Hardwood Tree Genomics: Unlocking Woody Plant Biology
Abstract
Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (“evo-devo”) approach to understanding the unique biology of largemore »
- Authors:
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA
- OSTI Identifier:
- 1487165
- Alternate Identifier(s):
- OSTI ID: 1493142; OSTI ID: 1616058
- Grant/Contract Number:
- AC05-00OR22725; AC02-05CH11231; USDA2016-51181-25408
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Plant Science
- Additional Journal Information:
- Journal Name: Frontiers in Plant Science Journal Volume: 9; Journal ID: ISSN 1664-462X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; tree habit; somatic mutations; evolutionary ecology; quantitative genetics; adaptive traits; comparative genomics
Citation Formats
Tuskan, Gerald A., Groover, Andrew T., Schmutz, Jeremy, DiFazio, Stephen Paul, Myburg, Alexander, Grattapaglia, Dario, Smart, Lawrence B., Yin, Tongming, Aury, Jean-Marc, Kremer, Antoine, Leroy, Thibault, Le Provost, Gregoire, Plomion, Christophe, Carlson, John E., Randall, Jennifer, Westbrook, Jared, Grimwood, Jane, Muchero, Wellington, Jacobson, Daniel, and Michener, Joshua K. Hardwood Tree Genomics: Unlocking Woody Plant Biology. Switzerland: N. p., 2018.
Web. doi:10.3389/fpls.2018.01799.
Tuskan, Gerald A., Groover, Andrew T., Schmutz, Jeremy, DiFazio, Stephen Paul, Myburg, Alexander, Grattapaglia, Dario, Smart, Lawrence B., Yin, Tongming, Aury, Jean-Marc, Kremer, Antoine, Leroy, Thibault, Le Provost, Gregoire, Plomion, Christophe, Carlson, John E., Randall, Jennifer, Westbrook, Jared, Grimwood, Jane, Muchero, Wellington, Jacobson, Daniel, & Michener, Joshua K. Hardwood Tree Genomics: Unlocking Woody Plant Biology. Switzerland. https://doi.org/10.3389/fpls.2018.01799
Tuskan, Gerald A., Groover, Andrew T., Schmutz, Jeremy, DiFazio, Stephen Paul, Myburg, Alexander, Grattapaglia, Dario, Smart, Lawrence B., Yin, Tongming, Aury, Jean-Marc, Kremer, Antoine, Leroy, Thibault, Le Provost, Gregoire, Plomion, Christophe, Carlson, John E., Randall, Jennifer, Westbrook, Jared, Grimwood, Jane, Muchero, Wellington, Jacobson, Daniel, and Michener, Joshua K. Mon .
"Hardwood Tree Genomics: Unlocking Woody Plant Biology". Switzerland. https://doi.org/10.3389/fpls.2018.01799.
@article{osti_1487165,
title = {Hardwood Tree Genomics: Unlocking Woody Plant Biology},
author = {Tuskan, Gerald A. and Groover, Andrew T. and Schmutz, Jeremy and DiFazio, Stephen Paul and Myburg, Alexander and Grattapaglia, Dario and Smart, Lawrence B. and Yin, Tongming and Aury, Jean-Marc and Kremer, Antoine and Leroy, Thibault and Le Provost, Gregoire and Plomion, Christophe and Carlson, John E. and Randall, Jennifer and Westbrook, Jared and Grimwood, Jane and Muchero, Wellington and Jacobson, Daniel and Michener, Joshua K.},
abstractNote = {Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (“evo-devo”) approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.},
doi = {10.3389/fpls.2018.01799},
journal = {Frontiers in Plant Science},
number = ,
volume = 9,
place = {Switzerland},
year = {2018},
month = {12}
}
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