DOI: 10.5068/d1hh31
title: Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations

description: Drought is a major stress for plants, creating a strong selection pressure
 for traits that enable plant growth and survival in dry environments. Many
 drought responses are conserved species-wide responses while others vary
 among populations distributed across heterogeneous environments. We tested
 how six populations of the widely-distributed California valley oak
 (Quercus lobata) sampled from contrasting climates would differ in their
 response to soil drying relative to well-watered controls in a common
 environment by measuring ecophysiological traits in 93 individuals and
 gene expression (RNA-seq) in 42 individuals. Populations did not differ in
 their adjustment of turgor loss point during soil-drying, suggesting a
 generalized species-wide response. Differential expression analysis
 identified 689 genes with a common response to treatment across
 populations, and 470 genes with population-specific responses. Weighted
 gene co-expression network analysis (WGCNA) identified groups of genes
 with similar expression patterns that may be regulated together (gene
 modules). Several gene modules responded differently to water stress among
 populations, suggesting regional differences in gene network regulation.
 Populations from sites with a high mean annual temperature responded to
 the imposed water stress with significantly greater changes in gene module
 expression, indicating that these populations may be locally adapted to
 respond to drought. We propose that this variation among valley oak
 populations provides a mechanism for differential tolerance to the
 increasingly frequent and severe droughts in California.
description: This
 dataset is for a study in which <i>Quercus lobata</i> (valley
 oak) seedlings from six sites were grown in a greenhouse and subjected to
 a water stress or control treatment for 10 or 20 days. Gene expression
 data for a subset of seedlings was obtained through RNAseq on leaf tissue
 for control and treated seedlings at 10 days.  
 Data
 processing for fastq files: Converted raw
 reads from qseq to fastq files. Reads failing
 the Illumina quality filter were removed and reads were
 demultiplexed. Scripts are available at
 github.com/alaynamead/RNAseq_scripts  
 Data
 processing for gene counts file: Converted raw
 reads from qseq to fastq files
 (github.com/alaynamead/RNAseq_scripts) The fastq files
 were demultiplexed (github.com/alaynamead/RNAseq_scripts) Reads were
 trimmed for quality (&lt;27) and adapters, and short reads (&lt;20
 bp) were removed (Cutadapt version 1.12) Aligned to
 <i>Q. lobata</i> transcriptome using end-to-end alignment with
 default 'sensitive' parameters (Bowtie2) Removed reads
 with mapping quality (MAPQ) score &lt;20 (Samtools version
 0.1.19) Removed potential exclusion amplification (ExAmp)
 duplicates (github.com/afontenot/mark-duplicates)
description: <strong>File descriptions</strong>
   fastq files: 42
 gzipped fastq files, one for each sequenced individual and named with
 individual ID. Files include the demultiplexed raw reads for each
 seedling. Reads failing the Illumina quality filter were removed but no
 other processing was done. Read names have
 6 fields, separated by a colon ":" – instrument name, run name,
 lane number, tile number, x coordinate, y coordinate.  
 experiment_design.csv: Includes collection site, treatment,
 maternal family, sequencing lane, and library preparation batch for each
 individual sequenced.  
 gene_counts.csv: Raw transcript counts for each gene (rows)
 and each seedling (columns).  
 seedling_trait_data.csv: Data for each seedling with the
 following information. Includes some missing values as "NA" when
 a measurement was not collected for an individual. Site: location
 acorn was collected from Tree: individual
 seedling ID mom: maternal family ID Treatment:
 control1 and drought1 (control and water stress treatment after 10 days)
 or control2 and drought2 (control and water stress treatment after 20
 days). Family_Wt: acorn weight of family (g) Days_to_germ:
 average days to germination for seedlings from the same maternal
 family Diameter: seedling basal diameter (cm) Height: seedling
 height (cm) larg_leaf_length, larg_leaf_width, larg_leaf_thick: length,
 width, and thickness of the largest leaf (mm) Ave_Thick (two
 measurements and average): average thickness of two leaves (mm)
 Osmometer_mpa (two measurements): osmometer measurement
 used for turgor loss point calculation TLP_mpa (two
 measurements and average): leaf water potential at turgor loss point
 (MPa) Area (two measurements and average): leaf area
 (mm) dry_mass (two measurements and average): leaf dry mass
 (g) soil_mass (two measurements and average): soil mass
 (g) soil water potential (two measurements and average): soil
 water potential (MPa) leaf_water_potential (two measurements and average): leaf
 water potential (MPa) Latitude,
 Longitude, Elevation_m: location of tree from which the acorn was
 collected (elevation in meters) WP_avg_leaf_soil_diff: average leaf water potential –
 average soil water potential (MPa)