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Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations

Citation

Mead, Alayna et al. (2019), Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations, Dryad, Dataset, https://doi.org/10.5068/D1HH31

Abstract

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.

Methods

This dataset is for a study in which Quercus lobata (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 (<27) and adapters, and short reads (<20 bp) were removed (Cutadapt version 1.12)

Aligned to Q. lobata transcriptome using end-to-end alignment with default 'sensitive' parameters (Bowtie2)

Removed reads with mapping quality (MAPQ) score <20 (Samtools version 0.1.19)

Removed potential exclusion amplification (ExAmp) duplicates (github.com/afontenot/mark-duplicates)

Usage Notes

File descriptions

 

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)

Funding

National Science Foundation, Award: IOS-#1444661

University of California Institute for Mexico and the United States