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

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

doi:10.1186/s12864-019-6160-9

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

Journal Article · Wed Nov 20 00:00:00 EST 2019 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-019-6160-9· OSTI ID:1578253

Guerra, Fernando P. ^[1]; Suren, Haktan ^[2]; Holliday, Jason ^[2]; Richards, James H. ^[3]; Fiehn, Oliver ^[3]; Famula, Randi ^[3]; Stanton, Brian J. ^[4]; Shuren, Richard ^[4]; Sykes, Robert W. ^[5];

^[5]; Neale, David B. ^[3]

Univ. of California, Davis, CA (United States); Univ. de Talca, Talca (Chile)
Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
Univ. of California, Davis, CA (United States)
GreenWood Resources, Portland, OR (United States)
National Renewable Energy Lab. (NREL), Golden, CO (United States)

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. 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. 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.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1578253

Report Number(s):: NREL/JA-2700-74675

Journal Information:: BMC Genomics, Vol. 20, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 14 works

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MOESM1 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566815.v1 The current record is supplemented by this dataset	dataset	January 2019
Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.c.4747373.v1 The current record is supplemented by this collection	collection	January 2019
MOESM1 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566815 The current record is supplemented by this dataset	dataset	January 2019
MOESM4 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566830.v1 The current record is supplemented by this text	text	January 2019
MOESM2 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566824.v1 The current record is supplemented by this text	text	January 2019
MOESM5 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566836.v1 The current record is supplemented by this text	text	January 2019
MOESM3 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566827.v1 The current record is supplemented by this text	text	January 2019
Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.c.4747373 The current record is supplemented by this collection	collection	January 2019
MOESM4 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566830 The current record is supplemented by this text	text	January 2019
MOESM5 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566836 The current record is supplemented by this text	text	January 2019
MOESM3 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566827 The current record is supplemented by this text	text	January 2019
MOESM2 of Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando; Suren, Haktan; Holliday, Jason https://doi.org/10.6084/m9.figshare.10566824 The current record is supplemented by this text	text	January 2019

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

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