006).

Longevity and Size

Trees, including woody shrubs, differ from other organisms in several key respects. They are perennial, often long-lived, organisms which need to be able to either endure environmental extremes and changes and/or persist in the soil seed bank or regrow from root suckers and coppice in order to survive long-term at a particular site. Angiosperms trees have high levels of genetic diversity, both a high number of genes,

e.g. more than 40,000 for poplar2, with high allelic variation; while gymnosperms have giga-genomes with an order of magnitude more DNA than other organisms, but with likely a similar number of genes to angiosperm trees distributed more sparsely in a large pool of non-coding DNA (RIgault et al. 2011, Mackay et al. 2012). The high genetic diversity that characterizes tree populations and individuals, and associated stress tolerance and disease resistance mechanisms, help explain their capacity to persist and thrive for long periods. The life span of tree species typically ranges from about 10-15 years (short lived pioneer species) to 200-300 years (many larger trees species and those found in arid zones). Root suckering clones provide the oldest known trees and woody shrubs, examples include aspen (Populus tremuloides) with one clone in central Utah (USA) estimated to be 80,000 years old (DeWoody et al. 2008) and with 5-10,000 year-old clones reputedly common. A sterile triploid clone of the woody angiosperm shrub king lomatia (Lomatia tasmanica) has been determined to be at least 46,300 years old (Lynch et al. 1998). A colony of Huon pine (Lagarostrobus franklinii ) trees covering one hectare on Mount Read, Tasmania (Australia) is estimated to be around 10,000 years old, with individual tree stems in this group more than 2,500 years old, as determined by tree ring samples (The Gymnosperm Database A specimen of Norway spruce (Picea abies) in Dalarna Province (Sweden) has been found to be at least 9,550 years old, surviving by resprouting from layered stems, rather than underground root suckering (Anon. 2008). Three species of bristlecone pines in USA may live for several thousand years with one specimen of Great Basin bristlecone pine (Pinus longaeva) in California determined to be c. 4,850 years old/ Interestingly almost all of the world’s oldest recorded trees are conifers (Rocky Mountain Tree Ring Research Accessed 18/10/2012). It is likely that different xylem structure and associated ability to survive lower conductivities and drought (Choat et al. 2012) contributes to the great longevity of gymnosperms and especially conifers, compared with angiosperms. Ancient trees occur in all three orders of conifers, viz. Pinales, Araucariales, and Cupressales: > 4000 years – Pinus longaeva, Picea abies; > 3000 years – alerce (Fitzroya cupressoides), giant sequoia (Sequoiadendron giganteum); > 2000 years – western juniper (Juniperus occidentalis), Huon pine (Lagarostrobus franklinii), Rocky Mountain bristlecone pine (Pinus aristata), foxtail pine (P. balfouriana), coast redwood (Sequoia sempervirens); and > 1000 years – Nootka cypress (Chamaecyparis nootkatensis), sugi (Cryptomeria japonica), Rocky Mountain juniper (Juniperus scopulorum), alpine larch (Larix lyalli), whitebark pine (Pinus albicaulis), pinyon pine (P. edulis), limber pine (P. flexilis), douglas fir (Pseudotsuga menziesii) and bald cypress (Taxodium distichum). The capacity of gymnosperms to persist, often almost unchanged in form, over millions of years, is evidenced by ginkgo (Ginkgo biloba) recently re-discovered in the wild in south-west China where glaciation was relatively weak (Tang et al. 2012), whereas it was previously only known from cultivation in Japanese and Chinese temple gardens and in fossils. Likewise, the discovery in 1994 of the Wollemi pine (Wollemia nobilis), in a valley near Sydney, eastern Australia and presumed to be the last remnant3 of a genus which evolved about 61 million years ago (Liu et al. 2009). There are less than 100 stems of this tree, all genetically identical; and likely a single clonal root suckering clump. The only comparable long-lived organisms to the oldest trees are corals, fungal mats and other clonal suckering plants such as creosote bush (Larrea tridentata).

Trees also provide the biggest and tallest organisms on the planet. Coast redwood (Sequoia sempervirens) has been recorded up to 115 m tall and weighing up to 3,300 MT/ The world’s tallest and biggest angiosperms are eucalypts in south-eastern Australia, viz. mountain ash (Eucalyptus regnans) from Victoria and Tasmania with trees measuring over 100 m, but historically to at least 114 m tall, and trunk volumes to 360 cubic metres. By contrast the largest animals to have evolved are blue whales which can weigh up to 180 MT. Populations of large old trees are rapidly declining in many parts of the world, with detrimental implications for ecosystem integrity and biodiversity (Lindenmayer et al. 2012). Throughout the tropics the biggest forest trees are disappearing partly due to selective targeting by loggers, but more recently as a result of forest fragmentation, climate change and exposure to drought.

Trees are the dominant structural element in forests and several other terrestrial ecosystems (agroforests, woodlands, and gardens), intercepting much of the radiant sunlight, dominating photosynthetic processes and carbon flows, comprising the greater proportion of the biomass, and central to the cycling of water and mineral nutrients (especially absorbing and returning nutrients from deeper root zones, mobilizing mineral elements through associations with mycorrhizal fungi and fixing atmospheric nitrogen through symbiosis with bacteria). Increasingly the diversity within and between tree species is being found to be critical to promoting and maintaining almost all other life forms present in forest ecosystems.
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