Genome-wide identification of cold responsive transcription factors in Brassica napus L

Abstract

Background: 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. 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. Results: Global 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. Conclusion: In 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.

Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus

“…This gene family has been described in several plant species, including Arabidopsis [ 6 ], rice [ 7 ], wheat [ 8 ], tomato [ 37 ], pepper [ 38 ], Chinese cabbage [ 21 ], and cucumber [ 39 ], among others, but not in B. napus . Functional characterisation of various DOF proteins has highlighted their role in key plant functions such as seed development and germination [ 40 , 41 ], light-regulated hypocotyl elongation [ 42 ], photosynthesis [ 10 , 43 ], flowering [ 44 , 45 , 46 ], lipid biosynthesis [ 47 , 48 ], carbon metabolism [ 5 ], pollen development [ 49 ], abiotic stress response [ 46 , 50 , 51 ], and several other biological processes. In this study, we performed in silico genome-wide identification, comparison, and evolutionary analysis of the Dof gene family in B. napus .…”

“…The majority of BnaDofs in our analysis were differentially regulated upon exposure to low temperatures. A recent study in B. napus exploring the cold-responsive TFs reported the changes in expression of Dof genes in response to the cold stress response and suggested their possible role in imparting cold tolerance [ 50 ]. In cotton, the overexpression of the GhDof1 gene enhanced cold tolerance during the seedling stage [ 48 ].…”

An Insight into the Responses of Early-Maturing Brassica napus to Different Low-Temperature Stresses

“…Similar as other plants, the expression of CBF and COR genes were induced by chilling and freezing stresses in different ecotypes rapeseed with different cold tolerance [11,36,[41][42][43][44][45]. CBFs (BnaAnng34260D/BnaCnng49280D/BnaC03g71900D/ BnaC07g39680D), Kin1 and COR15 all were upregulated in both winter and semiwinter ecotype rapeseeds after cold stress (4°C for 7 days), while BnaA08g30910D (a CBF-like gene) and BnCOR25 were not varied in expression in any cold stressed rapeseeds [41]. Furthermore, COR15A/B, COR413-PM1 and nine CBF1/2/4 genes all were strongly upregulated in winter and spring ecotype rapeseeds after cold stress (4°C for 12 h) [42].…”

Identification Of Arabidopsis genes associated with cold tolerance based on integrated bioinformatics analysis

“…Recently, 5742 genes were differentially expressed to reveal the gene regulators and pathways involved in cold tolerance in Brassica napus. These DEGs were related to the inhibition of photosynthesis and the primary biological processes (Ke et al 2020). To identify early responsive events in Oryza sativa under cold stress, a transcriptome profile was performed to identify 516 DEGs that were involved in Ca 2+ and ROS-mediated signaling, and the DREB/CBF pathway (Dasgupta et al 2020).…”