Comparative transcriptome analysis provides new insights into the molecular regulatory mechanism of adventitious root formation in ramie (Boehmeria nivea L.)

Abstract

Background: 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 RNA-Seq under water culture (treatment, T) and non-water culture conditions (control, CK) to reveal the regulatory mechanism of rooting. Results: Characterization of the cuttings of two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had high adventitious rooting rate but H4 had low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26723 genes were identified. In non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in 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 DEGs were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After water culture, more DEGs were up-regulated in Z2, but more DEGs were down-regulated in H4. Gene Ontology (GO) Gene functional analysis of the DEGs indicated that polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctive 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 identified in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) can interact with ethylene to regulate the occurrence and number of AR in Z2.Conclusions: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 adventitious root formation in ramie.

Comparative analysis of RNA-Seq data reveals adventitious root development is mediated by ChIFNα in lotus japonicus

“…During mulberry root development, hormone signal transduction, energy metabolism and starch metabolism, photosynthesis, sugar metabolism, and other processes were all found to be enriched [53]. Polysaccharide metabolism, carbohydrate metabolism, and photosynthesis were also enriched during ramie AR formation [31]. Taken together, these results suggest that the development of TP ARs is regulated by the above enriched processes and pathways, which are known to be involved in plant root growth, and involves more differentially expressed genes than WT.…”

“…For example, transcriptome technology was used to analyze the molecular regulatory network of root development in Chinese fir and Panax ginseng [29,30]. Similarly, this method was used to reveal the Gene Ontology (GO) of genes involved in the growth and development of ARs, which include cell carbohydrates, photosystems, polysaccharide metabolism, carbohydrate metabolism, and cell carbohydrate metabolism [26,31,32]. Additional genes related to AR formation, including photosynthesis and the starch and sucrose metabolism pathways, were revealed by comparison with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database [31,33].…”