T2T Genome-Based Identification of the PLR Gene Family in Flax (Linum usitatissimum L.) Reveals Candidate Genes Associated with Seed Lignan Accumulation

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.