Genome-wide identification and functional analysis of the TCP gene family in rye (Secale cereale L.)

Genome-wide analysis and expression profile of TCP gene family under drought and salinity stress condition in cowpea (Vigna unguiculata (L.) Walp.)

TCP transcription factors are known to regulate abiotic stress condition, but their role in V. unguiculata remains unexplored. So, in silico analysis and expression profile of the TCP gene family were performed in V. unguiculata to understand its role in response to heat and drought stress. A genome-wide search detected 28 TCPs (designated as VuTCPs) that were grouped into three subclasses by phylogenetic analysis. Gene structure, synteny, and phylogeny analyses of VuTCPs have shown a typical evolutionary path. One tandem and eight segmental duplication events were identified. Furthermore, identified duplicated, and orthologous VuTCP genes were under strong purifying selection pressure. A total of 15 SSRs were identified in the 12 VuTCPs, while 10 VuTCP genes were regulated by different miRNAs having a major role in abiotic stress tolerance. Analysed physicochemical properties, cis-acting elements, and gene ontology suggested that VuTCPs play various roles, including salinity and drought stress tolerance. qRT-PCR analysis showed that 11 and 15 VuTCPs were upregulated under drought and salinity stress conditions, respectively. Our findings provide comprehensive insights into the genomic characterization of the VuTCPs gene family in V. unguiculata, offering a foundation for understanding their structure, evolution, and role in abiotic stress tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03976-x.

GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

BACKGROUND

The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet.

RESULTS

In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement.

CONCLUSIONS

We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.

Genome-Wide Analysis of TCP Transcription Factors and Their Expression Pattern Analysis of Rose Plants (Rosa chinensis)

The plant-specific transcription factor TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) gene family plays vital roles in various biological processes, including growth and development, hormone signaling, and stress responses. However, there is a limited amount of information regarding the TCP gene family in roses (Rosa sp.). In this study, we identified 18 TCP genes in the rose genome, which were further classified into two subgroups (Group A and Group B) via phylogenetic analysis. Comprehensive characterization of these TCP genes was performed, including gene structure, motif composition, chromosomal location, and expression profiles. Synteny analysis revealed that a few TCP genes are involved in segmental duplication events, indicating that these genes played an important role in the expansion of the TCP gene family in roses. This suggests that segmental duplication events have caused the evolution of the TCP gene family and may have generated new functions. Our study provides an insight into the evolutionary and functional characteristics of the TCP gene family in roses and lays a foundation for the future exploration of the regulatory mechanisms of TCP genes in plant growth and development.