1
|
Li H, Liu C, Kan J, Lin J, Li X. Integrated Methylome and Transcriptome Analysis between Wizened and Normal Flower Buds in Pyrus pyrifolia Cultivar 'Sucui 1'. Int J Mol Sci 2024; 25:7180. [PMID: 39000285 PMCID: PMC11241763 DOI: 10.3390/ijms25137180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Here, cytosine methylation in the whole genome of pear flower buds was mapped at a single-base resolution. There was 19.4% methylation across all sequenced C sites in the Pyrus pyrifolia cultivar 'Sucui 1' flower bud genome. Meantime, the CG, CHG, and CHH sequence contexts (where H = A, T or C) exhibited 47.4%, 33.3%, and 11.9% methylation, respectively. Methylation in different gene regions was revealed through combining methylome and transcriptome analysis, which presented various transcription trends. Genes with methylated promoters exhibited lower expression levels than genes with non-methylated promoters, while body-methylated genes displayed an obvious negative correlation with their transcription levels. The methylation profiles of auxin- and cytokinin-related genes were estimated. And some of them proved to be hypomethylated, with increased transcription levels, in wizened buds. More specifically, the expression of the genes PRXP73, CYP749A22, and CYP82A3 was upregulated as a result of methylation changes in their promoters. Finally, auxin and cytokinin concentrations were higher in wizened flower buds than in normal buds. The exogenous application of paclobutrazol (PP333) in the field influenced the DNA methylation status of some genes and changed their expression level, reducing the proportion of wizened flower buds in a concentration-dependent manner. Overall, our results demonstrated the relationship between DNA methylation and gene expression in wizened flower buds of P. pyrifolia cultivar 'Sucui 1', which was associated with changes in auxin and cytokinin concentrations.
Collapse
Affiliation(s)
| | | | | | | | - Xiaogang Li
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (H.L.); (C.L.); (J.K.); (J.L.)
| |
Collapse
|
2
|
Jiang L, Guo T, Song X, Jiang H, Lu M, Luo J, Rossi V, He Y. MSH7 confers quantitative variation in pollen fertility and boosts grain yield in maize. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1372-1386. [PMID: 38263872 PMCID: PMC11022798 DOI: 10.1111/pbi.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/15/2023] [Accepted: 12/08/2023] [Indexed: 01/25/2024]
Abstract
Fertile pollen is critical for the survival, fitness, and dispersal of flowering plants, and directly contributes to crop productivity. Extensive mutational screening studies have been carried out to dissect the genetic regulatory network determining pollen fertility, but we still lack fundamental knowledge about whether and how pollen fertility is controlled in natural populations. We used a genome-wide association study (GWAS) to show that ZmGEN1A and ZmMSH7, two DNA repair-related genes, confer natural variation in maize pollen fertility. Mutants defective in these genes exhibited abnormalities in meiotic or post-meiotic DNA repair, leading to reduced pollen fertility. More importantly, ZmMSH7 showed evidence of selection during maize domestication, and its disruption resulted in a substantial increase in grain yield for both inbred and hybrid. Overall, our study describes the first systematic examination of natural genetic effects on pollen fertility in plants, providing valuable genetic resources for optimizing male fertility. In addition, we find that ZmMSH7 represents a candidate for improvement of grain yield.
Collapse
Affiliation(s)
- Luguang Jiang
- National Maize Improvement Center of China, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Ting Guo
- Institute of Genetics and Developmental Biology, Key Laboratory of Seed InnovationChinese Academy of SciencesBeijingChina
| | - Xinyuan Song
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro‐Biotechnology Research InstituteJilin Academy of Agricultural SciencesChangchunChina
| | - Huan Jiang
- National Maize Improvement Center of China, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Minhui Lu
- Center for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Jinhong Luo
- National Maize Improvement Center of China, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Institute of Genetics and Developmental Biology, Key Laboratory of Seed InnovationChinese Academy of SciencesBeijingChina
| | - Vincenzo Rossi
- Council for Agricultural Research and EconomicsResearch Centre for Cereal and Industrial CropsBergamoItaly
| | - Yan He
- National Maize Improvement Center of China, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Institute of Genetics and Developmental Biology, Key Laboratory of Seed InnovationChinese Academy of SciencesBeijingChina
| |
Collapse
|
3
|
Shi D, Huang H, Zhang Y, Qian Z, Du J, Huang L, Yan X, Lin S. The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111995. [PMID: 38266717 DOI: 10.1016/j.plantsci.2024.111995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.
Collapse
Affiliation(s)
- Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Huiting Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yuting Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
4
|
Qian Z, Shi D, Zhang H, Li Z, Huang L, Yan X, Lin S. Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants. Int J Mol Sci 2024; 25:566. [PMID: 38203741 PMCID: PMC10778882 DOI: 10.3390/ijms25010566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.
Collapse
Affiliation(s)
- Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Hongxia Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Zhenzhen Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China;
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
| |
Collapse
|
5
|
Hou Q, Wang L, Qi Y, Yan T, Zhang F, Zhao W, Wan X. A systematic analysis of the subtilase gene family and expression and subcellular localization investigation of anther-specific members in maize. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108041. [PMID: 37722281 DOI: 10.1016/j.plaphy.2023.108041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/20/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
Subtilases (SBTs), also known as Subtilisin-like serine proteases, are extracellular alkaline protease proteins. SBTs function in all stages of plant growth, development and stress responses. Maize (Zea mays L.) is a crop widely used worldwide as food, feed, and industrial materials. However, information about the members and their functions of the SBT proteins in maize is lacking. In this study, we identified 58 ZmSBT genes from the maize genome and conducted a comprehensive investigation of ZmSBTs by phylogenetic, gene duplication event, gene structure, and protein conserved motif analyses. The ZmSBT proteins were phylogenetically classified into seven groups, and collinearity analysis indicated that many ZmSBTs originate from tandem or segmental duplications. Structural and homolog protein comparison revealed ZmSBTs have conserved protein structures with reported subtilase proteins, suggesting the conserved functions. Further analysis showed that ZmSBTs are expressed in different tissues, and many are responses to specific abiotic stress. Analysis of the anther-specific ZmSBT genes showed their expression peaked at different developmental stages of maize anthers. Subcellular localization analysis of selected maize ZmSBTs showed they are located in different cellular compartments. The information provided in this study is valuable for further functional study of ZmSBTs.
Collapse
Affiliation(s)
- Quancan Hou
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Zhongzhi lnternational lnstitute of Agricultural Biosciences, Beijing, 100192, China
| | - Linlin Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yuchen Qi
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tingwei Yan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Fan Zhang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Wei Zhao
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Zhongzhi lnternational lnstitute of Agricultural Biosciences, Beijing, 100192, China.
| |
Collapse
|
6
|
Somers J, Nelms B. The sporophyte-to-gametophyte transition: The haploid generation comes of age. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102416. [PMID: 37441836 DOI: 10.1016/j.pbi.2023.102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Flowering plants alternate between two multicellular generations: the diploid sporophyte and haploid gametophyte. Despite its small size, the gametophyte has significant impacts on plant genetics, evolution, and breeding. Each male pollen grain and female embryo sac is a multicellular organism with independent gene expression, a functioning metabolism, and specialized cell types. In this review, we describe recent progress in understanding the process in which the haploid genome takes over expression from its diploid parent - the sporophyte-to-gametophyte transition. The focus is on pollen, but similar concepts may also apply to the female gametophyte. Technological advances in single-cell genomics offer the opportunity to characterize haploid gene expression in unprecedented detail, positioning the field to make rapid progress.
Collapse
Affiliation(s)
- Julian Somers
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
7
|
Zhao J, Zhang C, Li S, Yuan M, Mu W, Yang J, Ma Y, Guan C, Ma C. Changes in m 6A RNA methylation are associated with male sterility in wolfberry. BMC PLANT BIOLOGY 2023; 23:456. [PMID: 37770861 PMCID: PMC10540408 DOI: 10.1186/s12870-023-04458-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND N6-methyladenosine (m6A) modification is the most abundant type of RNA modification in eukaryotic cells, playing pivotal roles in multiple plant growth and development processes. Yet the potential role of m6A in conferring the trait of male sterility in plants remains unknown. RESULTS In this study, we performed RNA-sequencing (RNA-Seq) and m6A-sequencing (m6A-Seq) of RNAs obtained from the anther tissue of two wolfberry lines: 'Ningqi No.1' (LB1) and its natural male sterile mutant 'Ningqi No.5' (LB5). Based on the newly assembled transcriptome, we established transcriptome-wide m6A maps for LB1 and LB5 at the single nucleus pollen stage. We found that the gene XLOC_021201, a homolog of m6A eraser-related gene ALKBH10 in Arabidopsis thaliana, was significantly differentially expressed between LB1 and LB5. We also identified 1642 and 563 m6A-modified genes with hypermethylated and hypomethylated patterns, respectively, in LB1 compared with LB5. We found the hypermethylated genes significantly enriched in biological processes related to energy metabolism and lipid metabolism, while hypomethylation genes were mainly linked to cell cycle process, gametophyte development, and reproductive process. Among these 2205 differentially m6A methylated genes, 13.74% (303 of 2205) were differentially expressed in LB1 vis-à-vis LB5. CONCLUSIONS This study constructs the first m6A transcriptome map of wolfberry and establishes an association between m6A and the trait of male sterility in wolfberry.
Collapse
Affiliation(s)
- Jiawen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chujun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Sifan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mengmeng Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenlan Mu
- College of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China
| | - Jing Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yutong Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cuiping Guan
- College of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China.
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
8
|
Yan T, Hou Q, Wei X, Qi Y, Pu A, Wu S, An X, Wan X. Promoting genotype-independent plant transformation by manipulating developmental regulatory genes and/or using nanoparticles. PLANT CELL REPORTS 2023; 42:1395-1417. [PMID: 37311877 PMCID: PMC10447291 DOI: 10.1007/s00299-023-03037-2] [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: 02/01/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE This review summarizes the molecular basis and emerging applications of developmental regulatory genes and nanoparticles in plant transformation and discusses strategies to overcome the obstacles of genotype dependency in plant transformation. Plant transformation is an important tool for plant research and biotechnology-based crop breeding. However, Plant transformation and regeneration are highly dependent on species and genotype. Plant regeneration is a process of generating a complete individual plant from a single somatic cell, which involves somatic embryogenesis, root and shoot organogeneses. Over the past 40 years, significant advances have been made in understanding molecular mechanisms of embryogenesis and organogenesis, revealing many developmental regulatory genes critical for plant regeneration. Recent studies showed that manipulating some developmental regulatory genes promotes the genotype-independent transformation of several plant species. Besides, nanoparticles penetrate plant cell wall without external forces and protect cargoes from degradation, making them promising materials for exogenous biomolecule delivery. In addition, manipulation of developmental regulatory genes or application of nanoparticles could also bypass the tissue culture process, paving the way for efficient plant transformation. Applications of developmental regulatory genes and nanoparticles are emerging in the genetic transformation of different plant species. In this article, we review the molecular basis and applications of developmental regulatory genes and nanoparticles in plant transformation and discuss how to further promote genotype-independent plant transformation.
Collapse
Affiliation(s)
- Tingwei Yan
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Quancan Hou
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Yuchen Qi
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Suowei Wu
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Xueli An
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China.
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China.
| |
Collapse
|
9
|
Li J, Li C, Deng Y, Wei H, Lu S. Characteristics of Salvia miltiorrhiza methylome and the regulatory mechanism of DNA methylation in tanshinone biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad114. [PMID: 37577393 PMCID: PMC10419789 DOI: 10.1093/hr/uhad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/21/2023] [Indexed: 08/15/2023]
Abstract
Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value. Its roots produce a group of diterpenoid lipophilic bioactive components, termed tanshinones. Biosynthesis and regulation of tanshinones has attracted widespread interest. However, the methylome of S. miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown. Here we report single-base resolution DNA methylomes from roots and leaves. Comparative analysis revealed differential methylation patterns for CG, CHG, and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs. Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S. miltiorrhiza. DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference. Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root. Tanshinone biosynthesis-related enzyme genes, such as DXS2, CMK, IDI1, HMGR2, DXR, MDS, CYP76AH1, 2OGD25, and CYP71D373, were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March. Consistently, gene expression was up-regulated in S. miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production. It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S. miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.
Collapse
Affiliation(s)
- Jiang Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Caili Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yuxing Deng
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Shanfa Lu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| |
Collapse
|