Exome Resequencing and GWAS for Growth, Ecophysiology, and Chemical and Metabolomic Composition of Wood of Populus trichocarpa

Mark Davis, Fernando Guerra, Haktan Suren, Jason Holliday, James Richards, Oliver Fiehn, Randi Famula, Brian Stanton, Richard Shuren, David Neale, Robert Sykes

Research output: Contribution to journalArticlepeer-review

16 Scopus Citations

Abstract

Background: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation. Results: We identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others. Conclusions: SNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies.

Original languageAmerican English
Article number875
Number of pages14
JournalBMC Genomics
Volume20
Issue number1
DOIs
StatePublished - 2019

Bibliographical note

Publisher Copyright:
© 2019 The Author(s).

NREL Publication Number

  • NREL/JA-2700-74675

Keywords

  • Cellulose
  • Growth
  • GWAS
  • Lignin
  • Populus
  • Sequence capture
  • Stable isotopes
  • Wood metabolome

Fingerprint

Dive into the research topics of 'Exome Resequencing and GWAS for Growth, Ecophysiology, and Chemical and Metabolomic Composition of Wood of Populus trichocarpa'. Together they form a unique fingerprint.

Cite this