Researchers use RNA-Seq to understand the effects of climate change

Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome.

The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22° ± 3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. Researchers from the Indian Agricultural Research Institute assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress.


Work flow chart depicting the de novo sequencing of wheat under the heat stress. Control and HS-treated samples of wheat cv. HD2329 was used for the sequencing; Illumina HiSeq 2000 and Roche GS-FLX 454 platforms were used for the de novo assembly.

In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.

Kumar RR, Goswami S, Sharma SK, Kala YK, Rai GK, Mishra DC, Grover M, Singh GP, Pathak H, Rai A, Chinnusamy V, Rai RD. (2015) Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.). OMICS [Epub ahead of print]. [abstract]

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