Forest biotechnology: Innovative methods, emerging opportunities

Summary The productivity of plantation forests is essential to meet the future world demand for wood and wood products in a sustainable fashion and in a manner that preserves natural stands and biodiversity. Plantation forestry has enormously benefited from development and implementation of improved silvicultural and forest management practices during the past century. A second wave of improvements has been brought about by the introduction of new germplasm developed through genetics and breeding efforts for both hardwood and conifer tree species. Coupled with the genetic gains achieved through tree breeding, the emergence of new biotechnological approaches that span the fields of plant developmental biology, genetic transformation, and discovery of genes associated with complex multigenic traits have added a new dimension to forest tree improvement programs. Significant progress has been made during the past five years in the area of plant regeneration via organogenesis and somatic embryogenesis (SE) for economically important tree species. These advances have not only helped the development of efficient gene transfer techniques, but also have opened up avenues for deployment of new high-performance clonally replicated planting stocks in forest plantations. One of the greatest challenges today is the ability to extend this technology to the most elite germplasm, such that it becomes an, economically feasible means for large-scale production and delivery of improved planting stock. Another challenge will be the ability of the forestry research community to capitalize rapidly on current and future genomics-based elucidation of the underlying mechanisms for important but complex phenotypes. Advancements in gene cloning and genomics technology in forest trees have enabled the discovery and introduction of value-added traits for wood quality and resistance to biotic and abiotic stresses into improved genotypes. With these technical advancements, it will be necessary for reliable regulatory infrastructures and processes to be in place worldwide for testing and release of trees improved through biotechnology. Commercialization of planting stocks, as new varieties generated through clonal propagation and advanced breeding programs or as transgenic trees with high-value traits, is expected in the near future, and these trees will enhance the quality and productivity of our plantation forests.     

生物多样性与林木育种

保护生物多样性在林木育种中必须予以重视。传统的林木育种主要考虑遗传增益。长期育种则以维持育种群体的变异性为主要目的。具有丰富生物多样性的天然森林群体是长期育种的基础。长期育种研究应以物种生物学、群体遗传学和居群生态学等为理论基础。主要研究森林群体的性质及群体的动态变化规律。传统林木育种的研究方向、研究内容及林木育种学的教学内容等都应予以适当的调整和补充。     

The origin and genetic diversity of Pinus radiata in Australia

Summary Despite the fact that forest trees are in early stages of domestication there has been little direct evaluation of either the origin of, or genetic diversity within the breeding material in tree improvement programs. Allozyme variation was used to compare the total genetic diversity in the breeding programs of P. radiata within Australia and the five wild populations in North America. The current breeding populations were very similar genetically and were essentially homogenous with only 1.8% of the variation among programs. The total genetic diversity in the species was 0.12, which is a low estimate compared to most conifers. Overall in the Australian material the genetic diversity was somewhat less. The comparison of allelic frequencies in the five native populations with the Australian material indicates that the Monterey and Año Nuevo populations were probably the major source of the original introductions and that a substantial portion of the genetic diversity in the two populations has been captured in current breeding programs. The three southern populations do not appear to be currently represented in the breeding programs. The implications for future breeding strategies are discussed.     

Molecular Genetics and Developmental Physiology: Implications for Designing Better Forest Crops

Current tree biology related to tree genetics and breeding has two important developments that have not well been integrated in the literature. The first is the physiological and biochemical dissection of plant yield, whereas the second is the genetic mapping based on molecular markers, such as RFLPs, RAPDs, AFLPs, and microsatellites. Genetic mapping has revolutionized traditional quantitative genetic analysis by which the genetic variation of a character is described in terms of its mean and (co)variance without the knowledge of the underlying genes. By integrating physiological and developmental studies of yield traits, genetic mapping can provide a unique means for detecting key QTL that play important roles in affecting tree growth and metabolism. The incorporation of these QTL into commercial populations through gene transformation or marker-assisted selection will move current breeding programs strictly based on an empirism to an approach that is mechanistically oriented. In this review, we discuss how plant physiology and development are merged with genetic mapping to formulate the strategy of molecular breeding in which superior forest crops are selected at the gene level. It is anticipated that this novel breeding strategy can potentially provide major breakthroughs for tree breeding.     

A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.     

Biotechnological applications of tissue culture to forest tree improvement

Plant tissue culture techniques are of tremendous potential value to forest tree improvement. The technology is envisaged as playing a complementary role to traditional methods through exploiting spontaneous or induced genetic and epigenetic variability in culture, by use of haploidy and by the use of protoplasts. Haploids and protoplasts will aid in shortening breeding cycles and allow for unconventional crosses respectively. Clonal propagation is an integral part of any tree improvement program, and in addition can play an independent role in reforestation, clonal orchard establishment and in energy foresting. The goals, problems and limitations of these applications of tissue culture technology to forest tree improvement are indicated and assessed.     

From crop domestication to super-domestication

Research related to crop domestication has been transformed by technologies and discoveries in the genome sciences as well as information-related sciences that are providing new tools for bioinformatics and systems' biology. Rapid progress in archaeobotany and ethnobotany are also contributing new knowledge to understanding crop domestication. This sense of rapid progress is encapsulated in this Special Issue, which contains 18 papers by scientists in botanical, crop sciences and related disciplines on the topic of crop domestication. One paper focuses on current themes in the genetics of crop domestication across crops, whereas other papers have a crop or geographic focus. One feature of progress in the sciences related to crop domestication is the availability of well-characterized germplasm resources in the global network of genetic resources centres (genebanks). Germplasm in genebanks is providing research materials for understanding domestication as well as for plant breeding. In this review, we highlight current genetic themes related to crop domestication. Impressive progress in this field in recent years is transforming plant breeding into crop engineering to meet the human need for increased crop yield with the minimum environmental impact - we consider this to be 'super-domestication'. While the time scale of domestication of 10 000 years or less is a very short evolutionary time span, the details emerging of what has happened and what is happening provide a window to see where domestication might - and can - advance in the future.     

林木基因组及功能基因克隆研究概述

在美国能源部资助下, 首个多年生木本植物-- 杨树的全基因组测序已经完成且序列信息已对公众开放。杨树全基因组测序的完成标志着林木基因组进入后基因组研究时代。克隆控制重要性状的主效基因是林木后基因组时代的主要研究内容。近年来, 在一些重要作物, 如水稻、蕃茄及玉米中, 先后成功克隆了多个控制重要农艺性状的主效基因, 分子育种在作物中已进入实用阶段。林木相对于这些重要作物而言, 分子遗传学的研究起步较晚, 同时, 由于林木自身的一些生物学特性, 在林木中精确定位与克隆未知基因一度被视为遗传学研究领域的难点。随着技术和研究手段的不断进步, 以及林木基因组资源的快速积累, 有望在这一领域取得突破, 为在林木中开展分子育种创造条件。文章综述了国际上林木基因组与功能基因克隆研究的现状与新发展, 并对后基因组时代的林木功能基因克隆研究的预期成果进行了展望, 以期为从事该领域研究的科研人员提供参考。     

Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application

Genotype by environment interaction (G×E) refers to the comparative performances of genotypes differing among environments, representing differences in genotype rankings or differences in the level of expression of genetic differences among environments. G×E can reduce heritability and overall genetic gain, unless breeding programmes are structured to address different categories of environments. Understanding the impact of G×E, the role of environments in generating G×E and the problems and opportunities is vital to efficient breeding programme design and deployment of genetic material. We review the current main analytical methods for identifying G×E: factor analytic models, biplot analysis and reaction norm. We also review biological and statistical evidence of G×E for growth, form and wood properties in forest species of global economic importance, including some pines, eucalypts, Douglas-fir, spruces and some poplars. Among these species, high levels of G×E tend to be reported for growth traits, with low levels of G×E for form traits and wood properties. Finally, we discuss possible ways of exploiting G×E to maximise genetic gain in forest tree breeding. Characterising the role of environments in generating interactions is seen as the basic platform, allowing efficient testing of candidate genotypes. We discuss the importance of level-of-expression interaction, relative to rank-change interaction, as being greater than in many past reports, especially for deployment decisions. We examine the impacts of G×E on tree breeding, some environmental factors that cause G×E and the strategies for dealing with G×E in tree breeding, and the future role of genomics.     

Genetic mapping of a new race specific resistance allele effective to Puccinia hordei at the Rph9/Rph12locus on chromosome 5HL in barley

Background

Tea is one of the most popular beverages in the world. Many species in the Thea section of the Camellia genus can be processed for drinking and have been domesticated. However, few investigations have focused on the genetic consequence of domestication and geographic origin of landraces on tea plants using credible wild and planted populations of a single species. Here, C. taliensis provides us with a unique opportunity to explore these issues.

Results

Fourteen nuclear microsatellite loci were employed to determine the genetic diversity and domestication origin of C. taliensis, which were represented by 587 individuals from 25 wild, planted and recently domesticated populations. C. taliensis showed a moderate high level of overall genetic diversity. The greater reduction of genetic diversity and stronger genetic drift were detected in the wild group than in the recently domesticated group, indicating the loss of genetic diversity of wild populations due to overexploitation and habitat fragmentation. Instead of the endangered wild trees, recently domesticated individuals were used to compare with the planted trees for detecting the genetic consequence of domestication. A little and non-significant reduction in genetic diversity was found during domestication. The long life cycle, selection for leaf traits and gene flow between populations will delay the emergence of bottleneck in planted trees. Both phylogenetic and assignment analyses suggested that planted trees may have been domesticated from the adjacent central forest of western Yunnan and dispersed artificially to distant places.

Conclusions

This study contributes to the knowledge about levels and distribution of genetic diversity of C. taliensis and provides new insights into genetic consequence of domestication and geographic origin of planted trees of this species. As an endemic tea source plant, wild, planted and recently domesticated C. taliensis trees should all be protected for their unique genetic characteristics, which are valuable for tea breeding.     

Forestry's fertile crescent: the application of biotechnology to forest trees

Relative to crop plants, the domestication of forest trees is still in its infancy. For example, the domestication of many crop plants was initiated some 10,000 years ago in the so-called 'Fertile Crescent' of the Middle East. By contrast, the domestication of forest trees for the purposes of producing more fibre began in earnest in the last half century. The application of biotechnology to forest trees offers a great potential to hasten the pace of tree improvement for desirable end uses. This review outlines some of the progress that has been made in the application of biotechnology to forest trees, and considers the prospects for biotechnologically based tree improvement in the future.     

Isolation and characterization of microsatellite markers for Thujopsis dolabrata var. hondai (Cupressaceae)1

? Premise of the study: Microsatellite markers were developed for the endemic Japanese species Thujopsis dolabrata var. hondai for studies on forest ecology and tree breeding. ? Methods and Results: We characterized 10 dinucleotide microsatellite loci by screening primers developed using a simple sequence repeat-enriched library. The number of alleles per locus ranged from eight to 44 with an average of 20.3. The observed and expected heterozygosities ranged from 0.326 to 0.854 and from 0.670 to 0.976, respectively. ? Conclusions: The development of these markers can be used to assess useful genetic information for ecological studies and tree breeding in T. dolabrata var. hondai.     

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Buša breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.     

Integrating genomics into Eucalyptus breeding

The advent of high throughput genomic technologies has opened new perspectives in the speed, scale and detail with which one can investigate genes, genomes and complex traits in Eucalyptus species. A genomic approach to a more detailed understanding of important metabolic and physiological processes, which affect tree growth and stress resistance, and the identification of genes and their allelic variants, which determine the major chemical and physical features of wood properties, should eventually lead to new opportunities for directed genetic modifications of far-reaching economic impact in forest industry. It should be kept in mind, however, that basic breeding strategies, coupled with sophisticated quantitative methods, breeder's experience and breeder's intuition, will continue to generate significant genetic gains and have a clear measurable impact on production forestry. Even with a much more global view of genetic processes, genomics will only succeed in contributing to the development of improved industrial forests if it is strongly interconnected with intensive fieldwork and creative breeding. Integrated genomic projects involving multi-species expressed sequence tag sequencing and quantitative trait locus detection, single nucleotide polymorphism discovery for association mapping, and the development of a gene-rich physical map for the Eucalyptus genome will quickly move toward linking phenotypes to genes that control the wood formation processes that define industrial-level traits. Exploiting the full power of the superior natural phenotypic variation in wood properties found in Eucalyptus genetic resources will undoubtedly be a key factor to reach this goal.     

Strategies for genetic conservation of trees in the Peruvian Amazon

Forestry practices and high rates of land clearance for agriculture are causing genetic erosion of valuable tree species in the Peruvian Amazon, thereby endangering the economic sustainability of rural communities and limiting Peru's opportunities for the development of new timber and non-timber forest products. The potential utility and limitations of six low-input interventions to help forestall further genetic erosion in the region are discussed, with a focus on local community involvement. Improved agroforestry systems may help reduce deforestation by increasing farm productivity, although methods to increase the currently low adoption rate of these technologies need to be developed. Use of strategic tree domestication techniques can also improve farm productivity and prevent inadvertent genetic drift and inbreeding associated with traditional domestication practices, although to have a major impact, current programs need to be extended across the region. Woodlot forestry could supplant selective extraction of timber and offers an attractive opportunity for poverty alleviation if appropriate credit and land tenure policies can be developed. However, it may also result in increased deforestation if activities on public land cannot be controlled. The implementation of improved seed collection systems and simple seed transfer guidelines would help to reduce the collection of seed of poor quality and low genetic diversity, and avoid maladapted plantings, although such programs are difficult to monitor and seed costs may increase. Strategic identification and design of in situ conservation areas would help to ensure the viability of conserved populations, but requires the forfeiture of significant revenue from timber concessions.     

Geography and end use drive the diversification of worldwide winter rye populations

To meet the current challenges in human food production, improved understanding of the genetic diversity of crop species that maximizes the selection efficacy in breeding programs is needed. The present study offers new insights into the diversity, genetic structure and demographic history of cultivated rye (Secale cereale L.). We genotyped 620 individuals from 14 global rye populations with a different end use (grain or forage) at 32 genome‐wide simple sequence repeat markers. We reveal the relationships among these populations, their sizes and the timing of domestication events using population genetics and model‐based inference with approximate Bayesian computation. Our main results demonstrate (i) a high within‐population variation and genetic diversity, (ii) an unexpected absence of reduction in diversity with an increasing improvement level and (iii) patterns suggestive of multiple domestication events. We suggest that the main drivers of diversification of winter rye are the end use of rye in two early regions of cultivation: rye forage in the Mediterranean area and grain in northeast Europe. The lower diversity and stronger differentiation of eastern European populations were most likely due to more intensive cultivation and breeding of rye in this region, in contrast to the Mediterranean region where it was considered a secondary crop or even a weed. We discuss the relevance of our results for the management of gene bank resources and the pitfalls of inference methods applied to crop domestication due to violation of model assumptions and model complexity.     

Independent domestications of cultivated tree peonies from different wild peony species

An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programmes that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world; yet, the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, that is, the common and flare cultivated tree peonies, was a single event or whether independent domestications occurred. We used 14 nuclear microsatellite markers and a comprehensive set of 553 tree peonies collected across China, including common tree peonies, flare tree peonies and the wild species or subspecies that are potential contributors to the cultivated tree peonies, that is, Paeonia rockii ssp. rockii, P. rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods, a principal component analysis and approximate Bayesian computations provided clear evidence for independent domestications of these common tree and flare tree peonies from two distinct and allopatric wild species, P. jishanensis and P. rockii ssp. atava, respectively. This study provides the first example of independent domestications of cultivated trees from distinct species and locations. This work also yields crucial insight into the history of domestication of one of the most popular woody ornamental plants. The cultivated peonies represent an interesting case of parallel and convergent evolution. The information obtained in this study will be valuable both for improving current tree peony breeding strategies and for understanding the mechanisms of domestication, diversification and adaptation in plants.     

Dissection of complex traits in forest trees — opportunities for marker-assisted selection

Due to their long reproductive cycles and the time to expression of mature traits, marker-assisted selection is particularly attractive for tree breeding. In this review, we discuss different approaches used for developing markers and propose a method for application of markers in low linkage disequilibrium (LD) populations. Identification of useful markers for application in tree breeding is mainly based on two approaches, quantitative trait locus (QTL) mapping and association genetic studies. While several studies have identified significant markers, effect of the individual markers is low making it difficult to utilize them in breeding programs. Recently, genomic selection (GS) was proposed for overcoming some of these difficulties. In GS, high density markers are used for predicting phenotypes from genotypes. Currently small effective populations with high LD are being tested for GS in tree breeding. For wider application, GS needs to be applied in low LD populations which are found in many tree breeding programs. Here we propose an approach in which the significant markers from association studies may be used for developing prediction models in low LD populations using the same methods as in GS. Preliminary analyses indicate that a modest numbers of markers may be sufficient for developing prediction models in low LD populations. GS based on large numbers of random markers or small numbers of associated markers is poised to make marker-assisted selection a reality in forest tree breeding.     

Trends of genetic study of forest tree and development of useful traits for apple Biotechnology

Conclusion  Forest trees have long generation times and arc highly heterogeneous, so few extended pedigrees are available. Because of these limitations, there is a greater potential for DNA-markers to improve genetic analysis and to accelerate breeding in forest trees. In deciduous fruit plants, the most important traits are fruit qualities such as acidity, sugar content, fruit size, and total yield. As these are quantitative traits that appear to be controlled by a number of loci, it is difficult to make progress in the quick improvement of fruit quality, requiring the elucidation of the position and function of QTLs affecting these traits. Although QTL analysis is important for genetic enhancement, it is time consuming work. Also, for many years until now, DNA-markers have not been applied to practical tree improvement because of technical and theoretical limitations. High levels of heterozygosity and linkage equilibrium of markers in populations were considered to be serious limitations. Now, it is carefully suggested that molecular breeding should be primarily based on the cloning and characterization of useful agronomic traits for direct application to forest tree plants.For example, a monogenic trait that specifically contributes to flower and fruit development is useful for control of thinning. Biotechnology is likely to give valuable genetic improvement of tree species and the adopted strategy based upon biotechnology provides a model system in similar studies for other fruit and woody species. This paper was presented at the 11th Symposium on Plant Biotechnology entitled “Plant Genes and Genetic Resources” organized by Gynheung An, held July 4–5, 1997, by the Botanical Society of Korea     

是金子无论在何处都发光: 玉米和水稻驯化中的趋同选择

野生植物的驯化为人类定居与文明起源奠定了重要基础。在世界范围内不同地区生活的古人类分别对当地不同的野生植物进行了驯化, 而经过驯化的作物常常表现出相似的驯化综合性状。在基因组层面上对趋同选择规律的解析, 可为作物育种提供重要信息与遗传资源。近日, 中国农业大学杨小红/李建生和华中农业大学严建兵领衔的团队从单基因和全基因组2个层次系统解析了玉米(Zea mays)和水稻(Oryza sativa)趋同选择的遗传基础, 发现玉米KRN2与水稻OsKRN2受到了趋同选择, 并通过相似的途径调控玉米与水稻的粒数与产量。他们还发现玉米与水稻在全基因组范围内存在大量趋同选择同源基因对(gene pair), 这些基因在淀粉代谢、糖及辅酶合成等途径特异富集。该研究不仅克隆了在玉米与水稻中均具有重要育种价值的趋同选择同源基因对KRN2/OsKRN2, 而且在全基因组水平上揭示了玉米与水稻趋同选择的规律, 为进一步解析驯化综合性状形成的分子机理及其在育种中的应用奠定了重要理论基础。