Transcriptome data of cultivated tetraploid and hexaploid wheat variety during grain development

Pranab Kumar Mandal,Shubham Rai,Megha Kaushik,Subodh Kumar Sinha,Rajesh Kumar Gupta,Anju Mahendru

doi:10.1016/j.dib.2018.12.058

Pranab Kumar Mandal, Shubham Rai + Show 4 more

Open Access

https://doi.org/10.1016/j.dib.2018.12.058

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Abstract

Wheat is a major food crop and an important component of human diet throughout the world. There are two major types of cultivated wheat; one is tetraploid durum (pasta) wheat and another one is hexaploid bread wheat. Wheat grain is the reservoir of two major dietary components – carbohydrate and protein, which get accumulated during seed maturation and directly affects yield and quality. Hexaploid, having 6 copies of each chromosome differs to a great extent from tetraploid having 4 copies of each chromosome. Studying the gene expression pattern in developing grain would help in understanding the difference in metabolic process as well as involvement of the genes in these two types of wheat. A transcriptional comparison of developing grains was carried out between the two wheat genotypes; tetraploid (AABB:PDW233) and hexaploid (AABBDD:PBW343) using RNA-seq. Approximately 194 million raw reads were obtained from both libraries. After removal of contaminations, a huge proportion (>99%), of high quality reads were obtained, were aligned to reference genome. A total of 2324 up-regulated and 522 down-regulated genes were identified as differentially expressed between PDW233 vs PBW343. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes between durum and bread wheat. This information will help in understanding process grain reserve in tetraploid and hexaploid wheat in relation to their nutritional quality.

Highlights

Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes between durum and bread wheat. This information will help in understanding process grain reserve in tetraploid and hexaploid wheat in relation to their nutritional quality
Biology Transcriptomics Transcriptome sequences Illumina HiSeq. 2000 Raw data (FASTQ) RNA was isolated during grain development Datasets for hexaploid bread wheat and tetraploid durum wheat New Delhi, India http://www.ncbi.nlm.nih.gov/bioproject/503549
This is transcriptome analysis of two wheat genotypes i.e., tetraploid durum wheat (AABB: PDW233) and hexaploid bread wheat (AABBDD: PBW343) using RNA-seq. These are the most prominent and versatile varieties in North Western Plains of India. Owing to their bread and pasta making qualities, these genotypes were selected for transcriptome analysis during grain filling stages

Summary

Plant material and growing condition

Each genotype was grown with three replications, developing grain samples were collected 2 weeks after anthesis (WAA), 3WAA, 4WAA and 5WAA. Frozen grain samples of three biological replicates were pooled. Each pooled sample was ground in and total RNA was extracted using TRIzolsReagent according to standard protocol. RNA with an RNA integrity number (RIN) for PBW343 of 7.6 and PDW233 of 6.1 was only considered mRNA purification. Oligo dT beads (Illuminas TruSeqs RNA Sample Preparation Kit v2) were used to purify mRNA from one microgram of total RNA. Illumina adapters were ligated to the cDNA molecules after end repair and the addition of an ‘A’ base followed by SPRI clean-up. The resultant cDNA library was amplified using PCR for the enrichment of adapter-ligated fragments, quantified using a Nanodrop spectrophotometer (Thermo Scientific) and validated for quality with a Bioanalyzer (Agilent Technologies). The libraries were sequenced on Illumina Hiseq. 2000 platform at SciGenom Next-Gen sequencing facility, Cochin, India

Sequence data assembly and analysis

Functional annotation and biological classification of transcripts