Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. gaud (ramie)

Abstract

Background: Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie. Results: In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER.Conclusions: Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.

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

“…Gene for WAT1 was also up-regulated in hemp tissues, at the advanced stage of fiber development (Guerriero et al, 2017). In ramie stem, several genes for WAT1-related proteins were upregulated in the bark of elongating internode as compared to non-elongating one (Xie et al, 2020). Thus, two genes encoding proteins involved in keeping auxin sub-cellular homeostasis and specifically upregulated at flax fiber intrusive elongation are in the list of genes whose expression is highly related to the quality of technical fibers.…”

“…Since the TCW is known as a cellulose-rich structure, we added five genes related to cellulose biosynthesis: four cellulose synthase genes (LusCESA1, LusCESA3-B, LusCESA4, and LusCESA8-A) and the chitinase-like gene (LusCTL2). In ramie, the CESA3 and CESA8 were among the cell wall related DEGs revealed in comparative transcriptomics of stem bark samples collected from three regions associated with bast fiber development) (Xie et al, 2020); in hemp hypocotyl, the orthologs of A. thaliana CESA4, CESA7 and CESA8 were among the SCW-related genes upregulated at later stages of development (Behr et al, 2016). Along with cellulose, an important role in TCW formation and functioning is played by pectic RG-I, despite its relatively low content of around 7% (Gorshkova et al, 2018a).…”

“…Lower auxin conjugation may result in longer fibers in fiber flax cultivars, as compared to the remainder of the FLW group ( Supplementary Figure S2), leading to higher scutched fiber strength. Of note, putative IAA-amido synthetases GH3.9 (four isoforms) were activated in the fiber-containing bark peeled from elongating internode of ramie, as compared to fully elongated internode (Xie et al, 2020). Enhanced expression of GH3 genes in Arabidopsis leads to dwarf plants and de-etiolation in darkness (Hagen and Guilfoyle, 2002).…”

“…The LusGT47-1 gene encodes a glycosyltransferase, which is an enzyme that could potentially be associated with RG-I synthesis (Gorshkov et al, 2017), and it is included in a co-expression network with genes that are likely also related to RG-I biosynthesis and modification (LusGT31, LusGALS2, LusBGAL12-A, LusRRT1-A, and LusRRT1-B; Figure 3B). Probable glycosyltransferase homologous to At5g03795 (GT47) was activated in ramie bark from fully elongated internode region comparing to bark from elongating internode), as well as a number of galactosidases BGALs (Xie et al, 2020). LusWRKY2 is ortholog to At5g56270 that encodes (Goldberg et al, 2014).…”

Cell Wall Layer Induced in Xylem Fibers of Flax Upon Gravistimulation Is Similar to Constitutively Formed Cell Walls of Bast Fibers

“…The major obstacle in such studies is the impossibility of separating xylem fibers from other xylem tissues. However, comparisons of transcriptomes in different stem parts during certain stages of bast fiber development in several species of fiber crops provide important information (Roach and Deyholos, 2007;Guerriero et al, 2017;Xie et al, 2020). Unfortunately, different tissues also complicate this approach, and therefore, differences cannot be attributed solely to gelatinous fibers.…”