Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

Chhetri, Hari B.; Furches, Anna; Macaya-Sanz, David; Walker, Alejandro R.; Kainer, David; Jones, Piet; Harman-Ware, Anne E.; Tschaplinski, Timothy J.; Jacobson, Daniel; Tuskan, Gerald A.; DiFazio, Stephen P.

doi:10.3389/fpls.2020.545748

Title: Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

Journal Article · Wed Sep 09 00:00:00 EDT 2020 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2020.545748· OSTI ID:1658962

Chhetri, Hari B.; Furches, Anna; Macaya-Sanz, David; Walker, Alejandro R.; Kainer, David; Jones, Piet; Harman-Ware, Anne E.; Tschaplinski, Timothy J.; Jacobson, Daniel; Tuskan, Gerald A.; DiFazio, Stephen P.

To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office (BETO)

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231; AC36-08GO28308

OSTI ID:: 1658962

Alternate ID(s):: OSTI ID: 1665996; OSTI ID: 1677474

Report Number(s):: NREL/JA-2800-78068; 545748

Journal Information:: Frontiers in Plant Science, Journal Name: Frontiers in Plant Science Vol. 11; ISSN 1664-462X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: Switzerland

Language:: English

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