Comparative Transcriptome Analysis Provides New Insights into the Molecular Regulatory Mechanism of Adventitious Root Formation in Ramie (Boehmeria nivea L.)

Abstract

The occurrence of adventitious roots is necessary for the survival of cuttings. In this study, comparative transcriptome analysis between two ramie (Boehmeria nivea L.) varieties with different adventitious root (AR) patterns was performed by mRNA-Seq before rooting (control, CK) and 10 days water-induced adventitious rooting (treatment, T) to reveal the regulatory mechanism of rooting. Characterization of the two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had a high adventitious rooting rate but H4 had a low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26,723 genes were expressed. In the non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in the water culture condition, the number of the distinctive genes in Z2 was nearly 2 times of that in H4. A total of 4411 and 5195 differentially expressed genes (DEGs) were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After the water culture, more DEGs were upregulated in Z2, but more DEGs were downregulated in H4. Gene ontology (GO) functional analysis of the DEGs indicated that the polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctively significantly enriched in H4. Simultaneously, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, photosynthesis antenna proteins, and starch and sucrose metabolism pathways were distinctively significantly enriched in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) could interact with ethylene to regulate the occurrence and number of AR in Z2. This study reveals the transcriptomic divergence of two ramie varieties with high and low adventitious rooting rates, and provides insights into the molecular regulatory mechanism of AR formation in ramie.

Comprehensive Analysis of WUSCEL-Related Homeobox Gene Family in Ramie (Boehmeria nivea) Indicates Its Potential Role in Adventitious Root Development

“…The potential involvement of the ramie WOX genes in adventitious root formation was investigated using quantitative real-time PCR and transcriptomic analysis of the ramie tissues grown using stem cuttings according to previous reports [43,44]. The transcriptome analysis of tissue-specific expression of the WOX genes was performed using four different ramie tissues (bud, leaf, stem, and root) sequenced by our laboratory, which was previously reported by Chen et al [3].…”

“…Samples for transcriptome analysis were collected 20 days after the culture and immediately frozen in liquid nitrogen [3]. Total RNA was extracted using TRIzol Reagent and Plant RNA Purification reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.…”

“…The low germination rates and survival of conventional ramie seed propagation make vegetative propagation, such as hydroponic technology, the best option for large-scale production [2]. Due to a high degree of heterozygosity in ramie, vegetative propagation can increase its genetic stability and produce many clones within a short time, sustaining the increasing demand for raw ramie materials [3]. The availability of stable planting materials is critical in sustaining production and ensures profitable production and significant motivation to producers [4].…”

Integrated Transcriptomics and Metabolomics Analysis Promotes the Understanding of Adventitious Root Formation in Eucommia ulmoides Oliver

“…JA could also mutually interfere with ethylene signaling to facilitate auxin-induced AR in dark-grown Arabidopsis thaliana seedlings [ 19 ]. In Boehmeria nivea L., JA could interact with ethylene to regulate the occurrence and number of AR [ 20 ]. ABA regulated indole-3-acetic acid (IAA) oxidase activity and the AR development of mung bean seedlings under cadmium stress [ 21 ].…”

Comparative transcriptomic and hormonal analyses reveal potential regulation networks of adventitious root formation in Metasequoia glyptostroboides Hu et Cheng

“…Alongside the uctuation in endogenous hormones, various key genes, proteins and pathways are involved in AR development [27][28][29][30]. Transcriptome sequencing revealed that most candidate genes involved in AR formation encoded polar auxin transport carriers, auxin-regulated proteins, and cell wall remodeling enzymes, leading to an enrichment of the biosynthesis of secondary metabolites, plant hormone signal transduction, starch and sucrose metabolism, and other metabolic processes [31][32][33][34]. In the absence of PGRs and other growth regulators, genes related to the synthesis, transport, metabolism and recognition of plant hormones were involved in AR formation from Populus euramericana microcuttings [35].…”