Genome-Wide Identification and Characterization of the CsFHY3/FAR1 Gene Family and Expression Analysis under Biotic and Abiotic Stresses in Tea Plants (Camellia sinensis)

Abstract

The FHY3/FAR1 transcription factor family, derived from transposases, plays important roles in light signal transduction, and in the growth and development of plants. However, the homologous genes in tea plants have not been studied. In this study, 25 CsFHY3/FAR1 genes were identified in the tea plant genome through a genome-wide study, and were classified into five subgroups based on their phylogenic relationships. Their potential regulatory roles in light signal transduction and photomorphogenesis, plant growth and development, and hormone responses were verified by the existence of the corresponding cis-acting elements. The transcriptome data showed that these genes could respond to salt stress and shading treatment. An expression analysis revealed that, in different tissues, especially in leaves, CsFHY3/FAR1s were strongly expressed, and most of these genes were positively expressed under salt stress (NaCl), and negatively expressed under low temperature (4 °C) stress. In addition, a potential interaction network demonstrated that PHYA, PHYC, PHYE, LHY, FHL, HY5, and other FRSs were directly or indirectly associated with CsFHY3/FAR1 members. These results will provide the foundation for functional studies of the CsFHY3/FAR1 family, and will contribute to the breeding of tea varieties with high light efficiency and strong stress resistance.

Keywords: CsFHY3/FAR1 family; biotic and abiotic stress; expression pattern; interaction network; light.

Figure 1

Phylogenetic analysis of the CsFHY3/FAR1 family in tea, Arabidopsis, grape, poplar, maize, and kiwifruit.

Figure 2

Comparative gene structure and motif analysis of CsFHY3/FAR1s. (a) Phylogenetic analysis and classification of CsFHY3/FAR1s. The subtree branch lines are colored in order to indicate the different subfamilies. (b) Motif analysis of CsFHY3/FAR1s. The top five motifs identified from the tea plant proteins obtained by the MEME analysis. (c) Exon-intron structures of CsFHY3/FAR1s. The exons are marked as yellow boxes, and the introns are represented by black lines; UTRs are shown as blue boxes.

Figure 3

Cis-acting elements in promoters of CsFHY3/FAR1s.

Figure 4

Putative interaction network of CsFHY3/FAR1s in tea plants. The homologous proteins in tea plants and Arabidopsis are shown in red and black, respectively.

Figure 5

The expression profiles of CsFHY3/FAR1s in different tissues. R: root; S: stem; L: leaf; F: flower.

Figure 6

Expression of tea plant CsFHY3/FAR1 transcripts in response to salt (a) and shade (b) stress. CK: control; S: shade stress; SALT: salt stress.

Figure 7

Expression analysis of the CsFHY3/FAR1 genes in tea plants under ABA, PEG, NaCl, low temperature, and high temperature treatments. The results are expressed as the mean ± standard deviation. The asterisks (* significant, and ** highly significant) denote significant variation (p < 0.05).