Systematic analysis and expression profiles of TCP gene family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stress

Abstract

Background As transcription factors, the TCP genes are considered to be promising targets for crop enhancement for their responses to abiotic stresses. However, information on the systematic characterization and functional expression profiles under abiotic stress of TCPs in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is limited. Results In this study, we identified 26 FtTCPs and named them according to their position on the chromosomes. Phylogenetic tree, gene structure, duplication events, and cis-acting elements were further studied and syntenic analysis was conducted to explore the bioinformatic traits of the FtTCP gene family. Subsequently, 12 FtTCP genes were selected for expression analysis under cold, dark, heat, salt, UV, and waterlogging (WL) treatments by qRT-PCR. The spatio-temporal specificity, correlation analysis of gene expression levels and interaction network prediction revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stresses. Moreover, subcellular localization confirmed that FtTCP15 and FtTCP18 localized in the nucleus function as transcription factors. Conclusions In this research, 26 TCP genes were identified in Tartary buckwheat, and their structures and functions have been systematically explored. Our results reveal that the FtTCP15 and FtTCP18 have special cis-elements in response to abiotic stress and conserved nature in evolution, indicating they could be promising candidates for further functional verification under multiple abiotic stresses.

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

“…Duplication event researches have shown that segmental duplications are the main driving force for expansion and evolution of the TCP gene family ( Cannon et al, 2004 ; Wang et al, 2012 ). In support to these findings, research in Tartary buckwheat ( Yang M. et al, 2022 ), and M. acuminata ( Wang J. et al, 2022 ) have shown that the segmental duplication was responsible for the expansion of TCP gene family, and that the TCP gene family has undergone three WGDs during evolution. Therefore, to further understand the gene duplication events of TCP members in 17 different plant species, we computed for duplication event types using the plant duplicate gene database, PDGD ( http://pdgd.njau.edu.cn8080 ) ( Lee et al, 2012 ) ( Figure 5 ).…”

Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development

“…Cis-acting regulatory elements (CAREs) control the precise initiation and transcription efficiency of gene transcription by binding to transcription factors ( Yang et al., 2022 ). This study extracted the upstream regions 2,000 bp of D. nobile TCP genes to identify putative CAREs and investigate their functions.…”

“…Since transcription factors regulate the transcription of target genes within the nucleus, DnTCPs are likely to be localized in the nucleus. Some studies have analyzed the subcellular localization of Class I TCPs ( Jin et al., 2022 ; Yang et al., 2022 ; Ren et al., 2023 ). In this study, Class I TCPs, especially DnTCP9 and DnTCP18, were selected to investigate their subcellular localization, which could have unique roles in perianth development via binding to specific MADS-box.…”

“…As shown in Figure 10 , 35S:: DnTCP9-GFP and 35S:: DnTCP18-GFP were localized to the nucleus according to the fluorescence signals, consistent with the results consistent with the prior hypothesis ( Supplementary Table 3 ). In addition, DnTCP9 showed weak fluorescence signals in the endoplasmic reticulum, indicating many unique situations of subcellular localization of transcription factors ( Yang et al., 2022 ).…”

Evolutionary and expression analysis of starch synthase genes from Tartary buckwheat revealed the potential function of FtGBSSII‐4 and FtGBSSII‐5 in seed amylose biosynthesis

“…Previous studies have shown that TFs that are highly or specifically expressed in seeds are the best candidates for regulating SS genes. To date, 17 TF families with 1075 genes have been identified in the TBG (J. Li et al., 2022; Liu et al., 2018; Liu, Fu, et al., 2019; Liu, Huang, Ma, et al., 2019; Liu, Huang, Sun, et al., 2019; Liu, Ma, et al., 2019; Liu, Sun, Ma, Huang, et al., 2019; Liu, Sun, Ma, Zheng, et al., 2019; Liu, Wang, et al., 2019; Liu, Wen, et al., 2019; Ma et al., 2019; W. Sun, Jin, Ma, Chen, & Liu, 2020; W. Sun, Ma, Chen, & Liu, 2020; Yan et al., 2021; Yang et al., 2022; Zhao et al., 2021). Unexpectedly, most TFs were not expressed in the Tartary buckwheat seeds after we analyzed their expression patterns in the roots, stems, leaves, flowers, and fruits based on the TBD.…”