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Transcript expression data. Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes

Citation

Setter, Tim; Oluwasanya, Deborah (2021), Transcript expression data. Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes, Dryad, Dataset, https://doi.org/10.5061/dryad.j9kd51ccn

Abstract

To advance understanding of the mechanistic factors regulating cassava flowering, the leaf transcriptomes at 1) two stages of plant development were compared in two genotypes at Ubiaja and Ibadan, Nigeria; and 2) three controlled-environment growth chambers.

Methods

For the first data set, three biological replicates were analyzed for two locations, two genotypes, and two stages of plant development.  Field experiments were conducted from June 2017 to January 2018 at two field stations in Nigeria: Ibadan (7.4° N and 3.9°E, 230 m asl) in Oyo State and Ubiaja (6.6° N and 6.4° E, 221 m asl) in Edo State.  At each location the land was tilled and ridged with no extra nutrients or soil amendments added. Fields were kept free of weeds with hand weeding.  Cassava stem cuttings of similar lengths (about 20 cm each), were planted simultaneously in June 17, 2017 at both locations. For the second data set in controlled-environment growth chambers, three biological replicates were analyzed for three temperatures, three genotypes, and two stages of plant development.  Plants were grown in three growth chambers set at 22°C/18°C, 28°C/24°C, and 34°C/30°C, day/ night temperatures, respectively. Photoperiod was held constant at 12 h light and 12 h dark.   Growth chambers were Conviron Controlled Environments, Ltd (Winnipeg, Manitoba, Canada) model PGW 36 walk-in growth rooms (135 X 245 X 180 cm [ht.]) with ten 400 W high pressure sodium and ten 400 W metal halide lamps providing about 600 μmol photons (400-700 nm) m-2 s-1 at 1 m above the soil surface.

RNA extraction:  In brief (see published paper for details): total RNA was extracted from each sample by a modified CTAB protocol. Samples were ground to a fine powder in a mortar and pestle chilled with liquid N2;  chloroform was added, mixed,  centrifuged and the top layer was used.  Samples were purified on silica RNA columns and eluted with RNAase-free water.  3 ́RNA-seq libraries were prepared  at the Cornell Genomics facility using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD.  See published paper for details.  The libraries were quantified with the intercalating dye QuantiFluor, evenly pooled sequenced on one lane of an Illumina NextSeq500 sequencer, single-end 1x86bp de-multiplexed based upon six base i7 indices using Illumina bcl2fastq2 software (version 2.18; Illumina, Inc., San Diego, CA).   Illumina adapters were removed from the de-multiplexed fastq files using Trimmomatic (version 0.36; Bolger et al. 2014). Poly-A tails and poly-G stretches of at least 10 bases in length were then removed keeping reads at least 18 bases in length after trimming The trimmed reads were aligned to the Manihot esculenta genome assembly 520_v6 (https://genome.jgi.doe.gov) using the STAR aligner (version 2.7.0f; (Dobin et al., 2012)).   Matrix table with raw gene counts for every gene and every sample.

Usage Notes

Metadata are provided in the uploaded file.

Funding

Bill and Melinda Gates Foundation, Award: OPPID INV‐007637