Transcriptional Profiling of Winter-Regulated Genes in Populus trichocarpa
Authors:
Raphael Ployet1,2*, Sara S. Jawdy1,2, Miguel Rodriguez1, Ann Wymore1, Ranjan Priya1, Wellington Muchero1,2, Chung-Jui Tsai2,3 ([email protected])
Institutions:
1Biosciences Division, Oak Ridge National Laboratory; 2Center for Bioenergy Innovation, Oak Ridge National Laboratory; 3Warnell School of Forestry and Natural Resources, University of Georgia
Goals
This project’s goals include (1) identification of genes that are specifically expressed during winter dormancy; (2) identifying their transcriptional regulators using expression quantitative trait loci (eQTL) mapping; and (3) transgenic validation of candidate genes and 4) incorporation of workflows into the KBase platform.
Abstract
Xylem and bark samples were collected from 800 natural accessions of mature black cottonwood (Populus trichocarpa) planted in a common garden in Clatskanie, OR. To investigate the molecular mechanisms involved in cell survival during dormancy, samples were collected at two time points: in December 2022, when trees were dormant, and during the growing season in July 2023.
Initially, a small set of core samples was collected from approximately 5-year-old field-grown poplar trees established at the University of Tennessee experimental field site in Alcoa, TN. These samples were then used to refine the sampling procedure to ensure (1) that the most RNA-rich tissues are collected (bark, cambium, and most recent xylem) to capture transcriptomic responses and (2) that both the sampling and subsequent sample processing steps are scalable and suited to study a large population under field conditions.
After this initial optimization, 818 genotypes of the population of natural variants of P. trichocarpa were sampled, generating a total of over 2,400 samples across dormancy and growing seasons. To optimize the transcriptomic analysis, a subset of 40 genotypes was selected based on contrasted growth (highest or lowest trunk diameter) and wood properties (highest or lowest wood density). For these genotypes, samples collected in winter were grinded, RNA were isolated and then used for RNA sequencing (RNA-seq).
Based on transcriptome sequencing results, workflows were tested, optimized, and established to perform comprehensive analyses to meet the project goals. Future efforts include completion of RNA-seq and differential gene expression analyses, eQTL mapping, and incorporation of workflows into the KBase platform.
Funding Information
This research was supported by the DOE Office of Science, BER program, grant no. DE-SC0023166. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S DOE under contract no. DE-AC05- 000R22725.