- Results: AR formation was significantly affected by light, and high light intensity accelerated AR development.. - Twenty differentially expressed genes (DEGs) were involved in the signal transduction pathway, 28 DEGs were related to the IAA response, and 35 DEGs were involved in sugar metabolism. - this was responsible for AR formation. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - China Full list of author information is available at the end of the article. - Conclusions: AR formation was regulated by IAA, even in the dark, where induction and developmental processes could also be completed. - In addition, 36 genes displayed altered expression in carbohydrate metabolism and ucrose metabolism was involved in AR development (expressed stage) according to gene expression and content change characteristics.. - Lotus is widely cultivated in the southern region of the Yellow River Basin. - Lotus rhizome can be continuously supplied to the local market as a vegetable owing to its simple storage in soil from October to April of the next year. - Light, including photoperiod, light quality, and light in- tensity, is a basic condition that is involved in several as- pects of plant development and growth, such as root formation, photosynthesis, flowering, fruit development, and plant morphogenesis [4–6]. - Many metabolic pro- cesses that depend on light signals during plant growth are induced by hormonal signaling [7, 8], suggesting that hormone action occurs downstream of the light signal transduction pathway [9–11]. - A number of factors involved in the light signaling pathway, such as re- active oxygen species, abscisic acid, and sugar, have been to found to affect root development [15–17]. - Depending on the exposure to light, IAA plays a critical role in the developmental process of adventitious roots (ARs), including induction, development, and expression of roots [20, 21]. - It has been reported that cytokinin, which regulates cell division, is also involved in AR formation due to its effect on auxin metabolism [20].. - Therefore, IAA is considered a direct regulator of the complex network in regulating AR formation.. - Analysis of gene expression or regulation in the whole genome is the most effective approach to understand AR formation. - Studies over recent decades involved in auxin metabolism or responses related to ARs have shown that many genes participate in IAA synthesis, transport, or response which help accelerate developmental processes of ARs [25]. - The above data indicate that various functions exist for members of the AUX1/LAX family, although these genes are involved in AR development. - PIN, as an efflux car- rier , is expressed in the root primordia and is required for root formation [29, 30]. - However, the principal root cannot be devel- oped in the plant owing to long periods of evolution;. - In general, the number of ARs in the seedling hypocotyl is lower than that in the internodes of storage organs owing to the considerable amount of nutrition that is needed for plant growth. - In the induced stage, meristematic cells are developed from normal cells. - In the initial developmental stage, the primor- dium relevant to ARs is formed and developed [38], and finally, ARs protrude from the epidermis [39]. - No ARs were formed in the lotus under darkness (Table 1), whereas lotus could de- velop ARs when exposed to light. - Thus, AR formation ap- pears to be dependent on light intensity. - Next, we observed the microstructure of the hypocotyl where the ARs emerged.. - the AR primordium was present, but failed to break out of the epidermis (Fig. - Analysis of quality control showed that the reads derived from RNA-seq libraries covered the whole lotus genome, as evidenced by the flat curve of the obtained reads (Additional file 1: Fig. - Approximately 83% reads were successfully mapped into the lotus genome and 73% of the reads were unique (Additional file 1: Table S1). - a Changes in the morphology of ARs in lotus under darkness, and under 5000 and 20,000 lx light intensities over 5 days. - b Changes in the microstructure of ARs in lotus under darkness, and under 5000 and 20,000 lx light intensities over 5 days. - 2 IAA and sucrose content during AR development. - In terms of the dramatic difference in AR develop- ment between the 3-d exposure of libraries D and F, we analyzed their DEGs using the KEGG tool. - Further analysis showed that 20 DEGs were involved in signal transduction in the group of environmental information processing and 36 DEGs were related to carbohydrate metabolism in the metabolism processing group (Fig. - In support, the expression of genes involved in plant hormone signal transduction and the metabolism of starch and sucrose was also altered (Fig. - Role of sucrose in lotus AR formation. - Based on these observations, we believe that sucrose might be involved in the expressed state of lotus AR formation (Fig. - We found that different light in- tensities have various roles in the formation of ARs in lotus. - Light regulation of AR de- velopment is often derived from the sucrose content of photosynthate, and this effect is mainly reflected in the root number [44, 45]. - (2005) found that the role of IAA in regulating AR formation in Arabidopsis thaliana is dependent on light conditions. - Number of DEGs in the D/CK, E/CK, and F/CK libraries. - b Selected expressed genes in the D/CK, E/CK, and F/CK libraries. - d Distribution of expression of these DEGs identified in the F/D libraries. - ARs are a necessary secondary organ for mainly water and nutrition uptake because no princi- pal roots occur in the plants [32, 46]. - We found that many fac- tors including plant hormones [32, 47], mechanical dam- age [33], and sucrose [data not shown] are all involved in AR development. - We found that a large number of genes enhanced expression and decreased expression in the three libraries (D/CK0, E/. - Based on these datasets, several key genes that demonstrated clear changes in ex- pression were also implored in the F/D libraries (Add- itional file 1: file S1). - Auxin metabolism, including auxin synthesis, transport, and homeostasis are known to be involved in the regulation of plant development, such as root formation, shoot development, and reproduction [53]. - In the past decades, many important genes relevant to IAA metabolism or the response involved in root for- mation have been identified [55, 56]. - We found that a total of 4884 genes and 2040 genes demonstrated in- creased expression and decreased expression, respectively, in the three libraries (D/CK0, E/CK0, and F/CK0, respect- ively,) (Fig. - 5 Functional analysis of DEGs in the F/D libraries. - b Display of the top 20 enriched pathway terms in F/D libraries. - repressed protein was identified in the F/D libraries. - Interestingly, we observed that the expression of auxin transport-relevant genes such as auxin efflux carrier component 1c and auxin transporter-like protein 2 were not severely affected by light intensity, which indicated that the difference in ARs formation was not a result from IAA transport in the darkness and 20,000 lx light intensity (Table 2).. - Sugar (especially sucrose) signals are involved in the above biological processes by indu- cing many important genes [59–62]. - In this study, we found that several important genes related to su- crose synthesis had enhanced expression in the F/D libraries, and the content of sucrose was higher than that in darkness.. - It has been shown that the expression of these genes can lead to an in- crease in the sucrose content [67]. - We observed that the expression of genes encoding sucrose synthase and sucrose-phosphatase was enhanced by 3.91- and 1.29-fold in the F/D libraries (Table 3). - Therefore, we believe that a new model of interaction between sucrose and IAA is involved in lotus root development.. - Therefore, we analyzed genome-wide gene expression by RNA-seq and deter- mined that and 1462 genes were upregu- lated and and 834 genes were downregulated in the D/CK0, E/CK0, and F/CK0 li- braries, respectively. - We observed that 20 DEGs were involved in signal transduction, and 36 DEGs were re- lated to carbohydrate metabolism. - In the F/D librar- ies, 28 genes relevant to auxin synthesis, transport, response, or binding were found to participate in AR development, and 24 genes related to sucrose metab- olism, glucose metabolism, and fructose metabolism changed their expression. - According to changes in IAA and sucrose content, we believe that IAA and sucrose cooperatively regulate lotus AR formation.. - In this study, Taikong 36, which was bred by the research base of the Guangchang space lotus (this species of lotus, Nelumbo nucifera Gaertn., has been deposited in a publicly available herbarium), was selected for all experimental analyses as there were abundant material resources for this plant. - Taikong 36 was harvested from Guangxi province, and grown in the ex- perimental field of the aquatic vegetables research group of Yangzhou University (latitude: 119.42, longitude: 32.39, alti- tude: 12 m), Southeast China with conventional management in spring. - In the growing season, the temperature was 30 ± 5 °C/day and 25 ± 5 °C/night, and the average water depth of field (the plant must be maintained in the water) was 30 ± 10 cm. - The seeds were harvested after 30 d of flowering and kept in the warehouse under normal temperature conditions. - Table 2 Gene expression involved in IAA metabolism in the D/CK, F/CK, and F/D libraries. - 1.00 – Auxin responsive protein IAA27. - 1.94 – Auxin responsive protein SAUR21. - 2.36 – Auxin induced protein 6B. - A vacuum condition in a the small container was made Table 3 Gene expression involved in sucrose, glucose, and fructose metabolism in D/CK, F/CK, and F/D libraries. - Functional analysis of the DEGs. - The DEGs in each library involved in molecular func- tion, cellular component, and biological process were annotated using the Gene Ontology (GO) tool. - The number of DEGs in- volved in the above three ontologies was computed after comparison with the GO database (http://www.geneon- tology.org. - the primers of the chosen genes are listed in Additional file 1: Table S2. - The total volume of the PCR reaction system was 25 μL includ- ing 12.5 μL Premix Ex Taq II (TliRNaseH Plus) (2×) SYBR (Tiangen, China), 10 μM each of forward and reverse primers, 2 μL cDNA solution, and 8.5 μL distilled water.. - The lower layer of the supernatant (900 mL) was extracted and dried with nitrogen. - The seeds of the first group were placed in water for germination, and the sec- ond group was treated with 150 μM IAA for 2 days and then transferred to water for germination. - The seeds of the third group were put into 20 g/L sucrose for 2 days and then transferred into water, and the seeds of the fourth group were placed into the solution with 20 g/L and 150 μM IAA for 2 days. - Table S2.The primers of genes used for mRNA level analysis qRT-PCR method.. - We extend our thanks to members of the BIG for their cooperation in obtaining the data during the AR formation of the lotus by RNA-seq tech- nique. - XX and CL participated in the sequence analysis. - All the funder lists in this manuscript have no role in the design and performance of all the exper- iments, analysis of data, and in the writing of the text file.. - Detailed data has been deposited in the NCBI database (Biosample number, CK0_1 ~ CK0_3:. - Genome of the Long living sacred lotus ( Nelumbo nucifera Gaertn. - Auxin and cytokinin control formation of the quiescent Centre in the adventitious root apex of Arabidopsis. - Role of auxin and polyamines in adventitious root formation in relation to changes in compounds involved in rooting. - Genetic dissection of the role of ethylene in regulating auxin-dependent lateral and adventitious root formation in tomato. - AUX1 promotes lateral root formation by facilitating indole-3-acetic acid distribution between sink and source tissues in the Arabidopsis seedling.. - Diversification and expression of the PIN, AUX/LAX, and ABCB families of putative auxin transporters in Populus. - A PIN1 family gene, OsPIN1, involved in auxin- dependent adventitious root emergence and tillering in Rice. - Efects of light intensity and plant growth regulators on callus proliferation and shoot regeneration in the ornamental succulent Haworthia. - Transcriptomic analysis reveals ethylene ’ s regulation involved in adventitious roots formation in lotus ( Nelumbo nucifera Gaertn. - Genome- wide analysis and characterization of the aux/iaa family genes related to floral scent formation in Hedychium coronarium. - Sugar control of the plant cell cycle: differential regulation of Arabidopsis D-type cyclin gene expression. - Control of the plant cell cycle by developmental and environmental cues. - Modification of the droplet-vitrification method of cryopreservation to enhance survival rates of adventitious roots of Panax ginseng. - A spatiotemporal dna endoploidy map of the arabidopsis root reveals roles for the endocycle in root development and stress adaptation
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