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. 2022 May 4:13:883654.
doi: 10.3389/fpls.2022.883654. eCollection 2022.

FAR1/FHY3 Transcription Factors Positively Regulate the Salt and Temperature Stress Responses in Eucalyptus grandis

Jiahao Dai  1   2 , Jin Sun  3 , Wenjing Peng  1 , Wenhai Liao  1   2 , Yuhan Zhou  1 , Xue-Rong Zhou  4 , Yuan Qin  5   6   7   8 , Yan Cheng  5   6   9 , Shijiang Cao  1   2
Affiliations

FAR1/FHY3 Transcription Factors Positively Regulate the Salt and Temperature Stress Responses in Eucalyptus grandis

Jiahao Dai et al. Front Plant Sci. .

Abstract

FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), which play pivotal roles in plant growth and development, are essential for the photo-induced phyA nuclear accumulation and subsequent photoreaction. The FAR1/FHY3 family has been systematically characterized in some plants, but not in Eucalyptus grandis. In this study, genome-wide identification of FAR1/FHY3 genes in E. grandis was performed using bioinformatic methods. The gene structures, chromosomal locations, the encoded protein characteristics, 3D models, phylogenetic relationships, and promoter cis-elements were analyzed with this gene family. A total of 33 FAR1/FHY3 genes were identified in E. grandis, which were divided into three groups based on their phylogenetic relationships. A total of 21 pairs of duplicated repeats were identified by homology analysis. Gene expression analysis showed that most FAR1/FHY3 genes were differentially expressed in a spatial-specific manner. Gene expression analysis also showed that FAR1/FHY3 genes responded to salt and temperature stresses. These results and observation will enhance our understanding of the evolution and function of the FAR1/FHY3 genes in E. grandis and facilitate further studies on the molecular mechanism of the FAR1/FHY3 gene family in growth and development regulations, especially in response to salt and temperature.

Keywords: Eucalyptus grandis; FAR1/FHY3; salt stress; temperature stress; transcription factors.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree of FAR1/FHY3 protein sequences in Eucalyptus grandis, Arabidopsis, and poplar. The prefix “Eg,” “At,” and “Ptr” stand for E. grandis, Arabidopsis, and poplar, respectively. “Group I,” “Group II,” “Group III,” and “Group IV” were symbolized by blue, orange, green, and cyan colored arcs, respectively.
Figure 2
Figure 2
Chromosome locations of FAR1/FHY3 genes on 11 Eucalyptus grandis chromosomes. The number of chromosomes was displayed at the top of each vertical line. The position data were shown on the left side of the chromosome and the gene name on the right side. Blue: FAR1/FHY3 Group I; Orange: FAR1/FHY3 Group II; Green: FAR1/FHY3 Group III; chr: chromosome.
Figure 3
Figure 3
Conserved motifs of FAR1/FHY3 proteins and intron–exon organizations of FAR1/FHY3 genes in Eucalyptus grandis. (A) The phylogenetic tree of FAR1/FHY3 in E. grandis. (B) The intron–exon organizations of FAR1/FHY3 genes. Blue boxes indicate exons; black lines indicate introns. The length of exons and introns for each FAR1/FHY3 gene is proportionally displayed. (C) Conserved motifs of FAR1/FHY3 proteins. Motifs with specific colors can be found on the respective FAR1/FHY3 proteins. The order of the motifs corresponds to their position within individual protein sequences.
Figure 4
Figure 4
Three-dimensional models of EgFAR1/FHY3 proteins. Blue indicates high quality, whereas red indicates low quality.
Figure 5
Figure 5
Homologous relationships of FAR1/FHY3 family genes in eucalyptus. Small segments of different colors represent different chromosomes. The genes' positions on the chromosomes are shown in the corresponding positions on the scale above the small segments. The blue curve represents the correlation between the stages and the genes copied in tandem.
Figure 6
Figure 6
The numbers of cis-elements in the promoters of EgFAR1/FHY3 genes.
Figure 7
Figure 7
Tissue-specific expression profiles of FAR1/FHY3 genes in Eucalyptus grandis. Expression profiles of FAR1/FHY3 genes in immature xylem, xylem, phloem, shoot tips, young leaf, and mature leaf of E. grandis are displayed. Hierarchical clustering of expression profiles of FAR1/FHY3 genes in different tissues and developmental stages. Red indicates high levels of transcript abundance, whereas blue indicates low levels. The color scale is shown on the right side.
Figure 8
Figure 8
Expressions of four FAR1/FHY3 genes in response to salt and temperature stresses. The qRT-PCRs were conducted after 0, 6, and 12 h of stress treatments. The low salinity was treated with 100 mM NaCl, and the high salinity was 200 mM NaCl, whereas the control was treated with distilled water. The low temperature was treated with 4°C and the high temperature was 40°C, whereas the control temperature was 25°C. Average data with standard errors is presented (*p < 0.05).
Figure 9
Figure 9
A model of the function of FAR1/FHY3 under salt stress (modified from Halfter et al., ; Shi et al., ; Zhou et al., 2018). Under high/low salt stress, due to different response activities, different FAR1/FHY3 genes were activated successively to further activate downstream salt stress-induced genes, and then achieved Na+ balance inside and outside the vacuole and cell membrane through SOS pathway.
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