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Sample GSM2251919

Query DataSets for GSM2251919

Status

Public on Jul 26, 2016

Title

F1_rep1

Sample type

SRA

Source name

Organism

Medicago sativa

Characteristics

strain: CW 064027
growth protocol: grown under 1.53 dS/m salt condition
tissue: leaf and stem

Treatment protocol

Three electrical conductivity (EC) test levels formulated together with hydroponic growth solutions were used to irrigate the tanks: 1.53 dSm-1 as the no-salt control solution, and 8.03 and 15.61 dSm-1 as salt-supplemented solutions containing increased concentrations of sulphate-based sodium, calcium, and magnesium salts (composition fully defined in Steppuhn et al., 2012). Each EC level was replicated three times, and the two salinity-tolerant populations were replicated four times among the tanks, such that a total of 100 genotypes per salt-tolerant population were in the experiment. This covered the entire genotypic variation within each outcrossed alfalfa population at each EC level, and the salt-sensitive Rangelander genotypes were included in every tank as a population and tank control (Figure 1D). Since growth was retarded in all populations irrigated at 15.61 dSm-1, high-EC tanks were also positioned at an outer edge so that small plants would not be over-shadowed by vigorously growing plants at the other EC levels (Figure 1D). Sand tanks were irrigated 4 times (for 5 min each) over a 24 h cycle with the hydroponic solutions. Harvest date was determined when the 4th-regrowth forage was at 10% flowering in populations growing at 1.53 dSm-1.

Growth protocol

Alfalfa forage samples were grown in hydroponic sand tanks situated in a greenhouse facility at the Canadian Salt Lab at Swift Current, SK, Canada. Seeds for each population were placed 13 mm deep into the sand bed and positioned 40 mm apart within and between the rows, resulting in 641 seed m-2. Upon completion of emergence (after 1 month), the surviving plants were thinned to 25 genotypes (individuals have unique genotypes within the overall population) per tank quadrant. Each tank held three randomly chosen salinity-tolerant populations (i.e., three quadrants) and the remaining quadrant (randomized for within-tank position) held 25 genotypes of a more salt-sensitive AC Rangelander population.

Extracted molecule

polyA RNA

Extraction protocol

RNA was extracted using Qiagen Rneasy Plant mini kit. RNA quantity and quality was assessed using a Qubit fluorometry assay (Invitrogen Corp., Carlsbad, CA, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), respectively.
Libraries were prepared using a Truseq stranded mRNA kit (Illumina, San Diego, USA) following the manufacturer’s instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

Data processing

QC with FastQC (defaults)
Trimming with Trimmomatic (defaults)
Mapping with Tophat (defaults)
Exp analysis using Cufflinks (cufflinks-2.1.1.Linux_x86_64) (defaults)
DE genes were visualized in MapMan software
Genome_build: Transcripts combined from two other papers as mentioned in the manuscript was used as reference (see Ali_alfalfa_reference_split.fasta linked as supplementary file on the Series record).
Supplementary_files_format_and_content: [gene_exp.diff] file reports FPKMs

Submission date

Jul 26, 2016

Last update date

May 15, 2019

Contact name

Dwayne Hegedus

E-mail(s)

[email protected]

Phone

(306) 385-9427

Organization name

Agriculture and Agri-Food Canada