Genes with bast fiber-specific expression in flax plants - Molecular keys for targeted fiber crop improvement

The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality

“…Bioinformatic analysis of previously published RNA-Seq data (Mokshina et al, 2020) was performed after normalization applied to all samples simultaneously to ensure that the expression values were comparable across all samples. The procedure of normalization was described previously (Mokshina et al, 2020). Briefly, Illumina raw reads (as FASTQ files) of each sample were filtered using the BBDuk utility of BBToolsv 37.02 3 .…”

“…The average length of individual fibers obtained from mature plants ranged from 14.7 ± 2.0 mm in L. angustifolium to 21.5 ± 1.2 mm in Drakkar. The proportion of fibers longer SAM, shoot apical meristem (Zhang and Deyholos, 2016); cPAR, cortical parenchyma; iFIB, intrusively growing fibers (Gorshkova et al, 2018b); tFIBa, fibers depositing tertiary cell wall, earlier stage (Gorshkov et al, 2019); tFIBb, fibers depositing tertiary cell wall, later stage (Gorshkov et al, 2017); sXYLa, xylem part, the same segment of the stem as for tFIBa (Gorshkov et al, 2019); sXYLb, xylem part, the same segment of the stem as for tFIBb (Mokshina et al, 2020); LEAF, upper leaves from individual plants under normal conditions (Dmitriev et al, 2016); ROOT, root tips, average for control samples (Dmitriev et al, 2017). When calculating the FC, to avoid division by zero, +1 was added to all the TGR values.…”

“…The current paper presents a more targeted functional approach based on the analysis of gene expression during specific stages of bast fiber development. The whole pipeline includes the identification of temporal and spatial localization of fiber intrusive elongation and TCW deposition in the stems of developing flax plants (Gorshkova et al, 2003(Gorshkova et al, , 2004, transcriptomic analysis of fibers at certain developmental stage (Gorshkov et al, 2017;Gorshkova et al, 2018b), identification of genes with fiber-specific expression by determination of tau score (Mokshina et al, 2020), and the relation of fiber quality parameters to the expression of genes important at key stages of bast fiber development (current paper). The identification of genes contributing to fiber intrusive elongation and TCW deposition is an important step in this pipeline because it reduces information noise in the analysis and determines the effectiveness of the subsequent steps.…”

“…These approaches considerably advanced the earlier important studies to large-scale molecular characterization of the flax genome and transcriptome (Day et al, 2005;Roach and Deyholos, 2007;Fenart et al, 2010). Further RNA-Seq experiments revealed those genes that are highly upregulated during intrusive growth (Gorshkova et al, 2018b) and TCW deposition (Gorshkov et al, 2017), and described genes with fiber-specific expression that are barely transcribed in other tissues (Mokshina et al, 2020). These studies opened the possibility of relating the structure and expression of genes important for fiber development to fiber quality.…”

“…In the current study, we concentrated on the establishment of a pipeline that could be used to select a few genes that have high potential for manipulating fiber quality. Our approach included five key steps: (1) selection of candidate genes using previously published RNA-Seq data (Gorshkov et al, 2017(Gorshkov et al, , 2019Mokshina et al, 2020); (2) evaluation of their expression in various developing flax genotypes; (3) determination of technical fiber quality parameters in these flax genotypes after plant harvest; (4) identification of the optimal sets of genes whose expression is closely related to fiber quality features by regularized regression models; and (5) analysis of SNP abundance across the coding regions of genes important for bast fiber development using RNA-Seq data obtained for several different flax genotypes. We suggest that the obtained results may help to advance conventional breeding and genome editing programs for flax and other fiber crops.…”