Hardwood Tree Genomics: Unlocking Woody Plant Biology

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.

doi:10.3389/fpls.2018.01799

Title: Hardwood Tree Genomics: Unlocking Woody Plant Biology

Journal Article · Mon Dec 17 00:00:00 EST 2018 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2018.01799· OSTI ID:1487165

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.

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231; USDA2016-51181-25408

OSTI ID:: 1487165

Alternate ID(s):: OSTI ID: 1493142; OSTI ID: 1616058

Journal Information:: Frontiers in Plant Science, Journal Name: Frontiers in Plant Science Vol. 9; ISSN 1664-462X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: Switzerland

Language:: English

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Cited by: 19 works

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