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The Genetic Architecture of Bamboo Growth and Development
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The Genetic Architecture of Bamboo Growth and Development

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 November 2024 | Viewed by 6807

Special Issue Editors

Dr. Yulong Ding

E-Mail Website
Guest Editor
Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
Interests: bamboo; bamboo breeding; bamboo tissue culture
Dr. Muthusamy Ramakrishnan

E-Mail Website
Guest Editor
Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
Interests: bamboo growth and development; genetic diversity; RNA and DNA modification; transposons
Special Issues, Collections and Topics in MDPI journals
Dr. Zishan Ahmad

E-Mail Website
Guest Editor
Bamboo Research Institute, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
Interests: bamboo epigenetics; tissue culture; genetic transformation; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bamboo has immense ecological, economic, and cultural importance worldwide. It is a versatile and rapidly renewable resource with numerous applications, including construction, furniture, papermaking and environmental remediation. In addition, bamboo plays an important role in mitigating climate change by sequestering carbon and conserving soil. Therefore, research on the genetic basis of bamboo growth and development is of paramount importance for the sustainable management and utilization of bamboo. The proposed Special Issue aims to bring together a diverse collection of research articles that address the genetic architecture of bamboo, focusing on various aspects such as shoot development, rhizome growth, flowering patterns, stress tolerance, and resistance to pests and diseases. By uncovering the molecular mechanisms that control these traits, we can gain valuable insights into the unique growth patterns of bamboo and optimize its productivity and quality. To ensure a comprehensive coverage of the topic, we invite researchers, academics and industry experts from around the world to contribute their original work, reviews, and perspectives. This Special Issue serves as a platform for sharing the latest findings, novel methodologies and theoretical frameworks related to the genetic regulation of bamboo growth and development.

Possible topics for this Special Issue include:

  • Genetic regulation of shoot and culm development in bamboo species
  • Molecular basis of bamboo rhizome growth and clonal propagation
  • Identification and characterization of key regulatory pathways in bamboo growth
  • Understanding flowering behaviour and reproductive biology of bamboo
  • Genetic diversity and population genetics studies in bamboo species
  • Genetic improvement of bamboo to enhance productivity and quality traits
  • Molecular mechanisms underlying bamboo response to abiotic and biotic stresses
  • Advances in bamboo genomics, transcriptomics and proteomics
  • Biotechnological applications for bamboo improvement and propagation
  • Sustainable management strategies for bamboo genetic resources

We believe that this Special Issue will make an important contribution to the existing body of knowledge on bamboo genetics and will be a valuable resource for researchers, policy makers and bamboo industry professionals. By fostering interdisciplinary collaboration and knowledge sharing, we can accelerate the development of innovative strategies for the sustainable cultivation, conservation and utilization of bamboo. We are also excited about the possibility of a collaboration between conferences in the field of plant sciences and the journal Plants. This collaboration would further promote the dissemination of research results and facilitate networking among experts in the field.

Dr. Yulong Ding
Dr. Muthusamy Ramakrishnan
Dr. Zishan Ahmad
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bamboo species
  • bamboo growth
  • bamboo improvement
  • bamboo propagation
  • bamboo genetic resources

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Published Papers (6 papers)

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Research

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14 pages, 3255 KiB  
Article
Integrated Analysis of microRNAs and Transcription Factor Targets in Floral Transition of Pleioblastus pygmaeus
by Wenjing Yao, Peng Shen, Meng Yang, Qianyu Meng, Rui Zhou, Long Li and Shuyan Lin
Plants 2024, 13(21), 3033; https://doi.org/10.3390/plants13213033 - 30 Oct 2024
Viewed by 414
Abstract
Bamboo plants have erratic flowering habits with a long vegetative growth and an uncertain flowering cycle. The process of floral transition has always been one of the hot and intriguing topics in bamboo developmental biology. As master modulators of gene expression at the [...] Read more.
Bamboo plants have erratic flowering habits with a long vegetative growth and an uncertain flowering cycle. The process of floral transition has always been one of the hot and intriguing topics in bamboo developmental biology. As master modulators of gene expression at the post-transcriptional level, miRNAs play a crucial role in regulating reproductive growth, especially in floral transition of flowering plants. Pleioblastus pygmaeus is a kind of excellent ground cover ornamental bamboo species. In this study, we performed miRNA expression profiling of the shoot buds and flower buds from the bamboo species, to investigate flowering-related miRNAs in bamboo plants. A total of 179 mature miRNAs were identified from P. pygmaeus, including 120 known miRNAs and 59 novel miRNAs, of which 96 (61 known miRNAs and 35 novel miRNAs) were differentially expressed in the shoots at different growth stages. Based on target gene (TG) prediction, a total of 2099 transcription factors (TFs) were annotated to be TGs of the 96 differentially expressed miRNAs (DEMs), corresponding to 839 recordings of DEM-TF pairs. In addition, we identified 23 known DEMs involved in flowering and six known miRNAs related to floral organ development based on previous reports. Among these, there were 11 significantly differentially expressed miRNAs, with 124 TF targets corresponding to 132 DEM-TF pairs in P. pygmaeus. In particular, we focused on the identification of miR156a-SPL (SQUAMOSA Promoter-Binding protein-Like) modules in the age pathway, which are well-known to regulate the vegetative-to-reproductive phase transition in flowering plants. A total of 36 TF targets of miR156a were identified, among which there were 11 SPLs. The Dual-Luciferase transient expression assay indicated miR156a mediated the repression of the PpSPL targets in P. pygmaeus. The integrated analysis of miRNAs and TGs at genome scale in this study provides insight into the essential roles of individual miRNAs in modulating flowering transition through regulating TF targets in bamboo plants. Full article
(This article belongs to the Special Issue The Genetic Architecture of Bamboo Growth and Development)
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18 pages, 3908 KiB  
Article
Identification of New Cultivar and Different Provenances of Dendrocalamus brandisii (Poaceae: Bambusoideae) Using Simple Sequence Repeats Developed from the Whole Genome
by Ruiman Geng, Junlei Xu, Jutang Jiang, Zhanchao Cheng, Maosheng Sun, Nianhe Xia and Jian Gao
Plants 2024, 13(20), 2910; https://doi.org/10.3390/plants13202910 - 17 Oct 2024
Viewed by 504
Abstract
Dendrocalamus brandisii is a high-quality bamboo species that can be used for both bamboo shoots and wood. The nutritional components and flavors of D. brandisii vary from different geographical provenances. However, the unique biological characteristics of bamboo make morphological classification methods unsuitable for [...] Read more.
Dendrocalamus brandisii is a high-quality bamboo species that can be used for both bamboo shoots and wood. The nutritional components and flavors of D. brandisii vary from different geographical provenances. However, the unique biological characteristics of bamboo make morphological classification methods unsuitable for distinguishing them. Although the new cultivar ‘Manxie No.1’ has significant differences in the branch characteristics and the color of shoot sheaths compared to the D. brandisii, it still lacks precise genetic information at the molecular level. This study identified 231,789 microsatellite markers based on the whole genome of D. brandisii and analyzed their type composition and distribution on chromosomes in detail. Then, using TP-M13-SSR fluorescence-labeling technology, 34 pairs of polymorphic primers were screened to identify the new cultivar ‘Manxie No.1’ and 11 different geographical provenances of D. brandisii. We also constructed DNA fingerprinting profiles for them. At the same time, we mapped six polymorphic SSRs to the gene of D. brandisii, among which SSR673 was mapped to DhB10G011540, which is related to plant immunity. The specific markers selected in this study can rapidly identify the provenances and the new cultivar of D. brandisii and help explore candidate genes related to some important traits. Full article
(This article belongs to the Special Issue The Genetic Architecture of Bamboo Growth and Development)
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19 pages, 6032 KiB  
Article
Conservation and Divergence of PEPC Gene Family in Different Ploidy Bamboos
by Wenlong Cheng, Junlei Xu, Changhong Mu, Jutang Jiang, Zhanchao Cheng and Jian Gao
Plants 2024, 13(17), 2426; https://doi.org/10.3390/plants13172426 - 30 Aug 2024
Viewed by 558
Abstract
Phosphoenolpyruvate carboxylase (PEPC), as a necessary enzyme for higher plants to participate in photosynthesis, plays a key role in photosynthetic carbon metabolism and the stress response. However, the molecular biology of the PEPC family of Bambusoideae has been poorly studied, and the function [...] Read more.
Phosphoenolpyruvate carboxylase (PEPC), as a necessary enzyme for higher plants to participate in photosynthesis, plays a key role in photosynthetic carbon metabolism and the stress response. However, the molecular biology of the PEPC family of Bambusoideae has been poorly studied, and the function of its members in the growth and development of Bambusoideae is still unclear. Here, we identified a total of 62 PEPC family members in bamboo. All the PEPC genes in the bamboo subfamily were divided into twelve groups, each group typically containing significantly fewer PEPC members in Olyra latifolia than in Phyllostachys edulis, Dendrocalamus latiflorus and Dendrocalamus brandisii. The results of an intraspecific and interspecies collinearity analysis showed that fragment replication and whole genome replication were the main driving forces of bamboo PEPC members. Furthermore, the Ka/Ks values of collinear genes showed that bamboo PEPC experienced purification selection. In addition, the promoter region of PEPC genes contains cis-acting elements related to light response, plant hormone response and response to stress. An analysis of the expression levels of the PEPC family in different developmental stages and tissues of bamboo shoots has shown that PhePEPC7, PhePEPC9 and PhePEPC10 were highly expressed in the leaves of non-flowering plants and culms. Furthermore, PhePEPC6 was significantly upregulated in leaves after GA treatment. Further research has shown that PhePEPC6 was mainly localized in the cell membrane. This provides a solid bioinformatics foundation for further understanding the biological functions of the bamboo PEPC family. Full article
(This article belongs to the Special Issue The Genetic Architecture of Bamboo Growth and Development)
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13 pages, 5106 KiB  
Article
Understanding Water Utilization Mechanisms in Degrading Bamboo Shoots: A Cytological and Physiological Study
by Tianyi Hu, Zhengchun Wu, Meng Deng, Haiwen Liu, Jiao Xiao, Qiang Wei and Fen Yu
Plants 2024, 13(14), 1969; https://doi.org/10.3390/plants13141969 - 18 Jul 2024
Viewed by 729
Abstract
Degradation of shoots, characterized by stunted growth and signs of water deficit, is common in bamboo stands. However, the specific mechanisms underlying water utilization in degrading shoots remain unclear. This study sought to address this gap by harvesting bamboo shoots and culms of [...] Read more.
Degradation of shoots, characterized by stunted growth and signs of water deficit, is common in bamboo stands. However, the specific mechanisms underlying water utilization in degrading shoots remain unclear. This study sought to address this gap by harvesting bamboo shoots and culms of Phyllostachys edulis ‘Pachyloen’, employing cytological and physiological techniques to compare water utilization mechanisms between healthy and degrading shoots, and investigating the water supply to bamboo shoots by the parent bamboo. The water pressure in the degrading shoots was markedly lower compared to that of the healthy shoots, and it declined as the degradation progressed, resulting in reduced water content and the cessation of guttation in the degrading shoots. In conditions of water deficit, the percentage of free water in bamboo shoots decreased while the percentages of bound and semi-bound water increased, with the proportion of semi-bound water reaching as high as 88.13% in the late stages of degradation. The water potential of parent bamboo culms of different ages varied at different times of the day and during different growth stages of bamboo shoots, showing a strong association with the development of bamboo shoots. Conversely, the correlation between changes in the water potential of bamboo shoots and their degradation patterns was found to be comparatively minimal. The weakening of the connection between the bamboo shoots and the parent bamboo culms may play a significant role in the degradation of the bamboo shoots. This is evidenced by a decrease in the fluorescence intensity of the nucleus in bamboo shoots and the degradation of genetic material. This study lays the foundation for future research into the mechanisms of bamboo shoot degradation. Full article
(This article belongs to the Special Issue The Genetic Architecture of Bamboo Growth and Development)
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21 pages, 6202 KiB  
Article
Culm Morphological Analysis in Moso Bamboo Reveals the Negative Regulation of Internode Diameter and Thickness by Monthly Precipitation
by Qianwen Zhang, Xue Chu, Zhipeng Gao, Yulong Ding, Feng Que, Zishan Ahmad, Fen Yu, Muthusamy Ramakrishnan and Qiang Wei
Plants 2024, 13(11), 1484; https://doi.org/10.3390/plants13111484 - 28 May 2024
Cited by 1 | Viewed by 990
Abstract
The neglect of Moso bamboo’s phenotype variations hinders its broader utilization, despite its high economic value globally. Thus, this study investigated the morphological variations of 16 Moso bamboo populations. The analysis revealed the culm heights ranging from 9.67 m to 17.5 m, with [...] Read more.
The neglect of Moso bamboo’s phenotype variations hinders its broader utilization, despite its high economic value globally. Thus, this study investigated the morphological variations of 16 Moso bamboo populations. The analysis revealed the culm heights ranging from 9.67 m to 17.5 m, with average heights under the first branch ranging from 4.91 m to 7.67 m. The total internode numbers under the first branch varied from 17 to 36, with internode lengths spanning 2.9 cm to 46.4 cm, diameters ranging from 5.10 cm to 17.2 cm, and wall thicknesses from 3.20 mm to 33.3 mm, indicating distinct attributes among the populations. Furthermore, strong positive correlations were observed between the internode diameter, thickness, length, and volume. The coefficient of variation of height under the first branch showed strong positive correlations with several parameters, indicating variability in their contribution to the total culm height. A regression analysis revealed patterns of covariation among the culm parameters, highlighting their influence on the culm height and structural characteristics. Both the diameter and thickness significantly contribute to the internode volume and culm height, and the culm parameters tend to either increase or decrease together, influencing the culm height. Moreover, this study also identified a significant negative correlation between monthly precipitation and the internode diameter and thickness, especially during December and January, impacting the primary thickening growth and, consequently, the internode size. Full article
(This article belongs to the Special Issue The Genetic Architecture of Bamboo Growth and Development)
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Review

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26 pages, 1453 KiB  
Review
Advances in Single-Cell Transcriptome Sequencing and Spatial Transcriptome Sequencing in Plants
by Zhuo Lv, Shuaijun Jiang, Shuxin Kong, Xu Zhang, Jiahui Yue, Wanqi Zhao, Long Li and Shuyan Lin
Plants 2024, 13(12), 1679; https://doi.org/10.3390/plants13121679 - 18 Jun 2024
Cited by 1 | Viewed by 2199
Abstract
“Omics” typically involves exploration of the structure and function of the entire composition of a biological system at a specific level using high-throughput analytical methods to probe and analyze large amounts of data, including genomics, transcriptomics, proteomics, and metabolomics, among other types. Genomics [...] Read more.
“Omics” typically involves exploration of the structure and function of the entire composition of a biological system at a specific level using high-throughput analytical methods to probe and analyze large amounts of data, including genomics, transcriptomics, proteomics, and metabolomics, among other types. Genomics characterizes and quantifies all genes of an organism collectively, studying their interrelationships and their impacts on the organism. However, conventional transcriptomic sequencing techniques target population cells, and their results only reflect the average expression levels of genes in population cells, as they are unable to reveal the gene expression heterogeneity and spatial heterogeneity among individual cells, thus masking the expression specificity between different cells. Single-cell transcriptomic sequencing and spatial transcriptomic sequencing techniques analyze the transcriptome of individual cells in plant or animal tissues, enabling the understanding of each cell’s metabolites and expressed genes. Consequently, statistical analysis of the corresponding tissues can be performed, with the purpose of achieving cell classification, evolutionary growth, and physiological and pathological analyses. This article provides an overview of the research progress in plant single-cell and spatial transcriptomics, as well as their applications and challenges in plants. Furthermore, prospects for the development of single-cell and spatial transcriptomics are proposed. Full article
(This article belongs to the Special Issue The Genetic Architecture of Bamboo Growth and Development)
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