Genome-wide identification and characterization of aquaporin gene family in moso bamboo (Phyllostachys edulis)

Advances in bamboo genomics: Growth and development, stress tolerance, and genetic engineering

Bamboo is a fast-growing and ecologically significant plant with immense economic value due to its applications in construction, textiles, and bioenergy. However, research on bamboo has been hindered by its long vegetative period, unpredictable flowering cycles, and challenges in genetic transformation. Recent developments in advanced sequencing and genetic engineering technologies have provided new insights into bamboo's evolutionary history, developmental biology, and stress resilience, paving the way for improved conservation and sustainable utilization. This review synthesizes the latest findings on bamboo's genomics, biotechnology, and the molecular mechanisms governing its growth, development, and stress response. Key genes and regulatory pathways controlling its rapid growth, internode elongation, rhizome development, culm lignification, flowering, and abiotic stress responses have been identified through multi-omics and functional studies. Complex interactions among transcription factors, epigenetic regulators, and functionally important genes shape bamboo's unique growth characteristics. Moreover, progress in genetic engineering techniques, including clustered regularly interspaced short palindromic repeats-based genome editing, has opened new avenues for targeted genetic improvements. However, technical challenges, particularly the complexity of polyploid bamboo genomes and inefficient regeneration systems, remain significant barriers to functional studies and large-scale breeding efforts. By integrating recent genomic discoveries with advancements in biotechnology, this review proposes potential strategies to overcome existing technological limitations and to accelerate the development of improved bamboo varieties. Continued efforts in multi-omics research, gene-editing applications, and sustainable cultivation practices will be essential for harnessing bamboo as a resilient and renewable resource for the future. The review presented here not only deepens our understanding of bamboo's genetic architecture but also provides a foundation for future research aimed at optimizing its ecological and industrial potential.

Ethylene-Mediated RsCBF2 and RsERF18 Enhance Salt Tolerance by Directly Regulating Aquaporin Gene RsPIP2-1 in Radish (Raphanus sativus L.)

Salt stress is a major environmental factor limiting the production and quality of plants worldwide. Radish (Raphanus sativus L.), one of the most important root crops, is susceptible to salt stress worldwide. Plasma membrane intrinsic proteins (PIPs) have been identified to play a crucial role in regulating plants' salt tolerance. However, the underlying molecular regulatory mechanisms involved in salt stress tolerance are largely unknown. Here, a salt-induced water transport gene RsPIP2-1 associated with the regulatory mechanisms in response to salt stress was clarified in radish. Overexpression of RsPIP2-1 had high-water channel and H2O2 transport activity in Xenopus laevis oocytes and yeast, and it also conferred prominently salt tolerance through promoting reactive oxygen species (ROS) scavenging and enhancing antioxidant enzyme activity in transgenic radish. Moreover, yeast one-hybrid (Y1H) was used to screen the upstream regulators of RsPIP2-1, and two ethylene-responsive transcription factors including RsCBF2 and RsERF18 were identified. Y1H, dual-luciferase assay (DLA) and electrophoretic mobility shift assays (EMSA) showed that these two genes could active the transcription of RsPIP2-1 by directly binding to the DRE/CRT element and GCC-box element in its promoter. In addition, the salt tolerance and the expression levels of these two transcription factors could be significantly upregulated when treated with exogenous application of an ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), while the plants' resistance as well as the expression patterns could be reduced when exposure to the inhibitor of ethylene action (AgNO3), suggesting that RsCBF2 and RsERF18 positively regulated the salt tolerance in a manner of dependent on ethylene synthesis pathway. Taken together, these findings uncover a novel transcriptional regulatory module based on the RsCBF2/RsERF18-RsPIP2-1 underlying salt tolerance in radish and could provide new insights into the salt-tolerant vegetable crop breeding programs.

LTR retrotransposon-derived novel lncRNA2 enhances cold tolerance in Moso bamboo by modulating antioxidant activity and photosynthetic efficiency

In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived long non-coding RNA (TElncRNA) in response to cold stress remains unclear. In this study, several Pe-TElncRNAs were identified from Moso bamboo transcriptome data. qRT-PCR analysis showed that the expression of a novel Pe-TElncRNA2 in Moso bamboo seedlings reached its highest level at 8 hours of cold treatment at 4 °C and was significantly higher in the stems compared to the leaves, roots, and buds. Furthermore, cellular localization analysis revealed that Pe-TElncRNA2 expression was significantly higher in the cytoplasm than in the nucleus. Pe-TElncRNA2 overexpression in Moso bamboo protoplasts showed that Pe-TElncRNA2 positively regulated the expression of FZR2, NOT3, ABCG44 and AGD6 genes. Further validation of this lncRNA in Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity and proline content, as well as maximum photochemical efficiency PS II in dark-adapted leaves (F v/F m), in the transgenic plants compared to the wild-type controls. Conversely, malondialdehyde (MDA) content, a lipid peroxidation marker (a marker of oxidative stress), was significantly reduced in the transgenic plants. Notably, the expression levels of both Pe-TElncRNA2 and the genes that were regulated by this lncRNA were upregulated in the transgenic plants after two days of cold stress treatment. These findings elucidate the critical role of LTR retrotransposon-derived lncRNAs in mediating cold stress responses in Moso bamboo.

Comprehensive analysis of the CPP gene family in Moso bamboo: insights into their role in rapid shoot growth

Cysteine-rich polycomb-like proteins (CPPs), pivotal transcription factors crucial for evolution of plants from germination to maturity, and adaptation to environmental stresses, have not yet been characterized within the context of Moso bamboo. The CPP gene family of Moso bamboo was identified through bioinformatics, and the structural and functional attributes of the gene, including its physicochemical properties, evolutionary relationships, and gene-protein structures, were revealed. Additionally, the current study also offers valuable information on the patterns of gene expression in bamboo shoots during the period of accelerated development. The results show that the Moso bamboo genome contains 17 CPP members. Molecular phylogenetic relationships indicated that CPPs could be divided into three subfamilies and that CPP members of the same subfamily shared similar gene structures, motifs and conserved structural domains. The covariance analysis showed that the covariance between CPP and Oryza sativa was higher than that between Arabidopsis. Protein homology modeling showed that CPP proteins contain the DNA-binding domain of typical transcription factors. Transcriptomic data analysis revealed that CPP gene expression differs between tissues and organs. CPP could be regulated in response to exogenous gibberellin (GA) and naphthalene acetic acid (NAA). The qRT-PCR experiments demonstrated that CPP was crucial in the initial and fast expansion of bamboo shoots. Additionally, gene ontology (GO), KEGG enrichment and CPP regulatory network map analyses revealed multiple functional annotations of PeCPP-regulated downstream target genes. The results of this study will not only lay the foundation for further exploration of the detailed biological functions of CPP genes in the growth and development of Moso bamboo, but also establish the groundwork for future genetic enhancement of fast-growing forest trees.

Expression and function analysis of phenylalanine ammonia-lyase genes involved in Bamboo lignin biosynthesis

Bamboo, renowned as the fastest-growing plant globally, matures within an astonishingly short period of 40-50 days from shoots, reaching heights of 10-20 meters. Moreover, it can be harvested for various uses within 3-5 years. Bamboo exhibits exceptional mechanical properties, characterized by high hardness and flexibility, largely attributed to its lignin content. Phenylalanine ammonia-lyase (PAL) catalyzes the crucial initial step in lignin biosynthesis, but its precise role in bamboo lignification processes remains elusive. Thus, elucidating the functions of PAL genes in bamboo lignification processes is imperative for understanding its rapid growth and mechanical strength. Here, we systematically identified and classified PAL genes in Moso bamboo, ensuring nomenclature consistency across prior studies. Subsequently, we evaluated PAL gene expression profiles using publicly available transcriptome data. The downregulation of PePALs expression in Moso bamboo through in planta gene editing resulted in a decrease in PAL activity and a subsequent reduction in lignin content. In contrast, overexpression of PePAL led to enhanced PAL activity and an increase in lignin content. These findings highlight the critical role of PAL in the lignin biosynthesis process of Moso bamboo, which will help to unravel the mechanism underpinning bamboo's rapid growth and mechanical strength, with a specific emphasis on elucidating the functions of PAL genes.

Genome-Wide Analysis of Aquaporin Gene Family in Triticum turgidum and Its Expression Profile in Response to Salt Stress

During the response of plants to water stresses, aquaporin (AQP) plays a prominent role in membrane water transport based on the received upstream signals. Due to the importance of the AQP gene family, studies have been conducted that investigate the function and regulatory system of these genes. However, many of their molecular aspects are still unknown. This study aims to carry out a genome-wide investigation of the AQP gene family in Triticum turgidum using bioinformatics tools and to investigate the expression patterns of some members in response to salt stress. Our results show that there are 80 TtAQP genes in T. turgidum, which are classified into four main groups based on phylogenetic analysis. Several duplications were observed between the members of the TtAQP gene family, and high diversity in response to post-translational modifications was observed between TtAQP family members. The expression pattern of TtAQP genes disclosed that these genes are primarily upregulated in response to salt stress. Additionally, the qPCR data revealed that TtAQPs are more induced in delayed responses to salinity stress. Overall, our findings illustrate that TtAQP members are diverse in terms of their structure, regulatory systems, and expression levels.

Genome-wide identification and characterization of aquaporins in mangrove plant Kandelia obovata and its role in response to the intertidal environment

Aquaporins (AQPs) play important roles in plant growth, development and tolerance to environmental stresses. To understand the role of AQPs in the mangrove plant Kandelia obovata, which has the ability to acquire water from seawater, we identified 34 AQPs in the K. obovata genome and analysed their structural features. Phylogenetic analysis revealed that KoAQPs are homologous to AQPs of Populus and Arabidopsis, which are evolutionarily conserved. The key amino acid residues were used to assess water-transport ability. Analysis of cis-acting elements in the promoters indicated that KoAQPs may be stress- and hormone-responsive. Subcellular localization of KoAQPs in yeast showed most KoAQPs function in the membrane system. That transgenic yeast with increased cell volume showed that some KoAQPs have significant water-transport activity, and the substrate sensitivity assay indicates that some KoAQPs can transport H₂ O₂ . The transcriptome data were used to analyze the expression patterns of KoAQPs in different tissues and developing fruits of K. obovata. In addition, real-time quantitative PCR analyses combined transcriptome data showed that KoAQPs have complex responses to environmental factors, including salinity, flooding and cold. Collectively, the transport of water and solutes by KoAQPs contributed to the adaptation of K. obovata to the coastal intertidal environment.

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.

A bamboo leaf-specific aquaporin gene PePIP2;7 is involved in abiotic stress response

PePIP2;7, a leaf-specific aquaporin gene in bamboo, is upregulated under abiotic stresses. Overexpressing PePIP2;7 confers abiotic stresses tolerance in transgenic Arabidopsis plant and yeast. Aquaporins (AQPs) participate in the regulation of water balance in plants. However, the function of AQPs in bamboo remains unclear. Here, PePIP2;7 was identified as a leaf-specific aquaporin gene in moso bamboo based on the expression analysis of transcriptome data and PCR. In situ hybridization further indicated that PePIP2;7 was mainly expressed in mesophyll cells of mature leaves, while in immature leaves it was dominant in blade edge cells followed by mesophyll cells. Interestingly, PePIP2;7 was strongly expressed in the mesophyll cells near bulliform cells of immature leaves, suggesting that PePIP2;7 might function in water transport and contribute to leaf unfolding. The transient expression assay showed that PePIP2;7 was a plasma membrane intrinsic protein. Furthermore, PePIP2;7 was upregulated under abiotic stresses such as high light, drought, and NaCl. Compared with Col-0, transgenic Arabidopsis plants overexpressing PePIP2;7 had better seed germination rate, longer taproot length, higher SOD activity, and lower MDA content under abiotic stresses. Besides, yeasts expressing PePIP2;7 also had higher tolerance to stress compared to the control. Taken together, our results show that PePIP2;7 is leaf-specific and involved in stress response, which provides new insights into aquaporin function in bamboo.

Plant aquaporins alleviate drought tolerance in plants by modulating cellular biochemistry, root-architecture, and photosynthesis

Water is a vital resource for plants to grow, thrive, and complete their life cycle. In recent years, drastic changes in the climate, especially drought frequency and severity, have increased, which reduces agricultural productivity worldwide. Aquaporins are membrane channels belonging to the major intrinsic protein superfamily, which play an essential role in cellular water and osmotic homeostasis of plants under both control and water deficit conditions. A genome-wide search reveals the vast availability of aquaporin isoforms, phylogenetic relationships, different families, conserved residues, chromosomal locations, and gene structure of aquaporins. Furthermore, aquaporins gating and subcellular trafficking are commonly controlled by phosphorylation, cytosolic pH, divalent cations, reactive oxygen species, and stoichiometry. Researchers have identified their involvement in regulating hydraulic conductance, root system architecture, modulation of abiotic stress-related genes, seed viability and germination, phloem loading, xylem water exit, photosynthetic parameters, and post-drought recovery. Remarkable effects following the change in aquaporin activity and/or gene expression have been observed on root water transport properties, nutrient acquisition, physiology, transpiration, stomatal aperture, gas exchange, and water use efficiency. The present review highlights the role of different aquaporin homologs under water-deficit stress condition in model and crop plants. Moreover, the opportunity and challenges encountered to explore aquaporins for engineering drought-tolerant crop plants are also discussed here.

Two Aquaporin Genes, GhPIP2;7 and GhTIP2;1, Positively Regulate the Tolerance of Upland Cotton to Salt and Osmotic Stresses

Aquaporins (AQPs) facilitate the transport of water and small molecules across intrinsic membranes and play a critical role in abiotic stresses. In this study, 111, 54, and 56 candidate AQP genes were identified in Gossypium hirsutum (AD₁), Gossypium arboreum (A₂), and Gossypium raimondii (D₅), respectively, and were further classified into five subfamilies, namely, plasma intrinsic protein (PIP), tonoplast intrinsic protein (TIP), nodulin 26-like intrinsic protein (NIP), small basic intrinsic protein (SIP), and uncategorized X intrinsic protein (XIP). Transcriptome analysis and quantitative real-time PCR (qRT-PCR) revealed some high-expression GhPIPs and GhTIPs (PIP and TIP genes in G. hirsutum, respectively) in drought and salt stresses. GhPIP2;7-silenced plants decreased in the chlorophyll content, superoxide dismutase (SOD) activity, and peroxidase (POD) activity comparing the mock control (empty-vector) under 400 mM NaCl treatment, which indicated a positive regulatory role of GhPIP2;7 in salt tolerance of cotton. The GhTIP2;1-silenced cotton plants were more sensitive to osmotic stress. GhTIP2;1-overexpressed plants exhibited less accumulation of H₂O₂ and malondialdehyde but higher proline content under osmotic stress. In summary, our study elucidates the positive regulatory roles of two GhAQPs (GhPIP2;7 and GhTIP2;1) in salt and osmotic stress responses, respectively, and provides a new gene resource for future research.

Drought stress and re-watering affect the abundance of TIP aquaporin transcripts in barley

Tonoplast Intrinsic Proteins (TIP) are plant aquaporins that are primarily localized in the tonoplast and play a role in the bidirectional flux of water and other substrates across a membrane. In barley, eleven members of the HvTIP gene subfamily have been identified. Here, we describe the transcription profile of the HvTIP genes in the leaves of barley seedlings being grown under optimal moisture conditions, drought stress and a re-watering phase. The applied drought stress caused a 55% decrease in the relative water content (RWC) in seedlings, while re-watering increased the RWC to 90% of the control. Our analysis showed that all HvTIP genes, except HvTIP3;2, HvTIP4;3 and HvTIP5.1, were expressed in leaves of ten-day-old barley seedlings under optimal water conditions with the transcripts of HvTIP2;3, HvTIP1;2 and HvTIP1;1 being the most abundant. We showed, for the first time in barley, a significant variation in the transcriptional activity between the analysed genes under drought stress. After drought treatment, five HvTIP genes, which are engaged in water transport, were down-regulated to varying degrees, while two, HvTIP3;1 and HvTIP4;1, were up-regulated. The HvTIP3;1 isoform, which is postulated as transporting hydrogen peroxide, expressed the highest increase of activity (ca. 5000x) under drought stress, thus indicating its importance in the response to this stress. Re-hydration caused the return of the expression of many genes to the level that was observed under optimal moisture conditions or, at least, a change in this direction Additionally, we examined the promotor regions of HvTIP and detected the presence of the cis-regulatory elements that are connected with the hormone and stress responses in all of the genes. Overall, our results suggest that 7 of 11 studied HvTIP (HvTIP1;1, HvTIP1;2, HvTIP2;1, HvTIP2;2, HvTIP2;3, HvTIP3;1, HvTIP4;1) have an important function during the adaptation of barley to drought stress conditions. We discuss the identified drought-responsive HvTIP in terms of their function in the adaptation of barley to this stress.

Plant Aquaporins: Diversity, Evolution and Biotechnological Applications

The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles. While mammals have 15 types of AQPs described so far (displaying 18 paralogs), a single plant species can present more than 120 isoforms, providing transport of different types of solutes. Such aquaporins may be present in the whole plant or can be associated with different tissues or situations, including biotic and especially abiotic stresses, such as drought, salinity or tolerance to soils rich in heavy metals, for instance. The present review addresses several aspects of plant aquaporins, from their structure, classification, and function, to in silico methodologies for their analysis and identification in transcriptomes and genomes. Aspects of evolution and diversification of AQPs (with a focus on plants) are approached for the first time with the aid of the LCA (Last Common Ancestor) analysis. Finally, the main practical applications involving the use of AQPs are discussed, including patents and future perspectives involving this important protein family.

Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)

Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237-323 amino acids, with a theoretical molecular weight (MW) of 24.31-31.80 kDa and an isoelectric point (pI) value of 4.73-10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger's position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.

Genome-wide identification and expression analysis of aquaporin gene family related to abiotic stress in watermelon

The plant aquaporins (AQPs) are highly conserved integral membrane proteins that participate in multiple developmental processes and responses to various stresses. In this study, a total of 35 AQP genes were identified in the watermelon genome. The phylogenetic analysis showed that these AQPs can be divided into five types, including 16 plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight nodulin 26-like intrinsic proteins (NIPs), two small basic intrinsic proteins (SIPs), and one uncategorized X intrinsic protein (XIP). A number of cis-elements related to plant responses to hormones and stresses were detected in the promoter sequences of ClAQP genes. Chromosome distribution analysis revealed that the genes are unevenly distributed on eight chromosomes, with chromosomes 1 and 4 possessing the most genes. Expression analysis at different developmental stages in flesh and rind indicated that most of ClAQPs have tissue-specific expression. Meanwhile, some other AQP genes showed differential expression in response to cold, salt, and ABA treatments, which is consistent with the organization of the stress-responsive cis-elements detected in the promoter regions. Our results lay a foundation for understanding the specific functions of ClAQP genes to help the genetic improvement of watermelon.

Genome-wide identification, structure characterization, and expression pattern profiling of aquaporin gene family in cucumber

BACKGROUND

Aquaporin (AQP) proteins comprise a group of membrane intrinsic proteins (MIPs) that are responsible for transporting water and other small molecules, which is crucial for plant survival under stress conditions including salt stress. Despite the vital role of AQPs, little is known about them in cucumber (Cucumis sativus L.).

RESULTS

In this study, we identified 39 aquaporin-encoding genes in cucumber that were separated by phylogenetic analysis into five sub-families (PIP, TIP, NIP, SIP, and XIP). Their substrate specificity was then assessed based on key amino acid residues such as the aromatic/Arginine (ar/R) selectivity filter, Froger's positions, and specificity-determining positions. The putative cis-regulatory motifs available in the promoter region of each AQP gene were analyzed and results revealed that their promoter regions contain many abiotic related cis-regulatory elements. Furthermore, analysis of previously released RNA-seq data revealed tissue- and treatment-specific expression patterns of cucumber AQP genes (CsAQPs). Three aquaporins (CsTIP1;1, CsPIP2;4, and CsPIP1;2) were the most transcript abundance genes, with CsTIP1;1 showing the highest expression levels among all aquaporins. Subcellular localization analysis in Nicotiana benthamiana epidermal cells revealed the diverse and broad array of sub-cellular localizations of CsAQPs. We then performed RNA-seq to identify the expression pattern of CsAQPs under salt stress and found a general decreased expression level of root CsAQPs. Moreover, qRT-PCR revealed rapid changes in the expression levels of CsAQPs in response to diverse abiotic stresses including salt, polyethylene glycol (PEG)-6000, heat, and chilling stresses. Additionally, transient expression of AQPs in N. benthamiana increased leaf water loss rate, suggesting their potential roles in the regulation of plant water status under stress conditions.

CONCLUSIONS

Our results indicated that CsAQPs play important roles in response to salt stress. The genome-wide identification and primary function characterization of cucumber aquaporins provides insight to elucidate the complexity of the AQP gene family and their biological functions in cucumber.

Integrated approaches to study the drought tolerance mechanism in hot pepper (Capsicum annuum L.)

Drought is one of the predominant abiotic stresses which have phenomenal impact on crop productivity. Alterations in aquaporin gene expressions are part of complex molecular responses by plant in response to drought. To better understand the role of aquaporins in economically important crop chilli (Capsicum annuum), drought induced gene expression of twelve aquaporins was determined in drought tolerant-KCa-4884 and drought susceptible-G-4 genotypes. Conjointly, the effect of drought on leaf water status and photosynthetic parameters were evaluated. Gene expression of all examined 12 aquaporins was up-regulated in KCa-4884 and in contrast, all the aquaporin genes were down-regulated in G-4 under drought stress. Significant variations among two chilli genotypes have been recorded in photosynthetic rate (P _n ), stomatal conductance (G _s ), and relative water content (RWC), sub-stomatal CO₂ concentration (C _i ). KCa-4884 revealed significantly high rates of P _n and RWC and decreased G _s under water deficit conditions providing evidence for superior drought adaptive strategies. Differences in physiological parameters illustrate prevention of water loss during drought. Up-regulation of aquaporins in drought tolerant genotype implicates their possible role in water relations and photosynthetic performance even under extended drought conditions.

Transcriptome-Wide Characterization and Functional Identification of the Aquaporin Gene Family During Drought Stress in Common Vetch

Aquaporins (AQPs) are transmembrane channels that are essential for the movement of water and other small molecules between biofilms in various physiological processes in plants. In this study, based on transcriptome-wide data, we identified and described a total of 21 AQP genes in common vetch (Vicia sativa subsp. sativa), which is an economically important pasture legume worldwide. Based on phylogenetic analyses, the VsAQPs were sorted into four subfamilies, including four plasma membrane intrinsic proteins (PIPs), six tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins, and four small basic intrinsic proteins. Furthermore, chemical and physical properties of these VsAQPs, including the isoelectric point and theoretical molecular weight, were analyzed. Analyses of the AQP signature sequences and key residues indicated the substrate specificity of each VsAQP. A set of VsAQPs was selected for gene expression analysis in a number of tissues and after drought stress treatments using real-time quantitative reverse transcription/polymerase chain reaction assays. Most of the PIPs and TIPs were proposed to have critical roles in regulating the flow of water during drought stress. Heterologous expression experiments in yeast indicated that VsPIP1;2 and VsPIP2;2 are key candidate genes for improving drought stress tolerance. The results reported in this study could be a crucial resource for further practical analyses and for genetic improvement of drought stress tolerance in common vetch.

Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)

The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.

Whole-Genome and Expression Analyses of Bamboo Aquaporin Genes Reveal Their Functions Involved in Maintaining Diurnal Water Balance in Bamboo Shoots

Water supply is essential for maintaining normal physiological function during the rapid growth of bamboo. Aquaporins (AQPs) play crucial roles in water transport for plant growth and development. Although 26 PeAQPs in bamboo have been reported, the aquaporin-led mechanism of maintaining diurnal water balance in bamboo shoots remains unclear. In this study, a total of 63 PeAQPs were identified, based on the updated genome of moso bamboo (Phyllostachys edulis), including 22 PePIPs, 20 PeTIPs, 17 PeNIPs, and 4 PeSIPs. All of the PeAQPs were differently expressed in 26 different tissues of moso bamboo, based on RNA sequencing (RNA-seq) data. The root pressure in shoots showed circadian rhythm changes, with positive values at night and negative values in the daytime. The quantitative real-time PCR (qRT-PCR) result showed that 25 PeAQPs were detected in the base part of the shoots, and most of them demonstrated diurnal rhythm changes. The expression levels of some PeAQPs were significantly correlated with the root pressure. Of the 86 sugar transport genes, 33 had positive co-expression relationships with 27 PeAQPs. Two root pressure-correlated PeAQPs, PeTIP4;1 and PeTIP4;2, were confirmed to be highly expressed in the parenchyma and epidermal cells of bamboo culm, and in the epidermis, pith, and primary xylem of bamboo roots by in situ hybridization. The authors’ findings provide new insights and a possible aquaporin-led mechanism for bamboo fast growth.

Genome-Wide Identification and Transcriptional Regulation of Aquaporin Genes in Bread Wheat (Triticum aestivum L.) under Water Stress

Aquaporins (AQPs) are transmembrane proteins essential for controlling the flow of water and other molecules required for development and stress tolerance in plants, including important crop species such as wheat (Triticum aestivum). In this study, we utilized a genomic approach for analyzing the information about AQPs available in public databases to characterize their structure and function. Furthermore, we validated the expression of a suite of AQP genes, at the transcriptional level, including accessions with contrasting responses to drought, different organs and water stress levels. We found 65 new AQP genes, from which 60% are copies expanded by polyploidization. Sequence analysis of the AQP genes showed that the purifying selection pressure acted on duplicate genes, which was related to a high conservation of the functions. This situation contrasted with the expression patterns observed for different organs, developmental stages or genotypes under water deficit conditions, which indicated functional divergence at transcription. Expression analyses on contrasting genotypes showed high gene transcription from Tonoplast Intrinsic Protein 1 (TIP1) and 2 (TIP2), and Plasma Membrane Intrinsic Protein 1 (PIP1) and 2 (PIP2) subfamilies in roots and from TIP1 and PIP1 subfamilies in leaves. Interestingly, during severe drought stress, 4 TIP genes analyzed in leaves of the tolerant accession reached up to 15-fold the level observed at the susceptible genotype, suggesting a positive relationship with drought tolerance. The obtained results extend our understanding of the structure and function of AQPs, particularly under water stress conditions.

Expression and functional analysis of two PsbS genes in bamboo (Phyllostachys edulis)

Higher plants have an array of photoprotection mechanisms alleviating the harmful effects of light. Non-photochemical quenching (NPQ) is one of the photoprotective mechanisms, which dissipates the excess of light energy absorbed in the light-harvesting complexes (LHCs) into thermal energy. The photosystem II subunit S (PsbS), a member of the LHC family thought to be present exclusively in higher plants, is supposed to activate NPQ through interactions with antenna proteins. However, the roles of PsbS in bamboo remain unclear. Here, two genes of bamboo (Phyllostachys edulis), PePsbS1 and PePsbS2, are investigated and functionally analyzed. PePsbS1 and PePsbS2 have a similar gene structure with three introns separated by two exons, which encode 269 and 268 amino acid residues, respectively. Tissue-specific analysis showed that PePsbS1 and PePsbS2 are highly expressed in leaf blade. Besides, they are both upregulated in the leaf blade when plantlets are submitted to an increased and prolonged light intensity, suggesting that they are light-induced. Western blot analysis indicated that the accumulation level of total PePsbSs is consistent with what obtained by quantitative real-time polymerase chain reaction for PePsbS1 and PePsbS2. Transgenic Arabidopsis plants overexpressing PePsbS1 and PePsbS2 both displayed an enhanced photoprotection. Moreover, the expression of PePsbS1 and PePsbS2 could both rescue the NPQ of Arabidopsis npq4 mutant, indicating that the PsbSs are functionally conserved between monocots and dicots. These results indicated that both PePsbS1 and PePsbS2 could circumvent photoinhibition and enhance photoprotection, which are key factors for bamboo's adaptation to different light environment.

The R2R3MYB Gene Family in Phyllostachys edulis: Genome-Wide Analysis and Identification of Stress or Development-Related R2R3MYBs

The MYB transcription factor (TF) is one of the largest gene families in plants and involved to multiple biological processes. However, little is known about the MYB family and its functional role in the genome of moso bamboo. In the present study, a total of 114 R2R3MYB genes were first identified from moso bamboo genome and full-length non-chimeric (FLNC) reads. Phylogenetic analysis coupled with gene structure analysis and motif determination resulted in the division of these PheR2R3MYBs into 17 subgroups. The position of eight proteins along an external branch in the phylogenetic tree suggested their relatively ancient origin. The genes in this group were all substituted by (Met, M)/(Arg, R) at conservative W residues in both R2 and R3 repeats, and half were found to possess no transcriptional activation activity. The analysis of evolutionary patterns and divergence suggests that the expansion of PheMYBs was mainly attributable to whole genome duplication (WGD) under different selection pressures. Expressional analysis based on microarray and qRT-PCR data performed diverse expression patterns of R2R3MYBs in response to both various abiotic stimuli and flower development. Furthermore, the co-expression analysis of R2R3MYBs suggested an intricate interplay of growth- and stress-related responses. Finally, we found a hub gene, PheMYB4, was involved in a complex proteins interaction network. Further functional analysis indicated that ectopic overexpression of its homologous gene, PheMYB4-1, could increase tolerance to cold treatment and sensitivity to drought and salt treatment of transgenic Arabidopsis seedlings. These findings provide comprehensive insights into the MYB family members in moso bamboo and offer candidate MYB genes for further studies on their roles in stress resistance.

Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola

Aquaporins (AQPs) are of vital importance in the cellular transport system of all living organisms. In this study, genome-wide identification, distribution, and characterization of AQPs were determined in Arabidopsis lyrata, Capsella grandiflora, C. rubella, Eutrema salsugineum, Brassica rapa, B. oleracea, and B. napus (canola). Classification and phylogeny of AQPs revealed the loss of XIPs and NIP-IIIs in all species. Characterization of distinctive AQP features showed a high level of conservation in spacing between NPA-domains, and selectivity filters. Interestingly, TIP3s were found to be highly expressed in developing seeds, suggesting their role in seed desiccation. Analysis of available RNA-seq data obtained under biotic and abiotic stresses led to the identification of AQPs involved in stress tolerance mechanisms in canola. In addition, analysis of the effect of ploidy level, and resulting gene dose effect performed with the different combinations of Brassica A and C genomes revealed that more than 70% of AQPs expression were dose-independent, thereby supporting their role in stress alleviation. This first in-depth characterization of Brassicaceae AQPs highlights transport mechanisms and related physiological processes that could be exploited in breeding programs of stress-tolerant cultivars.

The bamboo aquaporin gene PeTIP4;1-1 confers drought and salinity tolerance in transgenic Arabidopsis

PeTIP4;1-1, an aquaporin gene involved in bamboo shoot growth, is regulated by abiotic stresses. Overexpression of PeTIP4;1-1 confers drought and salinity tolerance in transgenic Arabidopsis. Aquaporins play a central role in numerous physiological processes throughout plant growth and development. PeTIP4;1-1, an aquaporin gene isolated from moso bamboo (Phyllostachys edulis), comprises an open reading frame (ORF) of 756 bp encoding a peptide of 251 amino acids. The genomic sequence corresponding to the ORF of PeTIP4;1-1 was 1777 bp and contained three exons separated by two introns. PeTIP4;1-1 was constitutively expressed at the highest level in culms, and the expression level was elevated with increasing height of the bamboo shoot. PeTIP4;1-1 was significantly up-regulated in response to drought and salinity stresses in bamboo roots and leaves. To investigate the role of PeTIP4;1-1 in response to drought and salinity stresses, transgenic Arabidopsis plants overexpressing PeTIP4;1-1 under the control of CaMV 35S promoter were generated and subjected to morphological and physiological assays. Compared with Col-0, the transgenic plants showed enhanced tolerance to drought and salinity stresses and produced longer taproots, which had more green leaves, higher F _v/F _m and NPQ values, higher activities of SOD, POD and CAT, lower MDA concentration and higher water content. Transcript levels of three stress-related genes (AtP5CS, AtNHX1 and AtLEA) were enhanced. These results indicated that PeTIP4;1-1 might play an important function in response to drought and salinity stresses, and is a candidate gene for breeding of stress tolerance in other crops through genetic engineering.

The apoplasmic pathway via the root apex and lateral roots contributes to Cd hyperaccumulation in the hyperaccumulator Sedum alfredii

Although the significance of apoplasmic barriers in roots with regards to the uptake of toxic elements is generally known, the contribution of apoplasmic bypasses (ABs) to cadmium (Cd) hyperaccumulation is little understood. Here, we employed a combination of stable isotopic tracer techniques, an ABs tracer, hydraulic measurements, suberin lamellae staining, metabolic inhibitors, and antitranspirants to investigate and quantify the impact of the ABs on translocation of Cd to the xylem in roots of a hyperaccumulating (H) ecotype and a non-hyperaccumulating (NH) ecotype of Sedum alfredii. In the H ecotype, the Cd content in the xylem sap was proportional to hydrostatic pressure, which was attributed to pressure-driven flow via the ABs. The contribution of the ABs to Cd transportation to the xylem was dependent on the Cd concentration applied to the H ecotype (up to 37% at the highest concentration used). Cd-treated H ecotype roots showed significantly higher hydraulic conductance compared with the NH ecotype (76 vs 52 × 10–8 m s–1MPa–1), which is in accordance with less extensive suberization due to reduced expression of suberin-related genes. The main entry sites of apoplasmically transported Cd were localized in the root apexes and lateral roots of the H ecotype, where suberin lamellae were not well developed. These findings highlight the significance of the apoplasmic bypass in Cd hyperaccumulation in hyperaccumulating ecotypes of S. alfredii.

Cloning and Preliminary Functional Analysis of PeUGE Gene from Moso Bamboo (Phyllostachys edulis)

UDP-galactose-4-epimerase (UGE) is a key enzyme involved in galactose metabolism by catalyzing the interconversion of UDP-glucose to UDP-galactose. The cDNA encoding UGE was isolated from Phyllostachys edulis by reverse transcription-polymerase chain reaction and by 5' and 3' rapid amplification of cDNA ends, and was designated as PeUGE. The full-length cDNA of PeUGE was 1778 bp, which contained an open reading frame (ORF) encoding a peptide of 420 amino acids, with a calculated molecular mass of 46.58 kDa and a theoretic isoelectric point of 9.07. The genomic sequence corresponding to the ORF of PeUGE was 2656 bp containing 10 exons separated by nine introns. Tissue-specific analysis showed that PeUGE was constitutively expressed with the highest level in shoots, which had an increasing trend with the growth of shoots. PeUGE was induced by abiotic stresses such as drought, salinity, and water stresses. Moreover, chlorophyll fluorescence parameters and lateral roots analysis of transgenic Arabidopsis thaliana plants overexpressing PeUGE systematically confirmed the crucial role of PeUGE in improving the tolerance to abiotic stresses. These results indicated that PeUGE might be one of the key genes involved in the biosynthesis of cell wall polysaccharides during the growth and development of bamboo and in response to stresses, which provided a candidate gene for molecular engineering to improve the quality of bamboo products.

Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is offered as a resource for AQP research.