De-novo transcriptome assembly and analysis of lettuce plants grown under red, blue or white light

Abstract

Lettuce (Lactuca sativa) is grown in various parts of the world for use as a leafy vegetable. Although the use of light-emitting diode (LED) in controlled plant production systems has been successfully used to enhance nutritional quality and plant growth efficiently, the molecular basis of lettuce’s response to varying light spectra is not studied. Using next-generation sequencing, we have analyzed the transcriptomes of leaf lettuce (Lactuca sativa var. ‘New Red Fire’) grown hydroponically in a modular agricultural production system under three different types of LED lighting: red, blue, and white light. Illumina HiSeq sequencing platform was used to generate paired-end sequence reads (58 Gb raw and 54 Gb clean data) of the transcriptome of lettuce leaves exposed to varying light spectra. The de novo assembled final transcriptome contained 74,096 transcripts. Around 53% and 39% of the assembled transcripts matched to the UniProt and RefSeq RNA sequences, respectively. The validation of the differentially expressed transcripts using RT-qPCR showed complete agreement with RNA-Seq data for 27 transcripts. A comparison of the blue versus red light treatments showed the highest number of significantly differentially expressed transcripts. Among the transcripts significantly up-regulated in blue-light-exposed leaves compared to white-light-exposed leaves, ~ 26% were involved in the ‘response to stress’. Among the transcripts significantly upregulated under red light compared to white light, ~ 6% were associated with ‘nucleosome assembly’ and other processes, such as ‘oxidation–reduction process’ and ‘response to water deprivation’ were significantly enriched. Thus, the result from the current study provides deeper insights into differential gene expression patterns and associated functional aspects under varying light qualities.

Transcriptomic Insights into Molecular Response of Butter Lettuce to Different Light Wavelengths

“…Such regulation occurs at the direct transcriptional level through the action of transcription factors. In lettuce, the blue light (460 nm) exposure up-regulated the transcripts related to stress responses while red light (630 nm) exposure up-regulated oxidation–reduction-related transcripts [ 25 ].…”

“…The photoperiod, strength, and quality are the main determinants of effects of light radiation [ 54 , 55 ]. In lettuce, the secondary metabolite-related transcripts were upregulated upon exposure to the different light wavelengths [ 25 ]. In Rhododendron molle, de novo transcriptome assembly was used to identify genes involved in the regulation of secondary metabolite synthesis [ 56 ].…”

“…A recent study showed that an increased illumination duration can stimulate the dry weight accumulation of lettuce [ 1 ]. The next-generation sequencing was performed to analyze the differential expression of genes in lettuce leaves in response to different light spectra [ 25 ]. A transcriptomic analysis was also performed to identify the circadian clock-related genes in lettuce [ 26 ].…”