The WOX (WUSCHEL-related homeobox) gene family plays pivotal roles in plant growth, development, and responses to biotic/abiotic stresses. Flax (Linum usitatissimum L.), a globally important oilseed and fiber crop, lacks a comprehensive characterization of its WOX family. Here, 18 LuWOX genes were systematically identified in the flax genome through bioinformatics analyses. Phylogenetic classification grouped these genes into three clades: Ancient, Intermediate, and WUS Clades, with members within the same clade exhibiting conserved exon–intron structures and motif compositions. Promoter analysis revealed abundant cis-acting elements associated with hormone responses (MeJA, abscisic acid) and abiotic stress adaptation (anaerobic induction, drought, low temperature). Segmental duplication events (nine gene pairs) contributed significantly to LuWOX family expansion. Protein–protein interaction networks implicated several LuWOX proteins in stress-responsive pathways. Expression profiling demonstrated that most LuWOX genes were highly expressed in 5-day-post-anthesis (DPA) flowers and embryonic tissues. qRT-PCR validation further uncovered distinct expression patterns of LuWOX genes under cold, drought, and salt stresses. This study established a foundational framework for leveraging LuWOX genes to enhance stress tolerance in flax breeding and functional genomics.

The PLATZ gene family influences plant growth, development, and responses to both biotic and abiotic stresses. Flax (Linum usitatissimum L.), an important oilseed and fiber crop, has not been extensively studied for its PLATZ genes. In this study, 27 LuPLATZ genes were identified in the recently assembled T2T (Telomere-to-Telomere) flax genome through bioinformatics analyses. Phylogenetic analysis grouped these genes into five subfamilies. Examination of gene structure and motifs showed conserved exon–intron arrangements and similar motif compositions within the same clade. Promoter analysis revealed that most cis-elements are associated with plant hormone responses (such as MeJA and ABA) and abiotic stresses, including anaerobic induction, drought, and low temperature. Duplication analysis identified 33 segmental duplication events, and miRNA target prediction indicated that lus-miR167 is the primary regulator of LuPLATZ genes. Expression profiling based on RNA-seq data showed high expression levels of most LuPLATZ genes in leaves and roots, and qRT-PCR confirmed their stress-responsive expression under cold, drought, and salt conditions, with LuPLATZ14 and LuPLATZ21 significantly upregulated in all treatments. Furthermore, overexpression of these two genes enhanced drought tolerance in yeast transformants.

Pinoresinol–lariciresinol reductase (PLR) catalyzes a key reductive step in plant lignan biosynthesis. Although flax (Linum usitatissimum L.) seeds are rich in lignans, the PLR gene family and its relationship with lignan accumulation during seed development remain insufficiently characterized. Here, 18 LuPLR genes were identified from the telomere-to-telomere genome assembly of the flax cultivar ‘Gaosi’ using BLASTP and HMMER searches. Their phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, duplication and syntenic relationships, promoter cis-acting elements, predicted microRNA targets, and expression profiles were analyzed. Seed lignan content at 5, 10, 20, 30, and 40 days after flowering was quantified by high-performance liquid chromatography, and candidate genes were screened using quantitative real-time PCR and Pearson correlation analysis. The LuPLR genes were unevenly distributed across eight chromosomes and exhibited substantial structural and regulatory diversity. Seed lignan content varied dynamically and reached its highest level at 40 days after flowering. LuPLR10, LuPLR11, and LuPLR16 showed positive correlations with lignan content. Among them, LuPLR10 was prioritized because its developmental expression pattern most closely paralleled lignan accumulation. Subcellular localization analysis indicated that the LuPLR10 protein was predominantly associated with chloroplasts. These findings provide a genomic framework for the flax PLR family and identify LuPLR10 as a priority candidate for further functional investigation.