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Rawat S, Jugran AK, Sharma H. Recent advancements in the physiological, genetic, and genomic research on Rhododendrons for trait improvement. 3 Biotech 2024; 14:164. [PMID: 38808301 PMCID: PMC11128433 DOI: 10.1007/s13205-024-04006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024] Open
Abstract
High species diversity, hybridization potential, broad geographical dispersal range and ornamental characteristics (i.e., attractive size, shape, structure, flowers, and evergreen) have fetched a good international market for Rhododendron. However, most species are restricted to specific geographic areas due to their habitat specificity in acidic soil and cold climates, resulting many species being classified under threat categories of the IUCN. In this review, advances in research on Rhododendron for improvement to floral display quality and stress resistance have been described. The low genetic barrier among species has created opportunities for extensive hybridization and ploidy alteration for introducing quality and adaptive traits during the development of new varieties. Recent technological advances have supported investigations into the mechanism of flower development, as well as cold tolerance and pathogen resistance mechanisms in the Rhododendron. However, most of the species have limited adaptability to drought, line-tolerance, pathogen resistance, and high-temperature conditions and this resistance ability present in few species largely remains unexplored. Additionally, the available genetic diversity and genomic information on species, and possibilities for their application in molecular breeding have been summarized. Overall, genomic resource data are scarce in the majority of the members of this genus. Finally, various research gaps such as genetic mapping of quality traits, understanding the molecular mechanism of quality-related traits and genomic assortment in Rhododendron members have been discussed in the future perspective section. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04006-6.
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Affiliation(s)
- Sandeep Rawat
- Sikkim Regional Centre, G. B. Pant National Institute of Himalayan Environment, Pangthang, Gangtok, Sikkim 737101 India
| | - Arun K. Jugran
- Garhwal Regional Centre, G. B. Pant National Institute of Himalayan Environment, Srinagar, Uttarakhand 246174 India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab 140306 India
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh 173229 India
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Zhaogao L, Yaxuan W, Mengwei X, Haiyu L, Lin L, Delin X. Molecular mechanism overview of metabolite biosynthesis in medicinal plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108125. [PMID: 37883919 DOI: 10.1016/j.plaphy.2023.108125] [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: 07/21/2023] [Revised: 09/21/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
Medicinal plants are essential and rich resources for plant-based medicines and new drugs. Increasing attentions are paid to the secondary metabolites of medicinal plants due to their unique biological activity, pharmacological action, and high utilization value. However, the development of medicinal plants is constrained by limited natural resources and an unclear understanding of the mechanisms underlying active medicinal ingredients, thereby rendering the utilization and exploration of secondary metabolites more challenging. Besides, with the advancement of research on biosynthesis and molecular metabolism of natural products from medicinal plants, the methods for studying the biological activity and pharmacological effects of these products are constantly evolving. In recent years, significant progress has been made in the biosynthetic pathways and related regulatory genes of secondary metabolites in medicinal plants, which has greatly advanced both basic research and the development of clinical applications for medicinal plants. In this review, we discuss the past two decades of international research on the development of medicinal plant resources, mainly focusing on the biosynthetic pathway of secondary metabolites, intracellular signal transduction processes, multi-omics applications, and the application of gene editing technology in related research progress. We also discuss future development trends to promote the deep mining and development of natural products from medicinal plants, providing a useful reference.
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Affiliation(s)
- Li Zhaogao
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China.
| | - Wang Yaxuan
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China.
| | - Xu Mengwei
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China; Department of Medical Instrumental Analysis, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China.
| | - Liu Haiyu
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China; Guizhou Provincial Demonstration Center of Basic Medical Experimental Teaching, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China.
| | - Li Lin
- Department of Cell Biology, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China.
| | - Xu Delin
- Department of Medical Instrumental Analysis, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China; Guizhou Provincial Demonstration Center of Basic Medical Experimental Teaching, Zunyi Medical University, No.6 Xuefuxi Road Xinpu District of Zunyi City, Zunyi, 563099, Guizhou, China.
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Nie S, Zhao SW, Shi TL, Zhao W, Zhang RG, Tian XC, Guo JF, Yan XM, Bao YT, Li ZC, Kong L, Ma HY, Chen ZY, Liu H, El-Kassaby YA, Porth I, Yang FS, Mao JF. Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color. HORTICULTURE RESEARCH 2023; 10:uhac241. [PMID: 36643737 PMCID: PMC9832866 DOI: 10.1093/hr/uhac241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/17/2022] [Indexed: 05/09/2023]
Abstract
The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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Affiliation(s)
- Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden
| | - Ren-Gang Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang 261322, China
| | - Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hui Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
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Jin C, Dong L, Wei C, Wani MA, Yang C, Li S, Li F. Creating novel ornamentals via new strategies in the era of genome editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1142866. [PMID: 37123857 PMCID: PMC10140431 DOI: 10.3389/fpls.2023.1142866] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Ornamental breeding has traditionally focused on improving novelty, yield, quality, and resistance to biotic or abiotic stress. However, achieving these goals has often required laborious crossbreeding, while precise breeding techniques have been underutilized. Fortunately, recent advancements in plant genome sequencing and editing technology have opened up exciting new frontiers for revolutionizing ornamental breeding. In this review, we provide an overview of the current state of ornamental transgenic breeding and propose four promising breeding strategies that have already proven successful in crop breeding and could be adapted for ornamental breeding with the help of genome editing. These strategies include recombination manipulation, haploid inducer creation, clonal seed production, and reverse breeding. We also discuss in detail the research progress, application status, and feasibility of each of these tactics.
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Affiliation(s)
- Chunlian Jin
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Liqing Dong
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Chang Wei
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Muneeb Ahmad Wani
- Department of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Chunmei Yang
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Shenchong Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
| | - Fan Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
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Shen J, Li X, Li M, Cheng H, Huang X, Jin S. Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum. FRONTIERS IN PLANT SCIENCE 2022; 13:969765. [PMID: 36212362 PMCID: PMC9532937 DOI: 10.3389/fpls.2022.969765] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Rhododendron × pulchrum, an important horticultural species, is widely distributed in Europe, Asia, and North America. To analyze the phylogenetic and organelle genome information of R. × pulchrum and its related species, the organelle genome of R. × pulchrum was sequenced and assembled. The complete mitochondrial genome showed lineage DNA molecules, which were 816,410 bp long and contained 64 genes, namely 24 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 37 protein-coding genes. The chloroplast genome of R. × pulchrum was reassembled and re-annotated; the results were different from those of previous studies. There were 42 and 46 simple sequence repeats (SSR) identified from the mitochondrial and chloroplast genomes of R. × pulchrum, respectively. Five genes (nad1, nad2, nad4, nad7, and rps3) were potentially useful molecular markers. The R. × pulchrum mitochondrial genome collinear alignment among five species of the Ericaceae showed that the mitochondrial genomes of these related species have a high degree of homology with R. × pulchrum in this gene region, and the most conservative genes were trnC-GCA, trnD-GUC, trnM-CAU, trnN-GUU, trnY-GUA, atp4, nad4, nad2, nad5, ccmC, and rrn26. The phylogenetic trees of mitochondrial genome showed that R. simsii was a sister to R. × pulchrum. The results verified that there was gene rearrangement between R. × pulchrum and R. simsii mitochondrial genomes. The codon usage bias of 10 Ericaceae mitochondrial genes and 7 Rhododendron chloroplast genes were influenced by mutation, while other genes codon usages had undergone selection. The study identified 13 homologous fragments containing gene sequences between the chloroplast and mitochondrial genomes of R. × pulchrum. Overall, our results illustrate the organelle genome information could explain the phylogenetics of plants and could be used to develop molecular markers and genetic evolution. Our study will facilitate the study of population genetics and evolution in Rhododendron and other genera in Ericaceae.
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Affiliation(s)
| | - Xueqin Li
- Jiyang College, Zhejiang A&F University, Zhuji, China
- Department of Life Science and Health, Huzhou College, Huzhou, Zhejiang, China
| | - Mingzhi Li
- Bio and Data Biotechnology Co., Ltd., Guangzhou, China
| | - Hefeng Cheng
- Jiyang College, Zhejiang A&F University, Zhuji, China
| | | | - Songheng Jin
- Jiyang College, Zhejiang A&F University, Zhuji, China
- Department of Life Science and Health, Huzhou College, Huzhou, Zhejiang, China
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Characterisation of the Complete Chloroplast Genomes of Seven Hyacinthus orientalis L. Cultivars: Insights into Cultivar Phylogeny. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and annotated from seven cultivars of Hyacinthus orientalis and two Scilloideae species including Bellevalia paradoxa and Scilla siberica. The chloroplast genomes of Hyacinthus cultivars ranged from 154,458 bp to 154,641 bp, while those of Bellevalia paradoxa and Scilla siberica were 154,020 bp and 154,943 bp, respectively. Each chloroplast genome was annotated with 133 genes, including 87 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Simple sequence repeats AAGC/CTTG and ACTAT/AGTAT were identified only in ‘Eros’, while AAATC/ATTTG were identified in all cultivars except ‘Eros’. Five haplotypes were identified based on 460 variable sites. Combined with six other previously published chloroplast genomes of Scilloideae, a sliding window analysis and a phylogenetic analysis were performed. Divergence hotspots ndhA and trnG-UGC were identified with a nucleotide diversity threshold at 0.04. The phylogenetic positions of Hyacinthus cultivars were different from the previous study using ISSR. Complete chloroplast genomes serve as new evidence in Hyacinthus cultivar phylogeny, contributing to cultivar identification, preservation and breeding.
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