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

Abstract

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 significantmore » 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.« less

Authors:
 [1];  [2];  [2];  [3];  [3];  [3];  [4];  [4];  [5]; ORCiD logo [5];  [3]
  1. Univ. of California, Davis, CA (United States); Univ. de Talca, Talca (Chile)
  2. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
  3. Univ. of California, Davis, CA (United States)
  4. GreenWood Resources, Portland, OR (United States)
  5. National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1578253
Report Number(s):
NREL/JA-2700-74675
Journal ID: ISSN 1471-2164
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; populus; GWAS; sequence capture; growth; stable isotopes; lignin; cellulose; wood metabolome

Citation Formats

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., and Neale, David B. Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa. United States: N. p., 2019. Web. doi:10.1186/s12864-019-6160-9.
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. Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa. United States. https://doi.org/10.1186/s12864-019-6160-9
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., and Neale, David B. Wed . "Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa". United States. https://doi.org/10.1186/s12864-019-6160-9. https://www.osti.gov/servlets/purl/1578253.
@article{osti_1578253,
title = {Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa},
author = {Guerra, Fernando P. and Suren, Haktan and Holliday, Jason and Richards, James H. and Fiehn, Oliver and Famula, Randi and Stanton, Brian J. and Shuren, Richard and Sykes, Robert W. and Davis, Mark F. and Neale, David B.},
abstractNote = {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.},
doi = {10.1186/s12864-019-6160-9},
journal = {BMC Genomics},
number = 1,
volume = 20,
place = {United States},
year = {2019},
month = {11}
}

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