Sugar signal manipulation by T6P for yield on wheat grain - whole grain RNA-seq
Creators
- 1. Rothamsted Research
- 2. Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
- 3. CONICET- National Council of Scientific and Technical Research, Argentina
- 4. Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
Description
Trehalose 6-phosphate (T6P) is a powerful internal sugar signal in plants yet cannot be directly added nor
fully genetically controlled. A timed microdose of a plant-permeable T6P signalling precursor, DMNB-T6P, causes substantial yield improvements. This repository contains normalised counts table for a RNA-seq of wheat (Triticum aestivum) whole grains after spray with mock/DMNB-T6P.
DESeq2 normalised count table for raw reads deposited in ncbi SRA under Bioproject PRJNXXXX. Related manuscript submitted to XXX.
(...) Following RNA integrity analysis and quantitation (Bioanalyser; Agilent, USA), poly-A enriched cDNA libraries were generated and sequenced on an Illumina Novaseq 6000 sequencing platform generating 30–50 million 150 bp paired-end reads per sample. Low-quality reads and adaptor sequences were removed with Trimmomatic (trimmomatic-0.39.jar PE ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True TRAILING:30 MINLEN:40). The reads were aligned to the wheat reference genome (Triticum aestivum iwgsc_refseqv2.1 using HISAT2/2.2.1-foss-2019b with default parameters and converted to Bam format with SAMtools. Gene abundance was quantified using featureCounts with the High Confidence iwgsc_refseqv2.1 annotation (counting only primary alignments of read pairs with a quality cut-off of 10). Raw counts were normalized using the trimmed mean of M-values method by DESeq2.
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Funding
- Trehalose signalling: understanding and exploiting an emerging small molecule carbohydrate paradigm BB/D006112/1
- UK Research and Innovation
- IWYP Call 2: Transforming yield through source-sink synchronisation BB/S01280X/1
- UK Research and Innovation
- Spraying for Yield BB/R019606/1
- UK Research and Innovation