Genomics, Domestication, and Evolution of Forest Trees

Sederoff, Ronald R.; Myburg, Alexander Andrew; Kirst, Matias

doi:10.1101/sqb.2009.74.040

Cited by 12 publications

(5 citation statements)

References 147 publications

(154 reference statements)

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“…Genomics is defined as the branch of biotechnology that deals with the DNA sequence of the entire organism's genome (chromosome set) and includes two major disciplines namely functional (determines the biological function of all genes and their products) and structural (determines the three-dimensional structures of proteins). Genomics purpose in tree breeding technologies (Bhalerao et al 2003, Costanza andMcCord 2009) is foremost to describe and make efficient use of the abundant natural genetic variation present within undomesticated forest tree populations (Groover 2007) and contribute to an understanding of the genetic architecture underlying (ecological or industrial) traits of interest on a genomewide scale (Kirst et al 2004, Street et al 2006, Holliday et al 2008, Sederoff et al 2009, Porth et al 2012, Porth et al 2013a, Prunier et al 2013, Verta et al 2013, Beaulieu et al 2014, McKown et al 2014. While GE is the deliberate alteration of the genetic material of living organisms involving the introduction of alien genes from other taxa, resulting in the production of recombinant DNA, which in turn is used to create products (proteins), the original organism is incapable of producing without this alteration (Porth and El-Kassaby 2014).…”

Section: Introductionmentioning

confidence: 99%

“…With such tools in hand, it may be possible to address new or formerly intractable issues such as the understanding of the genetic underpinning of complex traits for applications in conservation and management of natural forests, the improved use of forest trees as carbon sinks, and their use as biofuels feedstock and in contributions to "green chemistry" (renewable biomaterials) (Groover 2007, Tsang et al 2007, Sederoff et al 2009). Thus, genomic basic research can provide both tool and resource development, functional genomics tools in "omics" technologies that relate to high throughput sequencing methods, bioinformatics, databases, and others, e.g., with respect to the development of improved agricultural crop varieties and increased crop productivity using marker-assisted breeding (see for example "Basic Research to Enable Agricultural Development, BREAD" within the National Plant Genome Initiative, USA).…”

Section: Introductionmentioning

confidence: 99%

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Forest genomics research and development in Canada: Priorities for developing an economic framework

Porth

Bull

Ahmed

et al. 2015

The Forestry Chronicle

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Forest genomics is a relatively recent research field and is often poorly understood both by the public and forest managers. Genomics in forestry, an expansion of forest biotechnology, seeks to develop generalized technologies for use in industrial plantations and/or natural forests as well as within process optimization, product development and international trade facilitation. With such tools it is possible to address formerly intractable issues such as understanding the underpinnings of complex traits for conservation management purposes, improved use of forest trees as carbon sinks, feedstock for biofuels and "green chemistry" through deeper understanding and effective utilization of forests' natural variation. Diverse end-users could benefit from genomics tools; for example, real-time detection and mapping of known and novel pathogens along with risk assessments to protect forest nurseries and natural forests from invasive pathogens and reduce economic losses associated with diseases. Since 2001, there has been approximately $123 million invested in Canadian forest genomics research; we thought it would be helpful to summarize projects in Canada and the USA and to identify research priorities and potential economic implications by: (a) developing a robust typology of forest sector genomics research relevant to Canadian application; (b) categorizing each initiative for its application potential (commercial, noncommercial); and, (c) demonstrating with silvicultural gain, insect resistance, and wood composition themes the application of modeling and economic analysis.Keywords: forest genomics, thematic areas, commercial applications, social and ecological dimensions, economic analysis, pest resistance, silvicultural gain, wood composition, market access, tree improvement RéSuméLa génomique forestière est un domaine de recherche relativement récent et souvent mal compris tant du public que des gestionnaires forestiers. La génomique forestière, une extension de la biotechnologie forestière, cherche à développer des technologies généralisées pouvant servir en plantation industrielle ou encore dans les forêts naturelles tout aussi bien que dans les processus d' optimisation, le développement de produit et la facilitation du commerce international. Avec de tels outils, il est possible d'aborder des problèmes autrefois insolubles comme comprendre les fondements des traits complexes utilisés en gestion de la conservation ou une meilleure utilisation des forêts comme réservoirs de carbone, comme source de biocarburants et pour « la chimie verte » rendus possibles grâce à une compréhension plus poussée et une utilisation efficace de la variabilité naturelle au sein des forêts. Plusieurs utilisateurs pourraient utiliser à leur avantage les outils de la génomique; par exemple, pour détecter et cartographier en temps réel les pathogènes connus et nouveaux et faire une éva-luation du risque afin de protéger les pépinières forestières et les forêts naturelles contre des pathogènes envahissants et réduire les pertes ...

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Forest genomics research and development in Canada: Priorities for developing an economic framework

Porth

Bull

Ahmed

et al. 2015

The Forestry Chronicle

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“…Fast-growing trees such as poplars and eucalypts with short rotation times, small genome sizes (500-600 Mbp), large genetic diversity, and established breeding populations are widely cultivated as woody biomass crops and are well suited for biotechnological improvement (5)(6)(7)(8). A tree's amenability to bioprocessing for pulp, paper, cellulose, and other bioproducts is dependent on the aggregate of its wood properties, which are a function of cellular architecture and the chemistry and ultrastructure of the secondary cell walls (SCWs) of wood fiber cells that compose the bulk of woody biomass (9).…”

mentioning

confidence: 99%

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Mizrachi

Verbeke

Christie

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.systems genetics | lignocellulosic biomass | cell wall | bioenergy | network-based data integration

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“…The forests of the world continue to be threatened by climate change, population growth, and loss to agriculture. The ability to conserve natural forests and meet the increasing demand for fuel, biomass, wood, and paper under climate changes, depends on fundamental understanding of tree growth and adaptation through the application of traditional methods and genomics (Sederoff et al 2009).…”

Section: Modeling Forest Biogeographic Patterns Geneticmentioning

confidence: 99%

Identification of Traits, Genes, and Crops of the Future

Pace

Ricciardi

Kumar

et al. 2013

Genomics and Breeding for Climate-Resilient Crops

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Studies on vulnerability and resilience of forest plant communities and crop species have multiplied with the growing realization that societal and scientific response is necessary to adapt to climate change impacts. The DPSIR (Driving forces, Pressure, State, Impact, Response) conceptual framework provides one of the simplest structure of indicators required to connect and model the dynamic systems of the causative and correlative components of climate envelopes and the genetic and genomic complexities regulating adaptive plant response to fluctuating environments and climate. Paleoclimate and vegetation type reconstruction from fossil records and species vicariance help in understanding the long-term dynamics of plant features and trait evolution associated with dispersal and climate changes. Comparative genomics demonstrated as alleles for those plant features (i.e., plant morphology and phenophase alteration), and for biotic (response to bacterial and fungal pathogens) and abiotic (i.e., drought, flooding) stress resistance are still part of the standing genetic endowment of the living gene pools of the crop and forest

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Genomics, Domestication, and Evolution of Forest Trees

Cited by 12 publications

References 147 publications

Forest genomics research and development in Canada: Priorities for developing an economic framework

Forest genomics research and development in Canada: Priorities for developing an economic framework

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Identification of Traits, Genes, and Crops of the Future

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