Abstract
BackgroundCold stress is one of the primary environmental factors that affect plant growth and productivity, especially for crops like Brassica napus that live through cold seasons. Till recently, although a number of genes and pathways involved in B. napus cold response have been revealed by independent studies, a genome-wide identification of the key regulators and the regulatory networks is still lack. In this study, we investigated the transcriptomes of cold stressed semi-winter and winter type rapeseeds in short day condition, mainly with the purpose to systematically identify the functional conserved transcription factors (TFs) in cold response of B. napus.ResultsGlobal modulation of gene expression was observed in both the semi-winter type line (158A) and the winter type line (SGDH284) rapeseeds, in response to a seven-day chilling stress in short-day condition. Function analysis of differentially expressed genes (DEGs) revealed enhanced stresses response mechanisms and inhibited photosynthesis in both lines, as well as a more extensive inhibition of some primary biological processes in the semi-winter type line. Over 400 TFs were differentially expressed in response to cold stress, including 56 of them showed high similarity to the known cold response TFs and were consistently regulated in 158A and SGDH284, as well as 25 TFs which targets were over-represented in the total DEGs. A further investigation based on their interactions indicated the critical roles of several TFs in cold response of B. napus.ConclusionIn summary, our results revealed the alteration of gene expression in cold stressed semi-winter and winter ecotype B. napus lines and provided a valuable collection of candidate key regulators involved in B. napus response to cold stress, which could expand our understanding of plant stress response and benefit the future improvement of the breed of rapeseeds.
Highlights
Cold stress is one of the primary environmental factors that affect plant growth and productivity, especially for crops like Brassica napus that live through cold seasons
Identification and general features of differentially expressed genes (DEGs) High-throughput sequencing generated an average of about 6.5 million qualified short reads from each samples of the semi-winter type (158A) and the winter type (SGDH284) B. napus lines, with around 70% of them were mapped to the reference genome (Additional file 1: Table S1)
In this work, derived from the estimated expression profiles of two B. napus lines, we found that expression of about 40% of the transcription factors (TFs) were detectable (FPKM ≥1) in at least one of the investigated samples. 692 and 708 TFs were differentially expressed during low-temperature exposure of 158A and SGDH284, respectively, including 402 TFs shared by two lines
Summary
Cold stress is one of the primary environmental factors that affect plant growth and productivity, especially for crops like Brassica napus that live through cold seasons. A number of genes and pathways involved in B. napus cold response have been revealed by independent studies, a genome-wide identification of the key regulators and the regulatory networks is still lack. We investigated the transcriptomes of cold stressed semi-winter and winter type rapeseeds in short day condition, mainly with the purpose to systematically identify the functional conserved transcription factors (TFs) in cold response of B. napus. I.e., a period of exposure to low but non-freezing temperature, would increase the frost tolerance in a wide range of plants [1]. In this process, a series of plant biochemical and physiological features are adjusted. Involvement of some CBF-independent regulatory pathways in cold response was characterized in many plants, such as the plant hormones of auxin, abscisic acid, ethylene, gibberellins and jasmonic acid [4]
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