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Cheng R, Bai X, Guo J, Huang L, Zhao D, Liu Z, Zhang W. Hyperspectral discrimination of ginseng variety and age from Changbai Mountain area. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123613. [PMID: 37976570 DOI: 10.1016/j.saa.2023.123613] [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: 08/22/2023] [Revised: 10/12/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The efficacy and market value of Panax ginseng Meyer are significantly influenced by its diversity and age. Traditional identification methods are prone to subjective biases and necessitate the use of destructive sample processing, leading to the loss and wastage of ginseng. Consequently, non-destructive in-situ identification has emerged as a crucial subject of interest for both researchers and the ginseng industry. The advancement of technology and the expansion of research have introduced spectral technology and image processing technology as novel approaches and concepts for non-destructive in-situ identification. METHODS Hyperspectral imaging (HSI) is a methodology that combines conventional spectroscopy and imaging to acquire comprehensive spectral and spatial data from various samples. In this study, we investigated the use of Support Vector Machine (SVM) and Spectral Angle Mapper (SAM) classifier algorithms, in conjunction with HSI classification technology, for quasi-Artificial Intelligence (quasi-AI) ginseng identification. To enhance the hyperspectral images prior to SVM classification, we compared the efficacy of Principal Component Analysis (PCA), Minimum Noise Fraction (MNF), and Independent Component Analysis (ICA). RESULTS The classification of ginseng based on age was accomplished through the utilization of Radial Basis Function (RBF) kernel SVM and SAM algorithm, which was trained on feature enhanced images. The classification of WMG, MCG, and GG is primarily based on age, with the endmember spectrum serving as the foundation for SAM and SVM. CONCLUSION The "endmember spectrum set" derived from the classification outcomes can serve as the "mutation point" for identifying ginseng of different ages.
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Affiliation(s)
- Ruiyang Cheng
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Xueyuan Bai
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jianying Guo
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Luqi Huang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Daqing Zhao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Zhaojian Liu
- Department of Cell Biology, School of Basic Medical Science, Shandong University, Jinan, China.
| | - Wei Zhang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.
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Jadhao KR, Kale SS, Chavan NS, Janjal PH. Genome-wide analysis of the SPL transcription factor family and its response to water stress in sunflower (Helianthus annuus). Cell Stress Chaperones 2023; 28:943-958. [PMID: 37938528 PMCID: PMC10746691 DOI: 10.1007/s12192-023-01388-z] [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: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023] Open
Abstract
SPL (SQUAMOSA promoter binding proteins-like) are plant-specific transcription factors that play essential roles in a variety of developmental processes as well as the ability to withstand biotic and abiotic stresses. To date, numerous species have been investigated for the SPL gene family, but so far, no SPL family genes have been thoroughly identified and characterized in the sunflower (Helianthus annuus). In this study, 25 SPL genes were identified in the sunflower genome and were unevenly distributed on 11 chromosomes. According to phylogeny analysis, 59 SPL genes from H. annuus, O. sativa, and A. thaliana were clustered into seven groups. Furthermore, the SPL genes in groups-I and II were demonstrated to be potential targets of miR156. Synteny analysis showed that 7 paralogous gene pairs exist in HaSPL genes and 26 orthologous gene pairs exist between sunflower and rice, whereas 21 orthologous gene pairs were found between sunflower and Arabidopsis. Segmental duplication appears to have played a vital role in the expansion processes of sunflower SPL genes, and because of selection pressure, all duplicated genes have undergone purifying selection. Tissue-specific gene expression analysis of the HaSBP genes proved their diverse spatiotemporal expression patterns, which were predominantly expressed in floral organs and differentially expressed in stem, axil, and root tissues. The expression pattern of HaSPL genes under water stress showed broad involvement of HaSPLs in the response to flood and drought stresses. This genome-wide identification investigation provides detailed information on the sunflower SPL transcription factor gene family and establishes a strong platform for future research on sunflower responses to abiotic stress tolerance.
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Affiliation(s)
- Kundansing R Jadhao
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India.
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Nilesh S Chavan
- Department of Microbiology and Environmental Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Pandharinath H Janjal
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India
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Li L, Lv B, Zang K, Jiang Y, Wang C, Wang Y, Wang K, Zhao M, Chen P, Lei J, Wang Y, Zhang M. Genome-wide identification and systematic analysis of the HD-Zip gene family and its roles in response to pH in Panax ginseng Meyer. BMC PLANT BIOLOGY 2023; 23:30. [PMID: 36639779 PMCID: PMC9838044 DOI: 10.1186/s12870-023-04038-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ginseng, Panax ginseng Meyer, is a traditional herb that is immensely valuable both for human health and medicine and for medicinal plant research. The homeodomain leucine zipper (HD-Zip) gene family is a plant-specific transcription factor gene family indispensable in the regulation of plant growth and development and plant response to environmental stresses. RESULTS We identified 117 HD-Zip transcripts from the transcriptome of ginseng cv. Damaya that is widely grown in Jilin, China where approximately 60% of the world's ginseng is produced. These transcripts were positioned to 64 loci in the ginseng genome and the ginseng HD-Zip genes were designated as PgHDZ genes. Identification of 82 and 83 PgHDZ genes from the ginseng acc. IR826 and cv. ChP genomes, respectively, indicated that the PgHDZ gene family consists of approximately 80 PgHDZ genes. Phylogenetic analysis showed that the gene family originated after Angiosperm split from Gymnosperm and before Dicots split from Monocots. The gene family was classified into four subfamilies and has dramatically diverged not only in gene structure and functionality but also in expression characteristics. Nevertheless, co-expression network analysis showed that the activities of the genes in the family remain significantly correlated, suggesting their functional correlation. Five hub PgHDZ genes were identified that might have central functions in ginseng biological processes and four of them were shown to be actively involved in plant response to environmental pH stress in ginseng. CONCLUSIONS The PgHDZ gene family was identified from ginseng and analyzed systematically. Five potential hub genes were identified and four of them were shown to be involved in ginseng response to environmental pH stress. The results provide new insights into the characteristics, diversity, evolution, and functionality of the PgHDZ gene family in ginseng and lay a foundation for comprehensive research of the gene family in plants.
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Affiliation(s)
- Li Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Boxin Lv
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Kaiyou Zang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Chaofan Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yanfang Wang
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Jun Lei
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China.
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Wang Y, Ruan Q, Zhu X, Wang B, Wei B, Wei X. Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses. Sci Rep 2023; 13:84. [PMID: 36596810 PMCID: PMC9810616 DOI: 10.1038/s41598-022-26911-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
The SQUAMOSA promoter binding-like protein (SPL) is a specific transcription factor that affects plant growth and development. The SPL gene family has been explored in various plants, but information about these genes in alfalfa is limited. This study, based on the whole genome data of alfalfa SPL, the fundamental physicochemical properties, phylogenetic evolution, gene structure, cis-acting elements, and gene expression of members of the MsSPL gene family were analyzed by bioinformatics methods. We identified 82 SPL sequences in the alfalfa, which were annotated into 23 genes, including 7 (30.43%) genes with four alleles, 10 (43.47%) with three, 3 (13.04%) with two, 3 (13.04%) with one allele. These SPL genes were divided into six groups, that are constructed from A. thaliana, M. truncatula and alfalfa. Chromosomal localization of the identified SPL genes showed arbitary distribution. The subcellular localization predictions showed that all MsSPL proteins were located in the nucleus. A total of 71 pairs of duplicated genes were identified, and segmental duplication mainly contributed to the expansion of the MsSPL gene family. Analysis of the Ka/Ks ratios indicated that paralogs of the MsSPL gene family principally underwent purifying selection. Protein-protein interaction analysis of MsSPL proteins were performed to predict their roles in potential regulatory networks. Twelve cis-acting elements including phytohormone and stress elements were detected in the regions of MsSPL genes. We further analyzed that the MsSPLs had apparent responses to abiotic stresses such as drought and salt and the biotic stress of methyl jasmonate. These results provide comprehensive information on the MsSPL gene family in alfalfa and lay a solid foundation for elucidating the biological functions of MsSPLs. This study also provides valuable on the regulation mechanism and function of MsSPLs in response to biotic and abiotic stresses.
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Affiliation(s)
- Yizhen Wang
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Qian Ruan
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaolin Zhu
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
| | - Baoqiang Wang
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Bochuang Wei
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaohong Wei
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
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He F, Long R, Wei C, Zhang Y, Li M, Kang J, Yang Q, Wang Z, Chen L. Genome-wide identification, phylogeny and expression analysis of the SPL gene family and its important role in salt stress in Medicago sativa L. BMC PLANT BIOLOGY 2022; 22:295. [PMID: 35705909 PMCID: PMC9199161 DOI: 10.1186/s12870-022-03678-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 06/03/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND SQUAMOSA promoter-binding protein-like (SPL) transcription factors are widely present in plants and are involved in signal transduction, the stress response and development. The SPL gene family has been characterized in several model species, such as A. thaliana and G. max. However, there is no in-depth analysis of the SPL gene family in forage, especially alfalfa (Medicago sativa L.), one of the most important forage crops worldwide. RESULT In total, 76 putative MsSPL genes were identified in the alfalfa genome with an uneven distribution. Based on their identity and gene structure, these MsSPLs were divided into eight phylogenetic groups. Seventy-three MsSPL gene pairs arose from segmental duplication events, and the MsSPLs on the four subgenomes of individual chromosomes displayed high collinearity with the corresponding M. truncatula genome. The prediction of the cis-elements in the promoter regions of the MsSPLs detected two copies of ABA (abscisic acid)-responsive elements (ABREs) on average, implying their potential involvement in alfalfa adaptation to adverse environments. The transcriptome sequencing of MsSPLs in roots and leaves revealed that 54 MsSPLs were expressed in both tissues. Upon salt treatment, three MsSPLs (MsSPL17, MsSPL23 and MsSPL36) were significantly regulated, and the transcription level of MsSPL36 in leaves was repressed to 46.6% of the control level. CONCLUSION In this study, based on sequence homology, we identified 76 SPL genes in the alfalfa. The SPLs with high identity shared similar gene structures and motifs. In total, 71.1% (54 of 76) of the MsSPLs were expressed in both roots and leaves, and the majority (74.1%) preferred underground tissues to aerial tissues. MsSPL36 in leaves was significantly repressed under salt stress. These findings provide comprehensive information regarding the SPB-box gene family for improve alfalfa tolerance to high salinity.
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Affiliation(s)
- Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chunxue Wei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunxiu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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