Abstract
Hidden underground, root systems constitute an important part of the plant for its development, nourishment and sensing the soil environment around it, but we know very little about its genetic regulation in crop plants like wheat. In the present study, we de novo assembled the root transcriptomes in reference cultivar Chinese Spring from RNA-seq reads generated by the 454-GS-FLX and HiSeq platforms. The FLX reads were assembled into 24,986 transcripts with completeness of 54.84%, and the HiSeq reads were assembled into 91,543 high-confidence protein-coding transcripts, 2,404 low-confidence protein-coding transcripts, and 13,181 non-coding transcripts with the completeness of >90%. Combining the FLX and HiSeq assemblies, we assembled a root transcriptome of 92,335 ORF-containing transcripts. Approximately 7% of the coding transcripts and ~2% non-coding transcripts are not present in the current wheat genome assembly. Functional annotation of both assemblies showed similar gene ontology patterns and that ~7% coding and >5% non-coding transcripts are root-specific. Transcription quantification identified 1,728 differentially expressed transcripts between root tips and maturation zone, and functional annotation of these transcripts captured a transcriptional signature of longitudinal development of wheat root. With the transcriptomic resources developed, this study provided the first view of wheat root transcriptome under different developmental zones and laid a foundation for molecular studies of wheat root development and growth using a reverse genetic approach.
Highlights
As the “hidden half” of a plant, root systems provide plant water, nutrients, and an anchorage from the soil, produce growth regulators and sense soil environmental changes such as pH, moisture, and mineral content
We sequenced the transcriptome of the Chinese Spring (CS) root tip using the 454 GS-FLX platform (Roche), which generated 1,086,240 raw reads from a single pyrosequencing run
As the evolution of sequencing technologies, we subsequently sequenced six libraries, three for the root tips and three from the rest of root tissues using HiSeq 2000 platform (Illumina), which generated 192,767,620 single-end sequence reads of 100 bp length
Summary
As the “hidden half” of a plant, root systems provide plant water, nutrients, and an anchorage from the soil, produce growth regulators and sense soil environmental changes such as pH, moisture, and mineral content. A well-developed root system is critical for sustainable crop production. Despite the important roles in plant development and growth, our understanding of root development and growth is still very limited as compared to the aboveground half. Most knowledge of root biology comes from the model plant Arabidopsis.
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