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ERX10931443: Illumina NovaSeq 6000 paired end sequencing; Drought tolerance mechanisms in chickpea studied through transcriptomic analysis
1 ILLUMINA (Illumina NovaSeq 6000) run: 9.3M spots, 1.9G bases, 645.3Mb downloads

Design: Drought tolerance mechanisms in chickpea studied through transcriptomic analysis
Submitted by: Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Italy (Department of Agriculture, Food, Environment and F)
Study: Drought tolerance mechanisms in chickpea studied through transcriptomic analysis
show Abstracthide Abstract
In order to identify genes and pathways involved in drought tolerance, RNA was isolated from control and 15-days drought-stressed chickpea plants. Two chickpea genotypes, Desi PI598080 (“D”) and Kabuli Flip07 318C (“K”), respectively sensitive and tolerant to drought stresses were used. The 12 extracted RNAs (2 genotypes x 2 water regimes x 3 biological replicates) were sequenced, and the transcriptomic changes between the genotypes and water conditions were analysed. The genotype with higher drought sensitivity showed a generally higher change of gene transcripts than the genotype with less sensitivity, upregulating genes involved in photophosphorylation process (transferases, oxygen lyases and oxidoreductases), hormones (brassinosteroids, abscissic acid and gibberellin response), solute transporters, nutrient uptake and cell wall properties (cellulose synthases, hemicellulose synthases, poligalacturonases, pectate lyases). These results will be helpful for further studies aiming at identifying genes and molecular markers to develop chickpea cultivars resilient to water stress.
Sample: DesS_2
SAMEA113577847 • ERS15572761 • All experiments • All runs
Organism: Cicer arietinum
Library:
Name: DesS_2_p
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: The leaves of 12 chickpea plants (3 biological replicates for each of the 2 genotypes and 2 water regimes) were collected, immediately frozen in liquid nitrogen and stored at −80 °C The two chickpea genotypes were used: Desi PI598080 and Kabuli Flip07 318C, respectively sensitive and tolerant to drought stresses. Seeds were planted in pots filled with potting soil (horticultural soil of the COMPO SANA® company). On the 21st day after sowing (DAS) the seedlings were thinned to one healthy plant per pot. The plants were well-watered until the beginning of the treatment. After 12 weeks from the germination, pots were separated into two groups: the first group was watered to 70% of the evapo-transpired (EVT) water (control), while the second group was watered to 30% of the EVT water (water stress conditions). The experiment was conducted in a greenhouse under natural light. The average daily temperature inside the greenhouse was the following: 21°C when the plants germinated and 26° C when the stress started. Plants were fertilized with commercial fertilizer (NPK 7:7:7) once a week. Frozen leaves (100mg) have been grounded to a fine powder with a previously sterilized mortar and pestle using liquid nitrogen to prevent RNA degradation. RNA extraction was performed using 100 mg of grounded material using the RNeasy Plant Mini kit (Qiagen). Final elutions were performed using 60 μL of RNase-free water. RNA quality was determined using the Agilent 2100 Bioanalyzer (RNA 6000 nano kit - Agilent Technologies). Twelve transcriptomic libraries were prepared using Illumina mRNA Prep kit, following the manufacturer instructions and a unique dual index combinations were used for each sample for barcoding. The concentration of each library was determined using Qubit™ 4 Fluorometer (dsDNA High Sensitivity Kit - Invitrogen).
Experiment attributes:
Experimental Factor: cultivar: Desi PI598080
Experimental Factor: environmental stress: drought stress
Runs: 1 run, 9.3M spots, 1.9G bases, 645.3Mb
Run# of Spots# of BasesSizePublished
ERR115261699,308,6871.9G645.3Mb2023-09-04

ID:
29250640

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