Comprehensive Characterization and Functional Analysis of the Lateral Organ Boundaries Domain Gene Family in Rice: Evolution, Expression, and Stress Response

Abstract

In this study, the LBD (Lateral Organ Boundaries Domain) gene family, a group of plant-specific transcription factors critical for plant growth and development as well as metabolic regulation, was comprehensively characterized in rice. We identified 36 LBD genes using multi-source genomic data and systematically classified them into Class I (31 genes) and Class II (5 genes). Analysis of their physicochemical properties revealed significant variations in amino acid length, molecular weight, isoelectric points, and hydropathicity. Motif analysis identified conserved LOB domains and other motifs potentially linked to functional diversity. Cis-acting element analysis indicated the involvement of these genes in various biological processes, including light response, hormone signaling, and stress response. Expression profiling demonstrated tissue-specific expression patterns, with several genes, such as XM_015770711.2, XM_015776632.2, and XM_015792766.2, showing relatively high expression in rice roots, implying their important role in root development. Transcriptome data further supported the involvement of specific genes in responses to phytohormones such as jasmonic acid (JA) and abscisic acid (ABA), as well as environmental stresses like cold and drought. Notably, XM_015770711.2, XM_015776632.2, and XM_015772758.2 may contribute to the regulation of rice environmental adaptability by mediating ABA and JA signaling pathways, respectively. In conclusion, this study identified members of the LBD gene family through the screening of two rice gene databases, and performed a comprehensive analysis of their physicochemical properties, evolutionary relationships, and expression profiles under various conditions. These findings provided valuable insights for further functional studies of LBD genes. Moreover, this study provides a foundation for targeting LBD genes to enhance stress resilience (e.g., drought/cold tolerance) and root architecture optimization. The LBD gene family possesses dual values in both stress resistance regulation and developmental optimization. The construction of its multidimensional functional map lays the theoretical and resource foundation for the precise design of high-yield and stress-resistant varieties.

Keywords: LBD gene family; gene expression; rice; stress response; system evolution.

Figure 1

Rice LBD family conserved domain protein sequence alignment.CX₂CX₆CX₃C, Gly-Ala-Ser and LX₆LX₃LX₆L constitute the LOB domain.

Figure 2

Subcellular localization of XM_015770711.2, XM_015773840.2, and XM_015776632.2. GFP is green fluorescent protein, DAPI is DAPI staining, BF is bright field, and Merge is a superimposed graph.

Figure 3

Analysis of phylogenetic tree, motif-structure, and gene structure of LBD gene family in rice.

Figure 4

Identification of cis-acting element analysis in the upstream 2000 bp promoter region of the rice LBD gene. The figures in the figures are the number of cis-acting elements that the gene has.

Figure 5

LBD gene interspecific phylogenetic tree. All genes can be divided into 2 subclasses, among which Class I has 5 subclasses.

Figure 6

Collinearity analysis of LBD genes in rice and Arabidopsis thaliana. Orange: collinear relationships within rice; red: collinear relationships within Arabidopsis thaliana; blue: colinear relationship between rice and Arabidopsis thaliana; green: collinear relationships within rice as well as between rice and Arabidopsis thaliana.

Figure 7

The gene expression heatmap of LBD gene family members in 4 different tissues of roots, stems, leaves, and seeds of rice. Red indicates high expression, and blue indicates low expression.

Figure 8

Transcriptome analysis of genes involved in phytohormone signaling and stress response. (A) Transcriptome data of rice at various periods and control samples after JA treatment; (B) transcriptome data of rice at various periods after ABA treatment and control samples; (C) transcriptome data of rice at various periods after cold treatment and control samples; (D) transcriptome data of rice at various periods after drought treatment and control samples. Red indicates high expression, and blue indicates low expression.