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

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

doi:10.1111/nph.20026

Title: Providing biological context for GWAS results using eQTL regulatory and co‐expression networks in Populus

Journal Article · 20 August 2024 · New Phytologist

DOI: https://doi.org/10.1111/nph.20026 · OSTI ID:2447203

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Biosciences Division Oak Ridge National Laboratory Oak Ridge 37831 TN USA, Center for Bioenergy Innovation Oak Ridge National Laboratory Oak Ridge 37831 TN USA
Biosciences Division Oak Ridge National Laboratory Oak Ridge 37831 TN USA, Center for Bioenergy Innovation Oak Ridge National Laboratory Oak Ridge 37831 TN USA, Department of Chemical and Biomolecular Engineering University of Tennessee Knoxville 37996 TN USA
Renewable Resources and Enabling Sciences Center National Renewable Energy Laboratory Golden 80401 CO USA
Department of Chemical and Biomolecular Engineering University of Tennessee Knoxville 37996 TN USA

Summary 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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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725; AC36-08GO28308

OSTI ID:: 2447203

Report Number(s):: NREL/JA-5H00-91227

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 2 Vol. 244; ISSN 0028-646X

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
BASIC BIOLOGICAL SCIENCES
Populus
expression quantitative trait loci
gene networks
genome-wide association studies
lignocellulose formation

Title: Providing biological context for GWAS results using eQTL regulatory and co‐expression networks in Populus

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