A Comprehensive Profiling of the Rice LATERAL ORGAN BOUNDARIES DOMAIN (LBD) Gene Family: Structure, Evolution, and Expressional Dynamics

The <i>LATERAL ORGAN BOUNDARIES DOMAIN</i> (<i>LBD</i>) gene family encodes plant-specific transcription factors that play vital roles in plant growth, development, and stress responses. Rice (<i>Oryza sativa</i> L.), a staple food for more than half of the world's population, also serves as an important model organism for monocot functional genomics. In this study, we conducted a comprehensive genomic survey of the <i>OsLBD</i> gene family in <i>Oryza sativa</i> ssp. <i>japonica</i> using the latest genomic sequence data. A total of 35 members of this family were identified through systematic characterization of their gene structures, conserved domains, phylogenetic relationships, and chromosomal distributions. Our analysis indicated that the expansion of <i>OsLBD</i> genes may have resulted mainly from segmental duplication, with these duplicated genes exhibiting diverse evolutionary fates ranging from functional conservation to expression divergence. Phylogenetic analysis further classified the <i>OsLBD</i> genes into two major groups: Class I and Class II. Expression profiling across various developmental stages demonstrated dynamic spatiotemporal regulation, with certain genes exhibiting tissue-specific expression, particularly in reproductive tissues. Furthermore, a comprehensive co-expression analysis of <i>OsLBD</i> genes and their co-regulators revealed multiple modules with tissue-specific roles in pollen cell wall synthesis and endosperm glycogen biosynthesis. Promoter analysis identified several <i>cis</i>-regulatory elements associated with hormone responses, stress adaptation, and developmental processes, consistent with the observed expression patterns under phytohormone treatments. Comparative genomics revealed a higher degree of synteny between rice and barley than between rice and <i>Arabidopsis</i>, highlighting the evolutionary conservation within the Poaceae family. This study provides a foundational framework for understanding the biological functions of <i>OsLBD</i> genes in rice and identifies promising candidate genes involved in vegetative and reproductive growth, development, and stress responses.