Gene expression analysis of flax seed development

Abstract

BackgroundFlax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed.ResultsWe describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development.ConclusionsWe have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as those encoding transcription factors. This has allowed us to delineate the spatio-temporal aspects of gene expression underlying the biosynthesis of a number of important seed constituents in flax. Flax belongs to a taxonomic group of diverse plants and the large sequence database will allow for evolutionary studies as well.

Natural Hypolignification Is Associated with Extensive Oligolignol Accumulation in Flax Stems

“…AC elements are also present in the promoter of the flax LuPLR1 gene (Hano et al, 2006b), suggesting that transcriptional regulation of lignan biosynthesis might also involve MYB factors. In support of this idea, a recent study has shown that MYB TF genes are expressed in flax seed tissues (Venglat et al, 2011). In this latter study, different MYB TF genes were expressed in flax stem tissues and seeds, although six MYB TF genes were also expressed in both tissues.…”

“…Previous gene expression analyses have demonstrated that a PLR gene is expressed in different flax seed tissues (Hano et al, 2006b;Venglat et al, 2011). Although promoter-GUS analyses and semiquantitative PCR indicated that the LuPLR1 gene cloned was not expressed in flax stem tissues (Hano et al, 2006b), the recent cloning of a second PLR gene (LuPLR2; Hemmati et al, 2010) from leaves and stems of flax plants, together with our results, suggest that PLR genes in flax form a small multigene family with organ-/tissuespecific expression patterns.…”

“…Although we did not detect any coexpression of TF gene expression and genes specifically involved in lignan biosynthesis such as PLR and PCBER, the observation that flax NAC genes are coregulated with monolignol biosynthetic genes, together with results (Venglat et al, 2011) showing that MYB TFs are expressed in developing seeds, could suggest that a similar transcriptional regulatory network plays a role in controlling (neo)lignan production in the flax stem.…”

“…In addition to providing novel information about the transcriptional regulation of lignification in flax plants, our study suggests that the natural hypolignification of outer stem tissues is associated with the accumulation of a wide range of phenolics. Recently, a number of tools have been developed for flax, including highdensity microarrays, cDNA libraries, physical and genetic maps, molecular markers, and mutant populations, which should allow an integrated approach to investigate different processes in this biologically interesting species (Cloutier et al, 2010;Fénart et al, 2010;Ragupathy et al, 2011;Venglat et al, 2011).…”

Choreography of Transcriptomes and Lipidomes ofNannochloropsisReveals the Mechanisms of Oil Synthesis in Microalgae

“…Extensive transcriptomic analyses suggested that FA synthesis may be another important regulatory step in TAG production in vascular plants (Bourgis et al, 2011;Troncoso-Ponce et al, 2011;Venglat et al, 2011). Pyruvate and acetyl-CoA, the precursors for FA biosynthesis, are synthesized via multiple metabolic routes.…”