Transcriptome analysis reveals key genes regulating signaling and metabolic pathways during the growth of moso bamboo (Phyllostachys edulis) shoots

Abstract

Moso bamboo (Phyllostachys edulis), a high-value bamboo used to produce food (young shoots), building, and industrial goods. To explore key candidate genes regulating signal transduction and metabolic processes during the initiation of stem elongation in moso bamboo, a transcriptome analysis of the shoots during three successive early elongation stages was performed. From cluster and differential expression analyses, 2984 differentially expressed genes (DEGs) were selected for an enrichment analysis. The DEGs were significantly enriched in the plant hormone signal transduction, sugar and starch metabolism, and energy metabolism pathways.Consequently, the DEG expression patterns of these pathways were analyzed, and the plant endogenous hormone and carbon metabolite (including sucrose, total soluble sugar, and starch) contents for each growth stage, of the shoot, were determined.The cytokinin-signaling pathway was continuously active in the three successive elongation stages, in which several cytokinin-signaling genes played indispensable roles. Additionally, many key DEGs regulating sugar, starch metabolism, and energy conversion, which are actively involved in energy production and substrate synthesis during the continuous growth of the shoots, were found. In summary, our study lays a foundation for understanding the mechanisms of moso bamboo growth and provides useful gene resources for breeding through genetic engineering. | INTRODUCTIONAt present, with a growing focus on the environment, the exploration of renewable resources to produce fuel, chemicals, and materials is becoming increasingly important (Matsakas et al., 2019). Thus, the development of fast-growing and high-yield wood resources for energy, chemical, and food products is vital, especially as agricultural and forestry biomass resources (FitzPatrick et al., 2010;Zhang et al., 2011). Moso bamboo (Phyllostachys edulis) is highly valuable because of its use food production (juvenile shoots), as building material, and the production of industrial goods. Additionally, it is a highly important and popular bamboo species, having great ecological, economic, and cultural values worldwide owing to its characteristics of easy reproduction, rapid growth, and high productivity (Peng et al., 2010). Understanding the characteristics of its early growth and development will be conducive in order to be able to utilize the moso bamboo resources better.Owing to its extraordinarily rapid growth, moso bamboo has been studied extensively. The rapid growth is largely achieved through cell division and the elongation of the intercalary meristem at the basal

Hormone and carbohydrate metabolism associated genes play important roles in rhizome bud full‐year germination of Cephalostachyum pingbianense

“…(Zhang et al, 2020) and grape ( Vitis vinifera L.) (Cong et al, 2013), in GBs, most of the key genes associated with EMP, PPP, and TCA cycle pathway were detected as upregulated in this study, such as the HK , PFK , and PK in glycolysis, G6PD in PPP, and CS in TCA cycle. This suggested that the GBs had more active respiration than dormant buds, providing much more immediate energy to maintain continuous cell division (Cui et al, 2012; Lan et al, 2021; Siqueira et al, 2018).…”

“…For example, sucrose promotes cell cycle progression by inducing the expression of D‐type cyclins (Riou‐Khamlichi et al, 2000), and accelerates stem branching by augmenting cytokinin accumulation (Salam et al, 2021). During the lateral bud germination and early growth in Moso bamboo rhizomes ( Phyllostachys edulis ), the expression patterns of genes involved in sugar, starch, and energy metabolism are altered dramatically (Lan et al, 2021; Shou et al, 2020), indicating that carbohydrate metabolism‐related genes may participate in the regulation of bamboo shoot growth and development. In addition, genes associated with environmental response (Malyshev, 2020), cell cycle (Vergara et al, 2017), cell wall biosynthesis (Zhao et al, 2020), and transcription factors (TFs) (Li, An, Cheng, et al, 2021) are probably involved in bud dormancy and growth (Bhandawat et al, 2017; Gamuyao et al, 2017).…”

Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance

“…Access to the moso bamboo genome [210,211] provides a chance to many researchers for genome-wide classifications of TFs such as aquaporin, AAAP, UBP, IQD, HD-Zip, Hexokinase, Aux/IAA and ARF, NAC, PeUGE, HSF, and CONSTANS-like in moso bamboo [188,[214][215][216][217][218][219][220][221][222][223]. Genome-wide classifications of TFs' families in moso bamboo have been carried out and have demonstrated a limited molecular characterization in model plants by exogenous gene transfer in rice and Arabidopsis and the expression profile against stresses [224][225][226]. The expression of PeLAC was high in stem and its promoter sequence contains ABRE cisregulatory element that responds to ABA and GA treatments by upregulating and downregulating the transcript of PeLAC, respectively [227].…”

“…Genome-wide classifications of TFs’ families in moso bamboo have been carried out and have demonstrated a limited molecular characterization in model plants by exogenous gene transfer in rice and Arabidopsis and the expression profile against stresses [ 224 , 225 , 226 ]. The expression of PeLAC was high in stem and its promoter sequence contains ABRE cisregulatory element that responds to ABA and GA treatments by upregulating and downregulating the transcript of PeLAC , respectively [ 227 ].…”

Genome-Wide Identification and Expression Analysis of the Plant U-Box Protein Gene Family in Phyllostachys edulis

“…Further research on its growth and resistance to environmental stresses is important to improve cultivation and downstream applications. Sequencing of the P. edulis V2 genome was completed in 2018 ( Zhao et al, 2018 ), and multiple growth ( Wang et al, 2019 ; Yang et al, 2019 ; Lan et al, 2020 ; Wang et al, 2021 ) and stress-related genes ( Hou et al, 2018 ; Cheng et al, 2019 ; Hou et al, 2020 ; Liu et al, 2020 ) have been extensively studied. However, research on the PUB gene family in P. edulis is lacking.…”