Comprehensive Characterization and Transcriptomic Profiling of the GH3 Gene Family in Brassica rapa and Its Involvement in Auxin-Mediated Growth and Stress Response

Abstract

The Gretchen Hagen 3 (GH3) gene family plays a central role in maintaining auxin homeostasis and regulating hormone-mediated growth and stress responses in plants. In this study, a comprehensive genome-wide analysis of the GH3 gene family in Brassica rapa identified 49 GH3 genes. Phylogenetic analysis classified these genes into five distinct groups, reflecting their evolutionary relationships. Gene structure and conserved motif analyses revealed considerable variation in exon–intron organization among GH3 genes, while motif composition remained highly conserved within each phylogenetic group, suggesting functional conservation. Promoter analysis identified numerous cis-acting regulatory elements associated with phytohormone responsiveness, including auxin, abscisic acid, salicylic acid, gibberellins, and jasmonates, as well as elements related to abiotic stresses such as drought, low temperature, light, and defense responses. In addition, multiple microRNAs were predicted to target B. rapaGH3 genes, indicating an additional layer of post-transcriptional regulation. Transcriptomic analysis further revealed distinct tissue-specific and developmental expression patterns of GH3 genes, highlighting their diverse regulatory roles during plant growth. Overall, this study provides a systematic framework for understanding the structural, regulatory, and expression characteristics of the GH3 gene family in B. rapa and offers valuable insights for future functional studies aimed at improving stress tolerance and developmental traits in Brassica crops.