Genome-Wide Identification and Pollen-Specific Promoter Analysis of the <i>DIR</i> Gene Family in <i>Rosa chinensis</i>

Genome-Wide Identification and Pollen-Specific Promoter Analysis of the <i>DIR</i> Gene Family in <i>Rosa chinensis</i>

Dirigent proteins (DIRs) are pivotal regulators of lignin/lignan biosynthesis and play multifaceted roles in plant development and stress adaptation. Despite their functional significance, <i>DIR</i> genes remain unexplored in <i>Rosa chinensis</i>, a globally important woody...

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Bibliographic Details
Main Authors: Qijing Dong, Qian Yang, Zitong Wang, Yuan Zhao, Sixu Guo, Yifang Peng, Qi Li, Yu Han
Format: Article
Language:English
Published: MDPI AG 2025-06-01
Series:Horticulturae
Subjects:
dirigent (DIR) gene family
<i>Rosa chinensis</i>
cis-regulatory elements
pollen-specific promoter
tandem gene cluster
Online Access:https://www.mdpi.com/2311-7524/11/7/717
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Summary:Dirigent proteins (DIRs) are pivotal regulators of lignin/lignan biosynthesis and play multifaceted roles in plant development and stress adaptation. Despite their functional significance, <i>DIR</i> genes remain unexplored in <i>Rosa chinensis</i>, a globally important woody ornamental species. This study identified 33 <i>RcDIRs</i> through whole-genome analysis, including their chromosomal distribution, phylogenetic relationships, collinearity, protein and gene structure, conserved motifs, and cis-acting element distribution, and classified them into three phylogenetically independent subgroups (DIR-a, DIR-b/d, and DIR-e). Notably, the DIR-e subgroup includes an exclusive tandem cluster comprising RcDIR7-RcDIR12, representing the largest lineage-specific RcDIR expansion in <i>R. chinensis</i>. Structural characterization revealed that most <i>RcDIRs</i> exhibit a conserved single-exon architecture. Promoter <i>cis</i>-element analysis uncovered abundant stress-/hormone-responsive elements and three pollen-specific motifs (AAATGA, POLLEN1LELAT52, GTGANTG10), with <i>RcDIR12</i> from the DIR-e cluster showing high pollen-specific regulatory potential. Experimental validation included cloning the <i>RcDIR12</i> promoter from <i>R. chinensis</i> ‘Old Blush’, constructing proRcDIR12::<i>GUS</i> vectors, and conducting histochemical GUS assays with pollen viability/DAPI staining in transgenic <i>Arabidopsis</i>. Histochemical assays demonstrated GUS activity localization in mature trinucleate pollen grains, marking the first experimental evidence of pollen-specific DIRs in rose. Our findings not only elucidate the <i>DIR</i> family’s genomic organization and evolutionary innovations in <i>R. chinensis</i> but also establish proRcDIR12 as a molecular tool for manipulating pollen development in plants.
ISSN:2311-7524

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