Abstract
Flaxseed/Linseed (Linum usitatissimum) is an annual crop of economic importance due to its diverse applications in food, nutraceuticals, and industry. Flowering time is a crucial trait in linseed; however, the gene expression landscapes underlying its regulation remain poorly characterized, constraining its understanding and effective application in crop improvement. Here, an integrative transcriptome and genome resequencing approach was used to identify key flowering regulators and allelic variants. Transcriptome sequencing of reproductive tissues including floral bud at two developmental stages, flower, and two vegetative tissues (leaf and stem) in two early flowering linseed genotypes, IC0523807 and IC0525939 were performed. A total of 47.4 GB of filtered data was obtained from 20 datasets, resulting in 34,869 mapped transcripts. Differential expression analysis between vegetative tissues vs. reproductive tissues in different combinations revealed a total of 14,244 differentially expressed genes, with 67 GO and 161 KEGG enriched terms. Several DEGs were involved in auxin, cytokinin, gibberellic acid, and abscisic acid signal transduction pathways. From the 109 major Arabidopsis flowering gene orthologs identified in linseed, 54 were differentially expressed, whereas 46 of the 143 putative candidate genes reported in earlier association studies were also represented among the differentially expressed genes. Overall, by integrating a three-way strategy involving differential gene expression, flowering gene orthologs, and candidate genes for flowering, three promising genes were identified, namely, flowering locus T (FT), the flowering repressor APETALA2-like transcription factor SCHLAFMÜTZE (SMZ), and a Dof-type domain-containing protein (CDF3). The whole-genome resequencing of two early- and late-flowering genotypes was performed, unravelling allelic variations in key flowering candidate genes, including AGAMOUS-like 19 (AGL19), della protein, flowering locus K (FLK), Target of EAT1 (TOE1), and Late Elongated Hypocotyl (LHY). This study provides a detailed insight into gene expression profile of early-flowering linseed genotypes, highlighting key flowering pathways, regulators and allelic variants of flowering associated genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40729-7.