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

Comprehensive investigation of BZR gene family in four dicots and the function of PtBZR9 and PtBZR12 under drought stress

Brassinazole-resistant (BZR) transcription factor plays an important role in plant growth and stress resistance through brassinosteroid (BR) signal transduction. However, systematic analysis of the BZR family in dicots remains limited. In this study, we conducted a genome-wide study of four typical dicots: Arabidopsis thaliana, Carica papaya, Vitis vinifera and Populus trichocarpa. Thirty-four BZR gene family members were identified and classified them into three subfamilies. Analysis of promoter and expression patterns revealed crucial role of a pair of homologous BZR genes, PtBZR9 and PtBZR12, in poplar may play a critical role under abiotic stress. PtBZR9 and PtBZR12 were localised in the nucleus and exhibited mutual interactions. Moreover, transient overexpression (OE) of PtBZR9 and PtBZR12 in poplar enhanced tolerance to drought stress. The phenotypic and physiological characteristics of PtBZR9 and PtBZR12 OE in Arabidopsis mirrored those of transient OE in the poplar. Additionally, PtBZR9 and PtBZR12 can bind to the E-box element. Under exogenous BR treatment, transgenic lines displayed a greater decrease in root length than the wild type. Thus, these findings provide a solid foundation for future research on the complex regulatory mechanisms of BZR genes.

Emerging Insights into the Roles of the Rhizome-Culm System in Bamboo Shoot Development through Analysis of Non-Structural Carbohydrate Changes

Non-structural carbohydrates (NSCs) required for bamboo shoot development, the critical stage that determines the yield of a bamboo stand, originate from the parent bamboo with the complex underground system. However, the metabolic mechanism of NSCs in the rhizome-culm system during bamboo shoot development remains unclear. In this study, we focused on the changes of NSCs in the rhizome-culm system and used anatomical, physiological, and biochemical methods to investigate the metabolism of NSCs in bamboo shoots of Phyllostachys edulis and the role of NSCs supply in the parent bamboo at different ages. The results showed that NSCs were accumulated and consumed from the bottom to the top in a bamboo shoot, which was consistent with the developmental pattern. The starch granules were stored in advance. The bamboo sheath stored starch from the dormant stage of shoot buds. The functions of culms and rhizomes showed age-dependent differences. Adult culms showed the highest capacity to provide NSCs, with more stored NSCs and higher β-amylase activity. Conversely, young culms seemed to prefer their growth, while old culms tended to store starch. Accordingly, adult rhizomes preferred sugar transport due to the lowest starch storage, lower ADP-glucose pyrophosphorylase (AGPase) activity, and higher β-amylase activity, while young and old rhizomes tended to prefer starch storage. These results provide a basis for further understanding of nutrient metabolism in bamboo stands.

Physio-Biochemical Integrators and Transcriptome Analysis Reveal Nano-Elicitation Associated Response during Dendrocalamus asper (Schult. and Schult. F.) Backer ex K. Heyne Micropropagation

Bamboos are perennial, arborescent, monocarpic and industrially important non-timber plants. They are important for various purposes, such as carbon sequestration, biodiversity support, construction, and food and fiber production. However, traditional vegetative propagation is insufficient for bamboo multiplication. Moreover, little is known about the mechanism of gold nanoparticles (AuNPs) in vitro proliferation and regulation of physiological and biochemical properties. In this study, we investigated the impacts of citrate and cetyltrimethylammonium bromide (CTAB) coated AuNPs on in vitro proliferation, photosynthetic pigment content and antioxidant potential of Dendrocalamus asper (Schult. and Schult. F.) Backer ex K. Heyne. Various morpho-physiological and biochemical parameters were differentially affected along the citrate- and CTAB-coated AuNPs concentration gradients (200-600 µM). In vitro shoot proliferation, photosynthetic pigment content and antioxidant activities were higher in D. asper grown on Murashige and Skoog medium supplemented with 2 mg·L-1 benzyladenine and 400 µM citrate-coated AuNPs than in those grown on Murashige and Skoog medium supplemented with 600 µM CTAB- coated AuNPs. Identification of genes regulating in vitro D. asper proliferation will help understand the molecular regulation of AuNPs-mediated elicitation for modulating various physiological and biochemical activities during micropropagation. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analyses identified differentially expressed genes associated with in vitro modulation of AuNPs-regulated biological processes and molecular functions. The findings of this study provide new insight into AuNPs-mediated elicitation of in vitro mass scale bamboo propagation.

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

Cephalostachyum pingbianense is the only woody bamboo species that can produce bamboo shoots in four seasons under natural conditions. So far, the regulatory mechanism of shoot bud differentiation and development is unknown. In the present study, indole-3-acetic acid (IAA), zeatin riboside (ZR), gibberellin A3 (GA₃ ) and abscisic acid (ABA) contents determination, RNA sequencing and differentially expressed gene analysis were performed on dormant rhizome bud (DR), growing rhizome bud (GR), and germinative bud (GB) in each season. The results showed that the contents of IAA and ZR increased while ABA content decreased, and GA₃ content was stable during bud transition from dormancy to germination in each season. Moreover, rhizome bud germination was cooperatively regulated by multiple pathways such as carbohydrate metabolism, hormone signal transduction, cell wall biogenesis, temperature response, and water transport. The inferred hub genes among these candidates were identified by protein-protein interaction network analyses, most of which were involved in hormone and carbohydrate metabolism, such as HK and BGLU4 in spring, IDH and GH3 in winter, GPI and talA/talB in summer and autumn. It is speculated that dynamic phytohormone changes and differential expression of these genes promote the release of rhizome bud dormancy and contribute to the phenological characteristics of full-year shooting. Moreover, the rhizome buds of C. pingbianense may not suffer from ecodormancy in winter. These findings would help accumulate knowledge on shooting mechanisms in woody bamboos and provide a physiological insight into germplasm conservation and forest management of C. pingbianense.

Systematic analysis of the Serine/Arginine-Rich Protein Splicing Factors (SRs) and focus on salt tolerance of PtSC27 in Populus trichocarpa

Serine/Arginine-Rich Protein Splicing Factors (SRs) are indispensable splicing factors, which play significant roles in spliceosome assembly, splicing regulation and regulation of plant stress. However, a comprehensive analysis and function research of SRs in the woody plant is still lacking. In this report, we conducted the identification and comprehensive analysis of the 71 SRs in poplar and three other dicots, including basic characterization, phylogenetic, conserved motifs, gene duplication, promoter and splice isoform of these genes. Based on the publicly available transcriptome data, expression pattern of SRs in poplar under low temperature, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC27 that responded to salt stress was screened. More importantly, overexpression of PtSC27 increased plant survival rate under salt stress, and enhanced salt tolerance by regulating malondialdehyde (MDA) content, peroxidase (POD) and catalase (CAT) enzyme activities in transgenic plants. Meanwhile, overexpression of PtSC27 made transgenic plants insensitive to exogenous ABA and improved the expression of some ABA signal-related genes under salt stress. Overall, our studies lay a foundation for understanding the structure and function of SRs in the poplar and provide useful gene resources for breeding through genetic engineering.

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

Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.

Comparative analysis of the stellacyanins (SCs) family and focus on drought resistance of PtSC18 in Populus trichocarpa

Stellacyanin (SC) is a type I (blue) copper protein, which plays a crucial role in plant growth and stress response. However, the comprehensive analysis and functional research of SCs in the woody plant is still lacking. Here, a total of 74 SCs were collected and identified from Arabidopsis, papaya, grape, rice and poplar. Bioinformatics was used to analyze the gene structure, protein structure and evolutionary relationship of 74 genes, especially 19 SCs in Populus trichocarpa. Based on the RNA-seq data, expression pattern of SCs in poplar under cold, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC18 that strongly responded to drought stress was screened. Subcellular localization experiment exhibited that PtSC18 was localized in the nucleus and plasma membrane. Overexpression of PtSC18 enhanced drought tolerance of transgenic Arabidopsis by improving water retention and reducing oxidative damage. Measurements of physiological indicators, including chlorophyll, H₂O₂, malondialdehyde content, peroxidase and catalase enzyme activities and electrical conductivity, all supported this conclusion. More importantly, PtSC18 enhanced the expression of some stress-related genes in transgenic Arabidopsis. Overall, our results lay a foundation for understanding the structure and function of PtSCs and provide useful gene resources for breeding through genetic engineering.

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

The U-box gene encodes a ubiquitin ligase that contains a U-box domain. The plant U-box (PUB) protein plays an important role in the plant stress response; however, very few studies have investigated the role of these proteins in Moso bamboo (Phyllostachys edulis). Thus, more research on PUB proteins is necessary to understand the mechanisms of stress tolerance in P. edulis. In this study, we identified 121 members of the PUB family in P. edulis (PePUB), using bioinformatics based on the P. edulis V2 genome build. The U-box genes of P. edulis showed an uneven distribution among the chromosomes. Phylogenetic analysis of the U-box genes between P. edulis and Arabidopsis thaliana suggested that these genes can be classified into eight subgroups (Groups I–VIII) based on their structural and phylogenetic features. All U-box genes and the structure of their encoded proteins were identified in P. edulis. We further investigated the expression pattern of PePUB genes in different tissues, including the leaves, panicles, rhizomes, roots, and shoots. The qRT-PCR results showed that expression of three genes, PePUB15, PePUB92, and PePUB120, was upregulated at low temperatures compared to that at 25°C. The expression levels of two PePUBs, PePUB60 and PePUB120, were upregulated under drought stress. These results suggest that the PePUB genes play an important role in resistance to low temperatures and drought in P. edulis. This research provides new insight into the function, diversity, and characterization of PUB genes in P. edulis and provides a basis for understanding their biological roles and molecular mechanisms.