Pan-Genomic Analysis and Functional Characterization of the ATXR Gene Family Highlights Its Role in Regulating Agronomic Traits in Rapeseed

Histone methyltransferases of the Trithorax-related (ATXR) family act as critical epigenetic regulators in plants. However, systematic characterization of this gene family remains limited in the economically important oilseed crop Brassica napus. In this study, we performed a pan-genomic analysis of the BnaATXR family genes using 11 genetically diverse rapeseed accessions and identified a total of 185 BnaATXR family members, among which BnaATXR5 was categorized as a dispensable gene. Pan-genomic and phylogenetic analyses grouped these genes into five distinct subfamilies and uncovered strong sequence conservation and pervasive purifying selection across the family. Whole-genome duplication (WGD) was identified as the major evolutionary force driving BnaATXR genes expansion. Cis-acting regulatory element analysis further revealed significant enrichment of stress- and phytohormone-responsive motifs in the promoter regions of BnaATXR genes. BnaATXR members exhibited divergent tissue expression profiles: subfamilies B and C displayed constitutive and broad expression across multiple tissues, whereas subfamilies A and E exhibited pronounced tissue-specific expression, with preferential enrichment in reproductive organs. Notably, CRISPR/Cas9-mediated knockout of BnaATXR6 led to delayed flowering time, shortened siliques, and decreased seed size, thereby demonstrating a key functional role of this gene in the modulation of yield-associated agronomic traits. Collectively, our findings present a genome-wide systematic characterization of the ATXR gene family and highlight their critical functional relevance to agronomically important traits in rapeseed.