RNASeq Analysis of the Shoot Apex of Flax (Linum usitatissimum) to Identify Phloem Fiber Specification Genes

All of the post-embryonic, above-ground structures of seed plants are generated from the shoot apical meristem (SAM), which acts as a reservoir of stem cells. Members of the flax genus (Linum spp.) have been used historically as models for the study of SAMs (Esau, 1942). Cultivated flax (Linum usitatissimum) is grown in more than 50 countries for its seeds or its stem phloem (bast) fibers (Rubilar et al., 2010). Due to prolonged intrusive growth, and a highly crystalline cellulosic secondary wall, flax phloem fibers are among the longest and strongest cells in plants (Mohanty et al., 2000). In flax, all phloem fibers are derived from primary growth in the shoot apex. Specification of phloem fibers occurs in the apical-most 0.5 mm of the stem, since young phloem fibers can be anatomically distinguished starting 0.4–0.5 mm from the shoot apex (Gorshkova et al., 2003). The molecular mechanisms that govern fiber identity are almost entirely unknown (Gorshkova et al., 2012). Also, in contrast to the significant progress obtained in the past decade toward understanding xylem differentiation, information about the phloem fiber differentiation is very scarce (De Rybel et al., 2016). In the past decade, shoot apex transcriptomes have been described in various plants, including maize, pea, soybean, rice, Arabidopsis and chickpea, but none of these produce significant primary phloem fibers (Ohtsu et al., 2007; Wong et al., 2008; Haerizadeh et al., 2009; Jiao et al., 2009; Yadav et al., 2009; Wang et al., 2014). Most molecular and cellular research on flax fiber has thus far focused on later stages of development (Day et al., 2005; Roach and Deyholos, 2007; Fenart et al., 2010). Differential transcript expression data from the region of the shoot apex in which fiber specification occurs would complement other approaches (e.g., mutant screening) aimed at understanding primary phloem fiber differentiation.