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Li G, Zhao X, Yang J, Hu S, Ponnu J, Kimura S, Hwang I, Torii KU, Hou H. Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39076061 DOI: 10.1111/pce.15050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024]
Abstract
Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome-level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis.
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Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shiqi Hu
- Laboratory of Marine Biological Resources Development and Utilization, Zhejiang Marine Development Research Institute, Zhoushan, Zhejiang, China
| | - Jathish Ponnu
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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van Veen H, Müller JT, Bartylla MM, Akman M, Sasidharan R, Mustroph A. Phylotranscriptomics provides a treasure trove of flood-tolerance mechanisms in the Cardamineae tribe. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39012097 DOI: 10.1111/pce.15033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/10/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
Flooding events are highly detrimental to most terrestrial plant species. However, there is an impressive diversity of plant species that thrive in flood-prone regions and represent a treasure trove of unexplored flood-resilience mechanisms. Here we surveyed a panel of four species from the Cardamineae tribe representing a broad tolerance range. This included the flood-tolerant Cardamine pratensis, Rorippa sylvestris and Rorippa palustris and the flood-sensitive species Cardamine hirsuta. All four species displayed a quiescent strategy, evidenced by the repression of shoot growth underwater. Comparative transcriptomics analyses between the four species and the sensitive model species Arabidopsis thaliana were facilitated via de novo transcriptome assembly and identification of 16 902 universal orthogroups at a high resolution. Our results suggest that tolerance likely evolved separately in the Cardamine and Rorippa species. While the Rorippa response was marked by a strong downregulation of cell-cycle genes, Cardamine minimized overall transcriptional regulation. However, a weak starvation response was a universal trait of tolerant species, potentially achieved in multiple ways. It could result from a strong decline in cell-cycle activity, but is also intertwined with autophagy, senescence, day-time photosynthesis and night-time fermentation capacity. Our data set provides a rich source to study adaptational mechanisms of flooding tolerance.
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Affiliation(s)
- Hans van Veen
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
- Evolutionary Plant Ecophysiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jana T Müller
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Malte M Bartylla
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Melis Akman
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Rashmi Sasidharan
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Angelika Mustroph
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
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Zang Y, Xu C, Yu L, Ma L, Xuan L, Yan S, Zhang Y, Cao Y, Li X, Si Z, Deng J, Zhang T, Hu Y. GHCU, a Molecular Chaperone, Regulates Leaf Curling by Modulating the Distribution of KNGH1 in Cotton. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402816. [PMID: 38666376 PMCID: PMC11234424 DOI: 10.1002/advs.202402816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/08/2024] [Indexed: 07/11/2024]
Abstract
Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial domain. Loss of GHCU function restricts KNGH1 to the adaxial epidermal region, leading to lower auxin response levels in the adaxial boundary compared to the abaxial. This spatial asymmetry in auxin distribution produces the upward-curled leaf phenotype of the cu mutant. By analysis of single-cell RNA sequencing and spatiotemporal transcriptomic data, auxin biosynthesis genes are confirmed to be expressed asymmetrically in the adaxial-abaxial epidermal cells. Overall, these findings suggest that GHCU plays a crucial role in the regulation of leaf flattening through facilitating cell-to-cell trafficking of KNGH1 and hence influencing the auxin response level.
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Affiliation(s)
- Yihao Zang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Chenyu Xu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Lishan Yu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Longen Ma
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Lisha Xuan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Sunyi Yan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Yayao Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Xiaoran Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
| | - Jieqiong Deng
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Sichuan, 610066, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
- Hainan Institute of Zhejiang University, Sanya, 572025, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 310058, China
- Hainan Institute of Zhejiang University, Sanya, 572025, China
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Koga H, Ikematsu S, Kimura S. Diving into the Water: Amphibious Plants as a Model for Investigating Plant Adaptations to Aquatic Environments. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:579-604. [PMID: 38424069 DOI: 10.1146/annurev-arplant-062923-024919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Amphibious plants can grow and survive in both aquatic and terrestrial environments. This review explores the diverse adaptations that enable them to thrive in such contrasting habitats. Plants with amphibious lifestyles possess fascinating traits, and their phenotypic plasticity plays an important role in adaptations. Heterophylly, the ability to produce different leaf forms, is one such trait, with submerged leaves generally being longer, narrower, and thinner than aerial leaves. In addition to drastic changes in leaf contours, amphibious plants display significant anatomical and physiological changes, including a reduction in stomatal number and cuticle thickness and changes in photosynthesis mode. This review summarizes and compares the regulatory mechanisms and evolutionary origins of amphibious plants based on molecular biology studies actively conducted in recent years using novel model amphibious plant species. Studying amphibious plants will enhance our understanding of plant adaptations to aquatic environments.
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Affiliation(s)
- Hiroyuki Koga
- Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-Ku, Tokyo, Japan
| | - Shuka Ikematsu
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, Japan;
| | - Seisuke Kimura
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, Japan;
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, Japan
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Horiguchi G, Oyama R, Akabane T, Suzuki N, Katoh E, Mizokami Y, Noguchi K, Hirotsu N. Cooperation of an external carbonic anhydrase and HCO3- transporter supports underwater photosynthesis in submerged leaves of the amphibious plant Hygrophila difformis. ANNALS OF BOTANY 2024; 133:287-304. [PMID: 37832038 PMCID: PMC11005787 DOI: 10.1093/aob/mcad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/12/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND AND AIMS HCO3- can be a major carbon resource for photosynthesis in underwater environments. Here we investigate the underlying mechanism of uptake and membrane transport of HCO3- in submerged leaves of Hygrophila difformis, a heterophyllous amphibious plant. To characterize these mechanisms, we evaluated the sensitivity of underwater photosynthesis to an external carbonic anhydrase (CA) inhibitor and an anion exchanger protein inhibitor, and we attempted to identify components of the mechanism of HCO3- utilization. METHODS We evaluated the effects of the external CA inhibitor and anion exchanger protein inhibitor on the NaHCO3 response of photosynthetic O2 evolution in submerged leaves of H. difformis. Furthermore, we performed a comparative transcriptomic analysis between terrestrial and submerged leaves. KEY RESULTS Photosynthesis in the submerged leaves was decreased by both the external CA inhibitor and anion exchanger protein inhibitor, but no additive effect was observed. Among upregulated genes in submerged leaves, two α-CAs, Hdα-CA1 and Hdα-CA2, and one β-carbonic anhydrase, Hdβ-CA1, were detected. Based on their putative amino acid sequences, the α-CAs are predicted to be localized in the apoplastic region. Recombinant Hdα-CA1 and Hdβ-CA1 showed dominant CO2 hydration activity over HCO3- dehydration activity. CONCLUSIONS We propose that the use of HCO3- for photosynthesis in submerged leaves of H. difformis is driven by the cooperation between an external CA, Hdα-CA1, and an unidentified HCO3- transporter.
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Affiliation(s)
- Genki Horiguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
- Japan Society for the Promotion of Science, Chiyoda, Tokyo, Japan
| | - Ryoma Oyama
- Faculty of Life Sciences, Toyo University, Itakura, Gunma, Japan
| | - Tatsuki Akabane
- Graduate School of Life Sciences, Toyo University, Itakura, Gunma, Japan
| | - Nobuhiro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Etsuko Katoh
- Faculty of Food and Nutritional Sciences Life Sciences, Toyo University, Itakura, Gunma, Japan
| | - Yusuke Mizokami
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Ko Noguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Naoki Hirotsu
- Faculty of Life Sciences, Toyo University, Itakura, Gunma, Japan
- Graduate School of Life Sciences, Toyo University, Itakura, Gunma, Japan
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Jia P, Wang Y, Sharif R, Dong QL, Liu Y, Luan HA, Zhang XM, Guo SP, Qi GH. KNOTTED1-like homeobox (KNOX) transcription factors - Hubs in a plethora of networks: A review. Int J Biol Macromol 2023; 253:126878. [PMID: 37703987 DOI: 10.1016/j.ijbiomac.2023.126878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
KNOX (KNOTTED1-like HOMEOBOX) belongs to a class of important homeobox genes, which encode the homeodomain proteins binding to the specific element of target genes, and widely participate in plant development. Advancements in genetics and molecular biology research generate a large amount of information about KNOX genes in model and non-model plants, and their functions in different developmental backgrounds are gradually becoming clear. In this review, we summarize the known and presumed functions of the KNOX gene in plants, focusing on horticultural plants and crops. The classification and structural characteristics, expression characteristics and regulation, interacting protein factors, functions, and mechanisms of KNOX genes are systematically described. Further, the current research gaps and perspectives were discussed. These comprehensive data can provide a reference for the directional improvement of agronomic traits through KNOX gene regulation.
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Affiliation(s)
- Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
| | - Yuan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, China
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Qing-Long Dong
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Yang Liu
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Hao-An Luan
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xue-Mei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Sup-Ping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Guo-Hui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
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Zhang Y, Van de Peer Y, Lu B, Zhang S, Che J, Chen J, Marchal K, Yang X. Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii. BMC Biol 2023; 21:244. [PMID: 37926805 PMCID: PMC10626718 DOI: 10.1186/s12915-023-01743-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Sterile-fertile heteroblasty is a common phenomenon observed in ferns, where the leaf shape of a fern sporophyll, responsible for sporangium production, differs from that of a regular trophophyll. However, due to the large size and complexity of most fern genomes, the molecular mechanisms that regulate the formation of these functionally different heteroblasty have remained elusive. To shed light on these mechanisms, we generated a full-length transcriptome of Ceratopteris chingii with PacBio Iso-Seq from five tissue samples. By integrating Illumina-based sequencing short reads, we identified the genes exhibiting the most significant differential expression between sporophylls and trophophylls. RESULTS The long reads were assembled, resulting in a total of 24,024 gene models. The differential expressed genes between heteroblasty primarily involved reproduction and cell wall composition, with a particular focus on expansin genes. Reconstructing the phylogeny of expansin genes across 19 plant species, ranging from green algae to seed plants, we identified four ortholog groups for expansins. The observed high expression of expansin genes in the young sporophylls of C. chingii emphasizes their role in the development of heteroblastic leaves. Through gene coexpression analysis, we identified highly divergent expressions of expansin genes both within and between species. CONCLUSIONS The specific regulatory interactions and accompanying expression patterns of expansin genes are associated with variations in leaf shapes between sporophylls and trophophylls.
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Affiliation(s)
- Yue Zhang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bei Lu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Jingru Che
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- Department of Information Technology, IDLab, IMEC, Ghent University, 9052, Ghent, Belgium.
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China.
- Hubei Ecology Polytechnic College, Wuhan, 430200, China.
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Hu Y, Tang F, Zhang D, Shen S, Peng X. Integrating genome-wide association and transcriptome analysis to provide molecular insights into heterophylly and eco-adaptability in woody plants. HORTICULTURE RESEARCH 2023; 10:uhad212. [PMID: 38046852 PMCID: PMC10689056 DOI: 10.1093/hr/uhad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/11/2023] [Indexed: 12/05/2023]
Abstract
Heterophylly is regard as an important adaptive mechanism in response to different environments within plants. However, the genetic mechanisms responsible for heterophylly in woody plants are still poorly understood. Herein, the divergence of heterophyllous leaves was investigated at morphogenesis and using microdissection and physiological indexes in paper mulberry, and the genetic basis of heterophylly was further revealed combined with genome-wide association study (GWAS), transcriptome analysis and weighted gene coexpression network analysis (WGCNA). Our results revealed that the flavonoid content and antioxidant activity increased gradually from the entire leaf to the palmatisect leaf, while the hormone content and net photosynthetic rate decreased. Through GWAS and transcriptome analysis, a total of 98 candidate genes and 2338 differentially expressed genes associated with heterophylly were identified. Importantly, we uncovered critical variations in the candidate genes Bp07g0981 (WOX) and Bp07g0920 (HHO), along with significant differences in haplotypes and expression levels among heterophyllous leaves. Our results also suggested that the genes involved in hormone signaling pathways, antioxidant activity, and flavonoid metabolism might be closely related to the heterophylly of paper mulberry, which could account for the physiological data. Indeed, CR-wox mutant lines showed significant changes in leaf phenotypes, and differential expression profile analysis also highlighted the expression of genes related to phytohormones and transcription factors. Together, the genetic variations and candidate genes detected in this study provide novel insights into the genetic mechanism of heterophylly, and would improve the understanding of eco-adaptability in heterophyllous woody plants.
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Affiliation(s)
- Yanmin Hu
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Feng Tang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Dan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
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Liu P, Bu C, Chen P, El-Kassaby YA, Zhang D, Song Y. Enhanced genome-wide association reveals the role of YABBY11-NGATHA-LIKE1 in leaf serration development of Populus. PLANT PHYSIOLOGY 2023; 191:1702-1718. [PMID: 36535002 PMCID: PMC10022644 DOI: 10.1093/plphys/kiac585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Leaf margins are complex plant morphological features that contribute to leaf shape diversity, which affects plant structure, yield, and adaptation. Although several leaf margin regulators have been identified to date, the genetic basis of their natural variation has not been fully elucidated. In this study, we profiled two distinct leaf morphology types (serrated and smooth) using the persistent homology mathematical framework (PHMF) in two poplar species (Populus tomentosa and Populus simonii, respectively). A combined genome-wide association study (GWAS) and expression quantitative trait nucleotide (eQTN) mapping were applied to create a leaf morphology control module using data from P. tomentosa and P. simonii populations. Natural variation in leaf margins was associated with YABBY11 (YAB11) transcript abundance in poplar. In P. tomentosa, PtoYAB11 carries a premature stop codon (PtoYAB11PSC), resulting in the loss of its positive regulation of NGATHA-LIKE1 (PtoNGAL-1) and RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE SUBUNIT (PtoRBCL). Overexpression of PtoYAB11PSC promoted serrated leaf margins, enlarged leaves, enhanced photosynthesis, and increased biomass. Overexpression of PsiYAB11 in P. tomentosa promoted smooth leaf margins, higher stomatal density, and greater light damage repair ability. In poplar, YAB11-NGAL1 is sensitive to environmental conditions, acts as a positive regulator of leaf margin serration, and may also link environmental signaling to leaf morphological plasticity.
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Affiliation(s)
- Peng Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
| | - Chenhao Bu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
| | - Panfei Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
| | - Yuepeng Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P.R. China
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