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Title: Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. Lastly, these polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.
Authors:
 [1] ;  [1] ;  [1] ;  [2] ;  [2] ;  [1] ;  [3] ;  [3] ;  [1] ;  [1] ;  [1]
  1. Univ. of Florida, Gainesville, FL (United States)
  2. Michigan State Univ., East Lansing, MI (United States)
  3. National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Report Number(s):
NREL/JA-5100-67133
Journal ID: ISSN 0028-646X
Grant/Contract Number:
AC36-08GO28308; FG02-05ER64114; SC0003893; IOS-1444543
Type:
Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 213; Journal Issue: 2; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Research Org:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; eastern cottonwood; exome resequencing; genome-wide association studies (GWAS); low-frequency single-nucleotide polymorphisms (SNPs); poplar; Populus deltoides
OSTI Identifier:
1337536
Alternate Identifier(s):
OSTI ID: 1401014

Fahrenkrog, Annette M., Neves, Leandro G., Resende, Jr., Marcio F. R., Vazquez, Ana I., de los Campos, Gustavo, Dervinis, Christopher, Sykes, Robert, Davis, Mark, Davenport, Ruth, Barbazuk, William B., and Kirst, Matias. Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides. United States: N. p., Web. doi:10.1111/nph.14154.
Fahrenkrog, Annette M., Neves, Leandro G., Resende, Jr., Marcio F. R., Vazquez, Ana I., de los Campos, Gustavo, Dervinis, Christopher, Sykes, Robert, Davis, Mark, Davenport, Ruth, Barbazuk, William B., & Kirst, Matias. Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides. United States. doi:10.1111/nph.14154.
Fahrenkrog, Annette M., Neves, Leandro G., Resende, Jr., Marcio F. R., Vazquez, Ana I., de los Campos, Gustavo, Dervinis, Christopher, Sykes, Robert, Davis, Mark, Davenport, Ruth, Barbazuk, William B., and Kirst, Matias. 2016. "Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides". United States. doi:10.1111/nph.14154. https://www.osti.gov/servlets/purl/1337536.
@article{osti_1337536,
title = {Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides},
author = {Fahrenkrog, Annette M. and Neves, Leandro G. and Resende, Jr., Marcio F. R. and Vazquez, Ana I. and de los Campos, Gustavo and Dervinis, Christopher and Sykes, Robert and Davis, Mark and Davenport, Ruth and Barbazuk, William B. and Kirst, Matias},
abstractNote = {Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. Lastly, these polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.},
doi = {10.1111/nph.14154},
journal = {New Phytologist},
number = 2,
volume = 213,
place = {United States},
year = {2016},
month = {9}
}

Works referenced in this record:

Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels
journal, March 2009