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. 2024 Dec 19;25(24):13592.
doi: 10.3390/ijms252413592.

Genome-Wide Identification and Analysis of BrTCP Transcription Factor Family Genes Involved in Cold Stress Tolerance in Winter Rapeseed (Brassica rapa L.)

Yanxia Xu  1 , Li Ma  1 , Xiucun Zeng  2 , Yaozhao Xu  2 , Xiaolei Tao  1 , Abbas Muhammad Fahim  1 , Lijun Liu  1 , Junyan Wu  1 , Gang Yang  1 , Yuanyuan Pu  1 , Tingting Fan  1 , Wangtian Wang  1 , Wancang Sun  1
Affiliations

Genome-Wide Identification and Analysis of BrTCP Transcription Factor Family Genes Involved in Cold Stress Tolerance in Winter Rapeseed (Brassica rapa L.)

Yanxia Xu et al. Int J Mol Sci. .

Abstract

TCP transcription factors are important during plant growth and stress responses. However, their role in the cold stress response of Brassica rapa L. remains poorly understood. In this research, we identified the TCPs gene family in B. rapa to learn the features of the BrTCP gene family, functionally annotating the interacting proteins of TCP4 and analyzing their expression levels. Our results illustrated the presence of 19 members of the BrTCPs family in B. rapa, exhibiting molecular weights ranging from 27,367.45 to 59,433.64 Da. All identified proteins were classified as unstable, with isoelectric points ranging from 5.5 to 9.48. Subcellular localization forecasted that TCP proteins were all positioned in the nucleus. The BrTCP gene structure is relatively simple, with only seven members possessing introns, and none of the members contain UTR regions. BrTCPs comprise hormone-, light-, and stress-responsive elements. We found that the frequency of photoresponsive elements was greatest in the promoter region, suggesting that BrTCP genes are regulated by light signals and function synergistically with plant growth and development. In addition, five candidate interaction proteins of BrTCP4 were identified using yeast two-hybrid screening. RNA-Seq and q-PCR analyses of the interacting genes revealed differential expression of BrTCP family genes across various tissues following cold stress. Significant responses were observed under low-temperature stress, drought stress, and rehydration treatment, suggesting that these genes play crucial roles as regulators of the molecular network mechanisms responding to stress. This study enhances our understanding of the BrTCP family and provides significant insights into the stress tolerance mechanisms of B. rapa.

Keywords: Brassica rapa; TCP transcription factor; abiotic stress.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
(A) Gene structure and conserved protein motif of the TCPs gene family in B. rapa; (B) distribution of cis-acting elements; (C) systematic evolutionary tree.
Figure 2
Figure 2
Analysis of collinearity and localization of TCPs genes: (A) Intraspecies collinearity; (B) interspecific collinearity; (C) chromosomal localization of BrTCPs gene family members.
Figure 3
Figure 3
(A) pGBKT7-TCP4 yeast self-activation assay; (B) screening of pGBKT7-TCP4 interacting proteins; (C,D) GO annotation and KEGG functional analysis of interacting proteins.
Figure 4
Figure 4
(A) One-to-one validation of yeast two-hybrid crosses of BrTCP4 and its reciprocal proteins; (B) transcriptome expression after cryogenic treatment; (C) expression of BrTCP4 interacting proteins at low temperature. Different lowercase letters indicated significant differences among different treatments (p < 0.05).
Figure 5
Figure 5
Graphical article summary. Different lowercase letters indicated significant differences among different treatments (p < 0.05).
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