Journal Article

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa

Shuren, Richard, Fiehn, Oliver, Davis, Mark F., Richards, James H., Neale, David B., Suren, Haktan, Stanton, Brian J., Sykes, Robert, Famula, Randi, Holliday, Jason, Guerra, Fernando P.

2019

Overview

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 δ 15 N. 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,Springer,BMC
• Subject: 09 BIOMASS FUELS / Analysis / Animal Genetics and Genomics / Architecture / Biodiesel fuels / Biomarkers / Biomass / Biomedical and Life Sciences / California / Carbon - metabolism / Cellulose / Chemical composition / Chromosomes / Cloning / Deoxyribonucleic acid / DNA / DNA biosynthesis / Ecophysiology / Energy metabolism / Environmental effects / Ethanol / Gene expression / Genes / Genetic aspects / Genetic diversity / Genetic improvement / Genetic Markers / Genetic polymorphisms / Genetic research / Genome, Plant / Genome-wide association studies / Genome-Wide Association Study / Genomes / Genomics / Genotyping / Growth / GWAS / Life Sciences / Lignin / Lignin - biosynthesis / Lignocellulose / Metabolic Networks and Pathways - genetics / Metabolites / Metabolome / Metabolomics / Microarrays / Microbial Genetics and Genomics / Morphology / Nitrogen - metabolism / Nucleotides / Organic chemistry / Phenology / Phenotypic variations / Plant Genetics and Genomics / Plant genomics / Plant Leaves - genetics / Plant Leaves - metabolism / Plant species / Polygenic inheritance / Polymorphism, Single Nucleotide / Polysaccharides / Population / Populus / Populus - genetics / Populus - metabolism / Populus trichocarpa / Protein biosynthesis / Protein synthesis / Protein turnover / Proteins / Proteomics / Quantitative Trait, Heritable / Research Article / Ribonucleic acid / RNA / Sequence capture / Single nucleotide polymorphisms / Single-nucleotide polymorphism / Stable isotopes / Technology / Whole Exome Sequencing / Wood / Wood - genetics / Wood - metabolism / wood metabolome