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. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.
School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.|Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.
Annette M
AM
Fahrenkrog
School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.|Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.
Leandro G
LG
Neves
School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.|Genetics and Genomics Graduate Program, University of Florida, PO Box 103610, Gainesville, FL, 32610, USA.
Márcio F R
MF
Resende
Department of Epidemiology and Biostatistics, Michigan State University, 909 Fee Road, East Lansing, MI, 48824, USA.
Ana I
AI
Vazquez
Department of Epidemiology and Biostatistics, Michigan State University, 909 Fee Road, East Lansing, MI, 48824, USA.|Statistics Department, Michigan State University, 619 Red Cedar Road, MI, 48824, USA.
Gustavo
G
de Los Campos
School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.
Christopher
C
Dervinis
National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
Robert
R
Sykes
National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
Mark
M
Davis
Biology Department, University of Florida, PO Box 118525, Gainesville, FL, 32611, USA.
Ruth
R
Davenport
Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.|Biology Department, University of Florida, PO Box 118525, Gainesville, FL, 32611, USA.|University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL, 32611, USA.
William B
WB
Barbazuk
School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.|Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.|University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL, 32611, USA.
Matias
M
Kirst
D000595:Amino Acid Sequence; D004734:Energy Metabolism / Q000235:genetics*; D017343:Genes, Plant; D056426:Genetic Loci; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D032107:Populus / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA
D005819:Genetic Markers; D010940:Plant Proteins

Populus deltoides
; eastern cottonwood; exome resequencing; genome-wide association studies (GWAS); low-frequency single-nucleotide polymorphisms (SNPs); poplar