Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax

Abstract

Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing methods to generate in-depth transcriptome profiles of flax tissues with emphasis on the reproductive phases of five key stages of embryogenesis (globular embryo, heart embryo, torpedo embryo, cotyledon embryo, and mature embryo), mature seed, and vegetative tissues viz. ovary, anther, and root. These datasets were used to establish the co-expression networks covering 36 gene modules based on the expression patterns for each gene through weighted gene co-expression network analysis (WGCNA). Functional interrogation with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) of dominantly expressed genetic modules in tissues revealed pathways involved in the development of different tissues. Moreover, the essential genes in embryo development and synthesis of storage reserves were identified based on their dynamic expression patterns. Together, this comprehensive dataset for developing embryos, mature seeds and vegetative tissues provides new insights into molecular mechanisms of seed development with potential for flax crop improvement.

Expression of FAD and SAD Genes in Developing Seeds of Flax Varieties under Different Growth Conditions

“…In contrast to most previous works evaluating SAD and FAD gene expression in flax [8,[16][17][18]20,21], we obtained individual expression data for all 25 known SAD and FAD genes rather than the expression levels for only a few genes from each family or common expression patterns for pairs of homologous genes. Due to the large number of works devoted to conducting transcriptome analyses of different flax organs and tissues [33][34][35][36][37][38][39][40][41][42][43][44], we were previously able to determine which of the 25 SAD and FAD genes are expressed at high levels in flax seeds and to estimate the expression levels of these genes in other organs and tissues [19]. However, in that work, because of the lack of transcriptomic data, we were unable to assess the dynamics of expression of these genes during seed development; thus, this was carried out in the present work for a representative set of flax varieties grown under different conditions affecting the FA composition of linseed oil.…”

Key FAD2, FAD3, and SAD Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data

“…Likely, these sequences in the short-read assembly also had errors. The CDC Bethune assembly is often used as a reference in different molecular genetic studies of flax [61,63,[75][76][77][78][79]. However, the errors in FAD sequences demonstrate that even a chromosome-level assembly can have inaccuracies in highly homologous regions.…”

“…The obtained flax genomes opened up new opportunities for the identification and comparison of the SAD, FAD2, and FAD3 genes of different flax genotypes. In addition to whole-genome sequencing, a significant number of transcriptomes have been obtained for flax plants in recent years [59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74][75]. Such studies enabled extensive analysis of SAD, FAD2, and FAD3 expression in different organs/tissues and during various developmental stages and under various stress conditions.…”

Expression of <em>FAD</em> and <em>SAD</em> Genes in Developing Seeds of Flax Varieties under Different Growth Conditions

“…In contrast to most previous works evaluating SAD and FAD gene expression in flax [8,[16][17][18]25,26], we obtained individual expression data for all 25 known SAD and FAD genes, rather than expression levels just for a few genes from each family or common expression patterns for pairs of homologous genes. Due to the large number of works devoted to transcriptome analysis of different flax organs and tissues [33][34][35][36][37][38][39][40][41][42][43][44], we were previously able to determine which of the 25 SAD and FAD genes are expressed at high levels in flax seeds, and to estimate expression levels of these genes in other organs and tissues [19]. However, in that work, due to the lack of transcriptomic data, we were unable to assess the dynamics of expression of these genes during seed development, which was done in the present work for a representative set of flax varieties grown under different conditions affecting the FA composition of linseed oil.…”