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. 2022 Aug 6;23(15):8762.
doi: 10.3390/ijms23158762.

Genome-Wide Identification of Brassicaceae Hormone-Related Transcription Factors and Their Roles in Stress Adaptation and Plant Height Regulation in Allotetraploid Rapeseed

Shengjie Ma  1   2 , Liwei Zheng  1   2 , Xiaohan Liu  3 , Kaiyan Zhang  1   2 , Linlin Hu  1   2 , Yingpeng Hua  1 , Jinyong Huang  1   2   3
Affiliations

Genome-Wide Identification of Brassicaceae Hormone-Related Transcription Factors and Their Roles in Stress Adaptation and Plant Height Regulation in Allotetraploid Rapeseed

Shengjie Ma et al. Int J Mol Sci. .

Abstract

Phytohormone-related transcription factors (TFs) are involved in regulating stress responses and plant growth. However, systematic analysis of these TFs in Brassicaceae is limited, and their functions in stress adaptation and plant height (PH) regulation remain unclear. In this study, 2115 hormone-related TFs were identified in nine Brassicaceae species. Specific domains were found in several Brassicaceae hormone-related TFs, which may be associated with diverse functions. Syntenic analysis indicated that expansion of these genes was mainly caused by segmental duplication, with whole-genome duplication occurring in some species. Differential expression analysis and gene co-expression network analysis identified seven phytohormone-related TFs (BnaWRKY7, 21, 32, 38, 52, BnaGL3-4, and BnaAREB2-5) as possible key genes for cadmium (Cd) toxicity, salinity stress, and potassium (K) and nitrogen (N) deficiencies. Furthermore, BnaWRKY42 and BnaARR21 may play essential roles in plant height. Weighted gene co-expression network analysis (WGCNA) identified 15 phytohormone-related TFs and their potential target genes regulating stress adaptation and plant height. Among the above genes, BnaWRKY56 and BnaWRKY60 responded to four different stresses simultaneously, and BnaWRKY42 was identified in two dwarf rapeseeds. In summary, several candidate genes for stress resistance (BnaWRKY56 and BnaWRKY60) and plant height (BnaWRKY42) were identified. These findings should help elucidate the biological roles of Brassicaceae hormone-related TFs, and the identified candidate genes should provide a genetic resource for the potential development of stress-tolerant and dwarf oilseed plants.

Keywords: Brassicaceae; abiotic stress; phytohormone; plant height; transcription factors.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Expression profiles of B. napus hormone-related TFs in response to Cd and salt toxicity. Cycle nodes represent genes and the size of the node represents the power of the inter-relationship among nodes by degree value; Color of the node represents log2FC value; Red indicates up-regulated genes and blue indicates down-regulated genes; Edges between nodes represent p-value. (a) Expression analysis of B. napus hormone-related TFs in response to Cd toxicity in shoots. (b) Co-expression network analysis of differentially expressed B. napus hormone-related TFs in response to Cd toxicity in shoots. (c) Expression analysis of B. napus hormone-related TFs in response to Cd toxicity in roots. (d) Co-expression network analysis of differentially expressed B. napus hormone-related TFs in response to Cd toxicity in roots. (e) Expression analysis of B. napus hormone-related TFs in response to salt toxicity in shoots. (f) Co-expression network analysis of B. napus hormone-related TFs in response to salt toxicity in shoots. (g) Expression analysis of B. napus hormone-related TFs in roots in response to salt toxicity. (h) Co-expression network analysis of B. napus hormone-related TFs in response to salt toxicity in roots.
Figure 2
Figure 2
Expression profiles of B. napus hormone-related TFs in response to K and N starvation. Cycle nodes represent genes and the size of the node represents the power of the inter-relationship among nodes by degree value; Color of the node represents log2FC value; Red indicates up-regulated genes and blue indicates down-regulated genes; Edges between nodes represent p-value. (a) Expression analysis of B. napus hormone-related TFs in response to K starvation in shoots. (b) Co-expression network analysis of differentially expressed B. napus hormone-related TFs in response to K starvation in shoots. (c) Expression analysis of B. napus hormone-related TFs in response to K starvation in roots. (d) Co-expression network analysis of differentially expressed B. napus hormone-related TFs under in response to K starvation in roots. (e) Expression analysis of B. napus hormone-related TFs in response to N starvation in shoots. (f) Expression analysis of B. napus hormone-related TFs in response to N starvation in roots. (g) Co-expression network analysis of differentially expressed B. napus hormone-related TFs in response to N starvation in shoots and roots.
Figure 3
Figure 3
Expression profiles of B. napus hormone-related TFs in response to PH. Cycle nodes represent genes and the size of the node represents the power of the inter-relationship among nodes by degree value; Color of the node represents log2FC value; Red indicates up-regulated genes and blue indicates down-regulated genes; Edges between nodes represent p-value. (a) Expression analysis of B. napus hormone-related TFs in a conventional rapeseed cultivar (Ningyou 18) and a dwarf mutant (df59). (b) Co-expression network analysis of differentially expressed B. napus hormone-related TFs in WT and df59. (c) Expression analysis of hormone-related TFs in an extreme dwarf mutant of rapeseed (ed1) and WT. (d) Co-expression network analysis of differentially expressed B. napus hormone-related TFs in ed1 and WT.
Figure 4
Figure 4
WGCNA of rapeseed genes in response to Cd stress. (a) Module-trait correlation showing the significance of module eigengene correlation with traits (SPAD and biomass). Left panel shows modules. (b) Cytoscape representation of the relationship of hormone-related TFs in “green” module. Key genes are represented by large red circles. (c) Cytoscape representation of the relationship of hormone-related TFs in “purple” module. Key genes are represented by large red circles. (d) W-box cis-element in promoter of BnaHMTSPs. (e) RR binding cis-element genes in promoter of BnaHMTSPs.
Figure 5
Figure 5
WGCNA of rapeseed genes in response to salt. (a) Module-trait correlation showing the significance of module eigengene correlation with traits (biomass and leaf area). Left panel shows modules. (b) Cytoscape representation of the relationship of hormone-related TFs in “salmon” module. Key genes are represented by large red circles. (c) Cytoscape representation of the relationship of hormone-related TFs in “blue” module. Key genes are represented by large red circles.
Figure 6
Figure 6
WGCNA of rapeseed genes in response to K starvation. (a) Module-trait correlation showing the significance of module eigengene correlation with traits (biomass and SPAD). Left panel shows modules. (b) Cytoscape representation of the relationship of hormone-related TFs in “lightcyan” module. Key genes are represented by large red circles. (c) Cytoscape representation of the relationship of hormone-related TFs in “turquoise” module. Key genes are represented by large red circles. (d) W-box and RR binding cis-element in promoters of BnaKUP5, BnaPCP, and BnaKUP6.
Figure 7
Figure 7
WGCNA of rapeseed genes in response to N deficiency. (a) Module-trait correlation showing the significance of module eigengene correlation with traits (SPAD). Left panel shows modules. (b) Cytoscape representation of the relationship of hormone-related TFs in “green” module. Key genes are represented by large red circles.
Figure 8
Figure 8
WGCNA of rapeseed genes identified in dwarf mutants. (a) Module-trait correlation showing the significance of module eigengene correlation with traits (PH). Left panel shows modules. (b) Cytoscape representation of the relationship of hormone-related TFs in “darkmagenta” module. Key genes are represented by large red circles. (c) RR-binding cis-element in the promoter of BnaARFs.
Figure 9
Figure 9
Venn diagram indicating various functions of B. napus hormone-related TFs in stress adaptation and PH regulation. (a) Number of rapeseed hormone-related TFs in response to Cd, K, N, and salt stress. (b) Number of rapeseed hormone-related TFs identified in rapeseed dwarf mutants.
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