Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus

Mengjun Shu; Timothy B. Yates; Cai John; Anne E. Harman-Ware; Renee M. Happs; Nathan Bryant; Sara S. Jawdy; Arthur J. Ragauskas; Gerald A. Tuskan; Wellington Muchero; Jin Gui Chen

doi:10.1111/nph.20026

Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus

Mengjun Shu, Timothy B. Yates, Cai John, Anne E. Harman-Ware, Renee M. Happs, Nathan Bryant, Sara S. Jawdy, Arthur J. Ragauskas, Gerald A. Tuskan, Wellington Muchero, Jin Gui Chen

Research output: Contribution to journal › Article › peer-review

Abstract

Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.

Original language	English
Pages (from-to)	603-617
Number of pages	15
Journal	New Phytologist
Volume	244
Issue number	2
DOIs	https://doi.org/10.1111/nph.20026
State	Published - Oct 2024

Funding

This material is based upon work supported by the Center for Bioenergy Innovation (CBI), US Department of Energy, Office of Science, Biological and Environmental Research Program under Award Number ERKP886. This research used resources of the Compute and Data Environment for Science (CADES) and the Oak Ridge Leadership Computing Facility (OLCF). Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the Office of Science of the U.S. Department of Energy under contract no.: DE-AC05-00OR22725. The work (proposal: 10.46936/10.25585/60001221) conducted by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under contract no.: DE-AC02-05CH11231. This material is based upon work supported by the Center for Bioenergy Innovation (CBI), US Department of Energy, Office of Science, Biological and Environmental Research Program under Award Number ERKP886. This research used resources of the Compute and Data Environment for Science (CADES) and the Oak Ridge Leadership Computing Facility (OLCF). Oak Ridge National Laboratory is managed by UT\u2010Battelle, LLC for the Office of Science of the U.S. Department of Energy under contract no.: DE\u2010AC05\u201000OR22725. The work (proposal: 10.46936/10.25585/60001221 ) conducted by the US Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 ), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under contract no.: DE\u2010AC02\u201005CH11231.

Keywords

Populus
expression quantitative trait loci
gene networks
genome-wide association studies
lignocellulose formation

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10.1111/nph.20026

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title = "Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus",

abstract = "Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.",

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author = "Mengjun Shu and Yates, {Timothy B.} and Cai John and Harman-Ware, {Anne E.} and Happs, {Renee M.} and Nathan Bryant and Jawdy, {Sara S.} and Ragauskas, {Arthur J.} and Tuskan, {Gerald A.} and Wellington Muchero and Chen, {Jin Gui}",

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language = "English",

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AU - Shu, Mengjun

AU - Yates, Timothy B.

AU - John, Cai

AU - Harman-Ware, Anne E.

AU - Happs, Renee M.

AU - Bryant, Nathan

AU - Jawdy, Sara S.

AU - Ragauskas, Arthur J.

AU - Tuskan, Gerald A.

AU - Muchero, Wellington

AU - Chen, Jin Gui

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AB - Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.

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Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus

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