Systems genetics of wood formation

Mizrachi, Eshchar; Myburg, Alexander Andrew

doi:10.1016/j.pbi.2016.02.007

Cited by 41 publications

(33 citation statements)

References 46 publications

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“…Some of these pathways, SCW polysaccharide and lignin biosynthesis in particular, represent a strong, irreversible carbon sink and directly or indirectly use core metabolites (glucose/ UDP-glucose and fructose) that are also used for growth and physiological/cellular homeostasis (energy metabolism, production of amino acids, etc.). These metabolic interdependencies and the multitude of biological processes involved result in woody biomass traits having complex genetic architectures, especially in highly outbred organisms such as forest trees (11).…”

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confidence: 99%

“…However, they have not necessarily yielded insight into the complex interactions of the genes that naturally affect cell wall chemistry and ultrastructure in ways that do not interfere with normal plant growth, form, and biomass accumulation. The characterization of natural genetic perturbations segregating in phenotypically wild-type individuals offers an attractive alternative tool to study properties that emerge from permissible genetic variation (11,13). With the availability of high-throughput genotyping and high-resolution linkage maps in Populus (14,15) and Eucalyptus (16)(17)(18)(19), genetic approaches such as quantitative trait locus (QTL) (14,20,21) and LD-based association mapping (22)(23)(24)(25) are becoming feasible to…”

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confidence: 99%

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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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confidence: 99%

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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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“…New Phytologist regulation in xylem tissue (Mizrachi & Myburg, 2016). These networks show that plastid and mitochondrial C metabolic pathway genes are central to, and co-expressed with, the distinct developmental processes of xylogenesis (Figs 1, 5).…”

Section: Researchmentioning

confidence: 97%

Organellar carbon metabolism is coordinated with distinct developmental phases of secondary xylem

et al. 2019

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Summary Subcellular compartmentation of plant biosynthetic pathways in the mitochondria and plastids requires coordinated regulation of nuclear encoded genes, and the role of these genes has been largely ignored by wood researchers. In this study, we constructed a targeted systems genetics coexpression network of xylogenesis in Eucalyptus using plastid and mitochondrial carbon metabolic genes and compared the resulting clusters to the aspen xylem developmental series. The constructed network clusters reveal the organization of transcriptional modules regulating subcellular metabolic functions in plastids and mitochondria. Overlapping genes between the plastid and mitochondrial networks implicate the common transcriptional regulation of carbon metabolism during xylem secondary growth. We show that the central processes of organellar carbon metabolism are distinctly coordinated across the developmental stages of wood formation and are specifically associated with primary growth and secondary cell wall deposition. We also demonstrate that, during xylogenesis, plastid‐targeted carbon metabolism is partially regulated by the central clock for carbon allocation towards primary and secondary xylem growth, and we discuss these networks in the context of previously established associations with wood‐related complex traits. This study provides a new resolution into the integration and transcriptional regulation of plastid‐ and mitochondrial‐localized carbon metabolism during xylogenesis.

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“…However, the approach can identify gene modules, which are groups of highly correlated gene expression patterns, to refine a candidate gene list. Furthermore, positive and negative correlations within networks, across developmental stages, different plant organs (such as whole leaf and oil glands), or from genetically modified plants compared with the wild type, will yield predictive models of pathway regulation and flux [70,71]. Otero et al…”

Section: A Systems-level Understanding Of Terpene Biosynthesismentioning

confidence: 99%

Plant-Derived Terpenes: A Feedstock for Specialty Biofuels

Mewalal

Rai

Kainer

et al. 2017

Trends in Biotechnology

145

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Research toward renewable and sustainable energy has identified specific terpenes capable of supplementing or replacing current petroleum-derived fuels. Despite being naturally produced and stored by many plants, there are few examples of commercial recovery of terpenes from plants because of low yields. Plant terpene biosynthesis is regulated at multiple levels, leading to wide variability in terpene content and chemistry. Advances in the plant molecular toolkit, including annotated genomes, high-throughput omics profiling, and genome editing, have begun to elucidate plant terpene metabolism, and such information is useful for bioengineering metabolic pathways for specific terpenes. We review here the status of terpenes as a specialty biofuel and discuss the potential of plants as a viable agronomic solution for future terpene-derived biofuels.

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Systems genetics of wood formation

Cited by 41 publications

References 46 publications

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

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

Organellar carbon metabolism is coordinated with distinct developmental phases of secondary xylem

Plant-Derived Terpenes: A Feedstock for Specialty Biofuels

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