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Title: Multitrait genome–wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits

Abstract

Genome–wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge.We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)–phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole–genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data.Broad–sense heritability (H2) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single–trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co–expression networks, metabolite analyses, and direct confirmation of gene function through RNAi.Multitrait association identified many more significant associations than single–trait association, potentially revealing pleiotropic effects of individual genes. Furthermore, this approach can be particularly useful for challenging physiological traits such as water–use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co–expressionmore » and co–methylation data.« less

Authors:
ORCiD logo [1];  [1];  [2];  [3];  [1];  [2];  [4];  [4];  [3];  [5];  [3];  [4]; ORCiD logo [2]; ORCiD logo [2];  [3]; ORCiD logo [2];  [6]; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [1]
  1. West Virginia Univ., Morgantown, WV (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Univ. of Georgia, Athens, GA (United States)
  4. ArborGen, Inc., Ridgeville, SC (United States)
  5. Portland State Univ., Portland, OR (United States)
  6. Oregon State Univ., Corvallis, OR (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1545212
Alternate Identifier(s):
OSTI ID: 1505666
Grant/Contract Number:  
AC05-00OR22725; AC05‐00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 223; Journal Issue: 1; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
adaptation; drought tolerance; genome‐wide association studies (GWAS); leaf morphology; pleiotropy; Populus

Citation Formats

Chhetri, Hari B., Macaya‐Sanz, David, Kainer, David, Biswal, Ajaya K., Evans, Luke M., Chen, Jin ‐Gui, Collins, Cassandra, Hunt, Kimberly, Mohanty, Sushree S., Rosenstiel, Todd, Ryno, David, Winkeler, Kim, Yang, Xiaohan, Jacobson, Daniel A., Mohnen, Debra, Muchero, Wellington, Strauss, Steven H., Tschaplinski, Timothy J., Tuskan, Gerald A., and DiFazio, Stephen P. Multitrait genome–wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. United States: N. p., 2019. Web. doi:10.1111/nph.15777.
Chhetri, Hari B., Macaya‐Sanz, David, Kainer, David, Biswal, Ajaya K., Evans, Luke M., Chen, Jin ‐Gui, Collins, Cassandra, Hunt, Kimberly, Mohanty, Sushree S., Rosenstiel, Todd, Ryno, David, Winkeler, Kim, Yang, Xiaohan, Jacobson, Daniel A., Mohnen, Debra, Muchero, Wellington, Strauss, Steven H., Tschaplinski, Timothy J., Tuskan, Gerald A., & DiFazio, Stephen P. Multitrait genome–wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. United States. doi:10.1111/nph.15777.
Chhetri, Hari B., Macaya‐Sanz, David, Kainer, David, Biswal, Ajaya K., Evans, Luke M., Chen, Jin ‐Gui, Collins, Cassandra, Hunt, Kimberly, Mohanty, Sushree S., Rosenstiel, Todd, Ryno, David, Winkeler, Kim, Yang, Xiaohan, Jacobson, Daniel A., Mohnen, Debra, Muchero, Wellington, Strauss, Steven H., Tschaplinski, Timothy J., Tuskan, Gerald A., and DiFazio, Stephen P. Thu . "Multitrait genome–wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits". United States. doi:10.1111/nph.15777.
@article{osti_1545212,
title = {Multitrait genome–wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits},
author = {Chhetri, Hari B. and Macaya‐Sanz, David and Kainer, David and Biswal, Ajaya K. and Evans, Luke M. and Chen, Jin ‐Gui and Collins, Cassandra and Hunt, Kimberly and Mohanty, Sushree S. and Rosenstiel, Todd and Ryno, David and Winkeler, Kim and Yang, Xiaohan and Jacobson, Daniel A. and Mohnen, Debra and Muchero, Wellington and Strauss, Steven H. and Tschaplinski, Timothy J. and Tuskan, Gerald A. and DiFazio, Stephen P.},
abstractNote = {Genome–wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge.We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)–phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole–genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data.Broad–sense heritability (H2) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single–trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co–expression networks, metabolite analyses, and direct confirmation of gene function through RNAi.Multitrait association identified many more significant associations than single–trait association, potentially revealing pleiotropic effects of individual genes. Furthermore, this approach can be particularly useful for challenging physiological traits such as water–use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co–expression and co–methylation data.},
doi = {10.1111/nph.15777},
journal = {New Phytologist},
number = 1,
volume = 223,
place = {United States},
year = {2019},
month = {3}
}

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Works referenced in this record:

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa
journal, August 2012


Functional identification of an Arabidopsis pectin biosynthetic homogalacturonan galacturonosyltransferase
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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
journal, September 2006