# Characterization of trehalose-6-phosphate synthase gene family in linseed (Linum usitatissimum L.) and its potential implications in flowering time regulation

## TL;DR

This study explores how trehalose-6-phosphate synthase (TPS) genes in linseed may influence flowering time, which is important for seed yield and quality.

## Contribution

The study identifies TPS gene family members in linseed and links them to flowering time regulation through gene expression, allelic variation, and cis-regulatory elements.

## Key findings

- 18 LuTPS genes were identified and grouped into two clusters, with some showing high expression and correlation with flowering-related genes.
- Allelic variations in LuTPS6.1 and LuTPS10.2 are associated with early or late flowering in linseed.
- Enriched cis-regulatory elements in TPS gene promoters suggest roles in gene regulation and evolution.

## Abstract

Linseed is an important oilseed crop with diverse applications in the food, nutraceutical, oil, and paint industries. Flowering time is a critical trait in linseed, as it greatly influences seed yield potential and quality across various agro-ecological zones. Trehalose-6-phosphate synthase (TPS) genes have been implicated in the regulation of flowering time in plants. Therefore, a comprehensive analysis of the TPS gene family in linseed, using comparative genomics and bioinformatics approaches, is essential for elucidating the genetic mechanisms underlying flowering time regulation in this crop.

A total of 18 LuTPS genes, including several paralogs, were identified in the linseed genome and clustered into two distinct groups. Gene expression analysis in developing floral buds, flower, and vegetative tissues revealed that most TPS genes exhibited basal expression levels. However, LuTPS6.1, LuTPS6.2, LuTPS10.1, LuTPS1.1, LuTPS1.2, LuTPS7.2, LuTPS7.3, LuTPS7.4, and LuTPS8.2 showed significantly higher expression and strong correlation with key flowering-related genes such as FT, FUL, and SOC1. Allelic variation analysis using early- and late-flowering linseed accessions revealed trait-specific SNPs in LuTPS6.1 and LuTPS10.2. A comprehensive analysis of cis-regulatory elements (CREs) in the promoter regions of LuTPS genes, compared to the entire linseed genome, identified several CREs that were significantly enriched in TPS gene promoters, as well as those that were consistently present across all LuTPS gene promoters. Furthermore, the genome-wide syntenic network analysis involving linseed and nine other plant genomes provided valuable insights into TPS-associated syntelogs and the evolutionary dynamics and expansion of the TPS gene family. The physical proximity of TPS genes to known flowering time QTLs/QTNs is also discussed.

This study, with TPS gene family characterization, gene expression and allelic variation highlights the potential role of the TPS genes in the regulation of flowering time in linseed. The identified enriched CREs in the promoters of TPS genes would be crucial to understand the regulation of TPS genes in growth, development and stress response. TPS-associated syntelogs provided valuable insights into the evolutionary history and expansion of the TPS gene family. Collectively, these findings represent a significant step toward understanding the complex genetic regulation of flowering time in linseed.

The online version contains supplementary material available at 10.1186/s12870-025-07559-7.