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

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family encodes plant-specific transcription factors that play vital roles in plant growth, development, and stress responses. Rice (Oryza sativa 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 OsLBD gene family in Oryza sativa ssp. japonica 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 OsLBD 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 OsLBD 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 OsLBD 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 cis-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 Arabidopsis, highlighting the evolutionary conservation within the Poaceae family. This study provides a foundational framework for understanding the biological functions of OsLBD genes in rice and identifies promising candidate genes involved in vegetative and reproductive growth, development, and stress responses.