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Numaguchi K, Kitamura Y, Kashiwamoto T, Morimoto T, Oe T. Genomic region and origin for selected traits during differentiation of small-fruit cultivars in Japanese apricot (Prunus mume). Mol Genet Genomics 2023; 298:1365-1375. [PMID: 37632570 DOI: 10.1007/s00438-023-02062-w] [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: 06/09/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The Japanese apricot (Prunus mume) is a popular fruit tree in Japan. However, the genetic factors associated with fruit trait variations are poorly understood. In this study, we investigated nine fruit-associated traits, including harvesting time, fruit diameter, fruit shape, fruit weight, stone (endocarp) weight, ratio of stone weight to fruit weight, and rate of fruit gumming, using 110 Japanese apricot accessions over four years. A genome-wide association study (GWAS) was performed for these traits and strong signals were detected on chromosome 6 for harvesting time and fruit diameters. These peaks were shown to undergo strong artificial selection during the differentiation of small-fruit cultivars. The genomic region defined by the GWAS and XP-nSL analyses harbored several candidate genes associated with plant hormone regulation. Furthermore, the alleles of small-fruit cultivars in this region were shown to have genetic proximity to some Chinese cultivars of P. mume. These results indicate that the small-fruit trait originated in China; after being introduced into Japan, it was preferred and selected by the Japanese people, resulting in the differentiation of small-fruit cultivars.
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Affiliation(s)
- Koji Numaguchi
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan.
- Wakayama Fruit Tree Experiment Station, 751-1, Oki, Aridagawa-cho, Arida-gun, Wakayama, 643-0022, Japan.
| | - Yuto Kitamura
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Tomoaki Kashiwamoto
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
| | - Takuya Morimoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Kitainayazuma, Seika-cho, Soraku-gun, Kyoto, 619-0244, Japan
| | - Takaaki Oe
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
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2
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Zhao W, Huang H, Wang J, Wang X, Xu B, Yao X, Sun L, Yang R, Wang J, Sun A, Wang S. Jasmonic acid enhances osmotic stress responses by MYC2-mediated inhibition of protein phosphatase 2C1 and response regulators 26 transcription factor in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 110:1182-1197. [PMID: 36534116 DOI: 10.1111/tpj.15731] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 02/09/2022] [Accepted: 03/06/2022] [Indexed: 05/22/2023]
Abstract
The jasmonic acid (JA) signaling pathway is involved in the plant response to drought stress. JA and other hormones synergistically regulate the drought response in plants. However, the molecular mechanism underlying this synergism remains poorly defined. In the present study, transcriptome analyses of guard cells and quantitative PCR experiments revealed that MYC2 negatively regulated the negative regulator of ABA signaling, SlPP2C1, and the type-B response regulator in the cytokinin pathway, SlRR26, and this negative regulation was direct. SlRR26 overexpression reduced drought tolerance in transgenic tomatoes, whereas slrr26cr lines were more tolerant to drought. SlRR26 negatively modulated reactive oxygen species levels in stomata and stomatal closure through RobhB. Moreover, SlRR26 overexpression counteracted JA-mediated stomatal closure, suggesting that SlRR26 played a negative role in the JA-mediated drought response. These findings suggest that MYC2 plays a key role in JA-regulated stomatal closure under drought stress by inhibiting SlPP2C1 and SlRR26.
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Affiliation(s)
- Wenchao Zhao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Huang Huang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Jingjing Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiaoyun Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Bingqin Xu
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Xuehui Yao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Lulu Sun
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Rui Yang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Jianli Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Aidong Sun
- Beijing Key Laboratory of Forest Food Processing and Safety, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083, China
| | - Shaohui Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
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Li P, Zhang Q, Shi B, Liu L, Zhang X, Wang J, Yi H. Integration of genome and transcriptome reveal molecular regulation mechanism of early flowering trait in Prunus genus ( Prunus mume and Prunus persica). FRONTIERS IN PLANT SCIENCE 2022; 13:1036221. [PMID: 36275593 PMCID: PMC9582937 DOI: 10.3389/fpls.2022.1036221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Flowering time is crucial for the survival and reproduction. Prunus genus belongs to the Rosaceae family and includes several hundred species of flowering trees and shrubs with important ornamental and economic values. However, the molecular mechanism underlying early flowering in Prunus genus is unclear. Here, we utilized the genome and transcriptome of P. mume and P. persica to explore the transcriptional regulation mechanism of early flowering. Comparative genomics found that genes accounting for 92.4% of the total P. mume genome and 91.2% of the total P. persica genome belonged to orthogroups. A total of 19,169 orthogroups were found between P. mume and P. persica, including 20,431 corresponding orthologues and 20,080 collinearity gene pairs. A total of 305 differentially expressed genes (DEGs) associated with early flowering were found, among which FT, TLI65, and NAP57 were identified as hub genes in the early flowering regulation pathway. Moreover, we identified twenty-five transcription factors (TFs) from nine protein families, including MADS-box, AP2/ERF, and MYB. Our results provide insights into the underlying molecular model of flowering time regulation in Prunus genus and highlight the utility of multi-omics in deciphering the properties of the inter-genus plants.
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Affiliation(s)
- Ping Li
- College of Landscape and Tourism, Hebei Agricultural University, Baoding, China
| | - Qin Zhang
- College of Landscape and Tourism, Hebei Agricultural University, Baoding, China
| | - Baosheng Shi
- College of Landscape and Tourism, Hebei Agricultural University, Baoding, China
| | - Liu Liu
- College of Landscape and Tourism, Hebei Agricultural University, Baoding, China
| | - Xiaoman Zhang
- College of Landscape and Tourism, Hebei Agricultural University, Baoding, China
| | - Jia Wang
- National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Haihui Yi
- College of Agronomy, Inner Mongolia Minzu University, Tongliao, China
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Zhu Y, Wei S, Cao X, Wang S, Chang Y, Ouyang H, He J. Multi-component pharmacokinetic study of prunus mume fructus extract after oral administration in rats using UPLC-MS/MS. Front Pharmacol 2022; 13:954692. [PMID: 36210842 PMCID: PMC9541882 DOI: 10.3389/fphar.2022.954692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Prunus mume fructus (MF) is used in traditional Chinese medicine and food, as it exerts pharmacological effects, such as antibacterial, antioxidant, antitumour, thirst-relieving, and antidiarrheal effects. In the present study, a reliable and sensitive ultra-high performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) method was developed and validated for the simultaneous determination of 16 prototype components (L-(-)-malic acid, 3,4-dihydroxybenzaldehyde, protocatechuic acid, vanillic acid, caffeic acid, D-(-)-quinic acid, citric acid, ferulic acid, syringic acid, cryptochlorogenic acid, neochlorogenic acid, chlorogenic acid, amygdalin, maslinic acid, corosolic acid, and rutin) in rat plasma after oral administration of the MF extract. Plasma samples were prepared via protein precipitation using acetonitrile. The 16 components were separated on an ACQUITY UPLC BEH C18 column (2.1 × 100 mm, 1.7 μm) with a gradient mobile phase system of methanol and 0.1% (v/v) formic acid aqueous solution at a flow rate of 0.3 ml/min. All components were quantitated using Agilent Jet Stream electrospray ionisation in negative ion mode. The intra-day and inter-day accuracies ranged from-9.4 to 9.4%, and the precision of the analytes was less than 14.8%. The extraction recovery rate of the analytes ranged from 63.59 to 109.44% and the matrix effects ranged from 49.25 to 109.28%. Stability studies proved that the analytes were stable under the tested conditions, with a relative standard deviation lower than 13.7%. Hence, the developed method was successfully applied to evaluate the pharmacokinetics of 16 components in the MF extract after oral administration in rats using UPLC-MS/MS.
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Affiliation(s)
| | | | | | | | | | | | - Jun He
- *Correspondence: Huizi Ouyang, ; Jun He,
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Iqbal S, Bai Y, Hayat F, Coulibaly D, Khalil-Ur-Rehman M, Shi T, Gao Z. Comprehensive transcriptomic and metabolomic analysis revealed distinct flavonoid biosynthesis regulation during abnormal pistil development in Japanese apricot. Genomics 2022; 114:110451. [PMID: 35988654 DOI: 10.1016/j.ygeno.2022.110451] [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: 02/13/2022] [Revised: 08/06/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
Japanese apricot is an imperative stone fruit plant with numerous processing importance. The failure of reproductive system is the most common cause of fruit loss, through which pistil abortion is the fundamental one. To understand this mechanism, we used a combination of transcriptomic and metabolomic approaches to investigate the biochemical and molecular basis of flavonoid biosynthesis. Due to the regulated expression of flavonoid pathway-related genes in plants, flavonoid biosynthesis is largely regulated at the transcriptional level. A total of 2272 differently expressed genes and 215 differential metabolites were found. The expression of the genes and metabolites encoding flavonoid biosynthesis was lower in abnormal pistils that are in line with the flavonoid quantification from abnormal pistils. Besides, a couple of genes were also detected related to MYB, MADS, NAC and bHLH transcription factors. Remarkably, we found 'hydroxycinnamoyl transferase (LOC103323133)' and flavonoid related metabolite '2-hydroxycinnamic acid' was lower expressed in abnormal pistil, proposing the cause of pistil abortion. Collectively, the present study delivers inclusive transcriptional and metabolic datasets that proposed valuable prospects to unravel the genetic mechanism underlying pistil abortion.
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Affiliation(s)
- Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Faisal Hayat
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Daouda Coulibaly
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | | | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Xiujun W, Zhenqi S, Yujing T, Kaifeng M, Qingwei L. Comparative transcriptome analysis linked to key volatiles reveals molecular mechanisms of aroma compound biosynthesis in Prunus mume. BMC PLANT BIOLOGY 2022; 22:395. [PMID: 35945501 PMCID: PMC9361687 DOI: 10.1186/s12870-022-03779-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/27/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Mei (Prunus mume) is the only woody plant in the genus Prunus with a floral fragrance, but the underlying mechanisms of aroma compound biosynthesis are unclear despite being a matter of considerable interest. RESULTS The volatile contents of the petals of two cultivars with significantly different aromas, Prunus mume 'Xiao Lve' and Prunus mume 'Xiangxue Gongfen', were characterised by GC-MS at different flowering periods, and a total of 44 volatile compounds were detected. Among these, the main substances forming the typical aroma of P. mume were identified as eugenol, cinnamyl acetate, hexyl acetate and benzyl acetate, with variations in their relative concentrations leading to sensory differences in the aroma of the two cultivars. We compiled a transcriptome database at key stages of floral fragrance formation in the two cultivars and used it in combination with differential analysis of floral volatiles to construct a regulatory network for the biosynthesis of key aroma compounds. The results indicated that PmPAL enzymes and PmMYB4 transcription factors play important roles in regulating the accumulation of key biosynthetic precursors to these compounds. Cytochrome P450s and short-chain dehydrogenases/reductases might also influence the biosynthesis of benzyl acetate by regulating production of key precursors such as benzaldehyde and benzyl alcohol. Furthermore, by analogy to genes with verified functions in Arabidopsis, we predicted that three PmCAD genes, two 4CL genes, three CCR genes and two IGS genes all make important contributions to the synthesis of cinnamyl acetate and eugenol in P. mume. This analysis also suggested that the downstream genes PmBGLU18-like, PmUGT71A16 and PmUGT73C6 participate in regulation of the matrix-bound and volatile states of P. mume aroma compounds. CONCLUSIONS These findings present potential new anchor points for further exploration of floral aroma compound biosynthesis pathways in P. mume, and provide new insights into aroma induction and regulation mechanisms in woody plants.
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Affiliation(s)
- Wang Xiujun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Song Zhenqi
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Ti Yujing
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Ma Kaifeng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Li Qingwei
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
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Zheng T, Li P, Zhuo X, Liu W, Qiu L, Li L, Yuan C, Sun L, Zhang Z, Wang J, Cheng T, Zhang Q. The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume. THE NEW PHYTOLOGIST 2022; 235:141-156. [PMID: 34861048 PMCID: PMC9299681 DOI: 10.1111/nph.17894] [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: 07/16/2021] [Accepted: 11/20/2021] [Indexed: 05/22/2023]
Abstract
Plant with naturally twisted branches is referred to as a tortuous-branch plant, which have extremely high ornamental value due to their zigzag shape and the natural twisting of their branches. Prunus mume is an important woody ornamental plant. However, the molecular mechanism underlying this unique trait in Prunus genus is unknown. Here, we present a chromosome-level genome assembly of the cultivated P. mume var. tortuosa created using Oxford Nanopore combined with Hi-C scaffolding, which resulted in a 237.8 Mb genome assembly being anchored onto eight pseudochromosomes. Molecular dating indicated that P. mume is the most recently differentiated species in Prunus. Genes associated with cell division, development and plant hormones play essential roles in the formation of tortuous branch trait. A putative regulatory pathway for the tortuous branch trait was constructed based on gene expression levels. Furthermore, after transferring candidate PmCYCD genes into Arabidopsis thaliana, we found that seedlings overexpressing these genes exhibited curled rosette leaves. Our results provide insights into the evolutionary history of recently differentiated species in Prunus genus, the molecular basis of stem morphology, and the molecular mechanism underlying the tortuous branch trait and highlight the utility of multi-omics in deciphering the properties of P. mume plant architecture.
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Affiliation(s)
- Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Ping Li
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Xiaokang Zhuo
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Weichao Liu
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Like Qiu
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Lulu Li
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Zhiyong Zhang
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants, Germplasm Innovation & Molecular BreedingNational Engineering Research Centre for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of the Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China
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Xu Z, Zhang X, Wang W, Zhang D, Ma Y, Zhang D, Chen M. Fructus Mume (Wu Mei) Attenuates Acetic Acid-Induced Ulcerative Colitis by Regulating Inflammatory Cytokine, Reactive Oxygen Species, and Neuropeptide Levels in Model Rats. J Med Food 2022; 25:389-401. [PMID: 35438553 DOI: 10.1089/jmf.2021.k.0155] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic idiopathic inflammatory disorder of the large intestine. Fructus mume (FM), a natural food with nutritive and pharmaceutical value, has demonstrated therapeutic efficacy against UC. In this study, we investigated the protective effects and mechanisms of FM against UC. We induced UC in rats with 4% (v/v) acetic acid (AA), orally administered 0.7 or 0.325 g/kg FM and 0.3 g/kg sulfasalazine (SASP) for 7 days, and explored the responses the drugs elicited in the rats. We assessed the general conditions of the rats by the disease active index. We evaluated colon tissue damage macroscopically and by Hematoxylin & Eosin, Alcian Blue-periodic acid-Schiff, and Masson's staining, and explored the potential mechanisms of FM on inflammation, oxidative stress, and neuropeptides by measuring TNF-α, IL-6, IL-8, IL-10, MMP9, CXCR-1, SOD, GSH-px, MDA, ROS, SIRT3, SP, VIP, ghrelin, and 5-HT. FM treatment significantly attenuated colon damage and submucosal fibrosis compared with the model. It lowered serum proinflammatory TNF-α, IL-8, and colonic MMP9 and CXCR-1, and raised serum anti-inflammatory IL-10 levels. FM upregulated the antioxidant enzymes SOD, GSH-px, and SITR3 protein but inhibited ROS and MDA production. It downregulated colonic SP, VIP, ghrelin, and 5-HT. The beneficial effects of FM might be dose dependent. Around 0.7 g/kg FM and SASP displayed similar efficacy for treating AA-induced colitis in rats. Our results provide empirical evidence that FM protects against AA-induced UC in rats via anti-inflammatory and antioxidant mechanisms, and regulates neuropeptides; thus, FM may be a promising, safe, and efficacious alternative therapy for UC, if its efficacy can be confirmed in human trials.
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Affiliation(s)
- Zongying Xu
- Department of Clinical Foundation of Chinese Medicine, College of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xueli Zhang
- Department of Clinical Foundation of Chinese Medicine, College of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wenya Wang
- Department of Clinical Foundation of Chinese Medicine, College of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Di Zhang
- Department of Clinical Foundation of Chinese Medicine, College of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yan Ma
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Dongmei Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Meng Chen
- Department of Clinical Foundation of Chinese Medicine, College of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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Li M, Sang M, Wen Z, Meng J, Cheng T, Zhang Q, Sun L. Mapping Floral Genetic Architecture in Prunus mume, an Ornamental Woody Plant. FRONTIERS IN PLANT SCIENCE 2022; 13:828579. [PMID: 35211141 PMCID: PMC8860970 DOI: 10.3389/fpls.2022.828579] [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: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Floral traits are both evolutionarily and economically relevant for ornamental plants. However, their underlying genetic architecture, especially in woody ornamental plants, is still poorly understood. We perform mapping experiments aimed at identifying specific quantitative trait loci (QTLs) that control the size, shape, architecture, color, and timing of flowers in mei (Prunus mume). We find that the narrow region of chromosome 1 (5-15 Mb) contains a number of floral QTLs. Most QTLs detected from this mapping study are annotated to candidate genes that regulate various biological functions toward the floral formation. We identify strong pleiotropic control on different aspects of flower morphology (including shape, petal number, pistil number, petal color, and calyx color) and flower timing, but find different genetic systems that mediate whether a flower produces pistils and how many pistils a flower produces. We find that many floral QTLs display pleiotropic effects on shoot length growth but shoot radial growth, implicating a possible association of floral display with light capture. We conduct a transcriptomic study to characterize the genomic signature of floral QTLs expressed in mei. Our mapping results about the genetic control of floral features make it promising to select superior varieties for mei carrying flowers of ornamental value.
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Affiliation(s)
- Mingyu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- School Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Zhenying Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Juan Meng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
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10
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Ooi SE, Feshah I, Nuraziyan A, Sarpan N, Ata N, Lim CC, Choo CN, Wong WC, Wong FH, Wong CK, Ong-Abdullah M. Leaf transcriptomic signatures for somatic embryogenesis potential of Elaeis guineensis. PLANT CELL REPORTS 2021; 40:1141-1154. [PMID: 33929599 DOI: 10.1007/s00299-021-02698-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Potentially embryogenic oil palms can be identified through leaf transcriptomic signatures. Differential expression of genes involved in flowering time, and stress and light responses may associate with somatic embryogenesis potential. Clonal propagation is an attractive approach for the mass propagation of high yielding oil palms. A major issue hampering the effectiveness of oil palm tissue culture is the low somatic embryogenesis rate. Previous studies have identified numerous genes involved in oil palm somatic embryogenesis, but their association with embryogenic potential has not been determined. In this study, differential expression analysis of leaf transcriptomes from embryogenic and non-embryogenic mother palms revealed that transcriptome profiles from non- and poor embryogenic mother palms were more similar than highly embryogenic palms. A total of 171 genes exhibiting differential expression in non- and low embryogenesis groups could also discriminate high from poor embryogenesis groups of another tissue culture agency. Genes related to flowering time or transition such as FTIP, FRIGIDA-LIKE, and NF-YA were up-regulated in embryogenic ortets, suggesting that reproduction timing of the plant may associate with somatic embryogenesis potential. Several light response or photosynthesis-related genes were down-regulated in embryogenic ortets, suggesting a link between photosynthesis activity and embryogenic potential. As expression profiles of the differentially expressed genes are very similar between non- and low embryogenic groups, machine learning approaches with several candidate genes may generate a more sensitive model to better discriminate non-embryogenic from embryogenic ortets.
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Affiliation(s)
- Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia.
| | - Ishak Feshah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Azimi Nuraziyan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Nabeel Ata
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Chin-Ching Lim
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Chin-Nee Choo
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Wei-Chee Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Foo-Hin Wong
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Choo-Kien Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
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11
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Yamane H, Singh AK, Cooke JEK. Plant dormancy research: from environmental control to molecular regulatory networks. TREE PHYSIOLOGY 2021; 41:523-528. [PMID: 33834235 DOI: 10.1093/treephys/tpab035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 05/26/2023]
Affiliation(s)
- Hisayo Yamane
- Graduate school of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834 003 India
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E9, Alberta, Canada
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12
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Li Y, Cao K, Li N, Zhu G, Fang W, Chen C, Wang X, Guo J, Wang Q, Ding T, Wang J, Guan L, Wang J, Liu K, Guo W, Arús P, Huang S, Fei Z, Wang L. Genomic analyses provide insights into peach local adaptation and responses to climate change. Genome Res 2021; 31:592-606. [PMID: 33687945 PMCID: PMC8015852 DOI: 10.1101/gr.261032.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/25/2021] [Indexed: 01/30/2023]
Abstract
The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach adaptation to diverse climates. A total of 2092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using genome-wide environmental association studies (GWEAS), a total of 2755 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UVB, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 yr of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and breeding.
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Affiliation(s)
- Yong Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430000, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Nan Li
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Gengrui Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Changwen Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xinwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jian Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Qi Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Tiyu Ding
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jiao Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Liping Guan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Junxiu Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Kuozhan Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430000, China
| | - Pere Arús
- IRTA-Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB-UB), Barcelona 08193, Spain
| | - Sanwen Huang
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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13
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Zhang M, Yang Q, Yuan X, Yan X, Wang J, Cheng T, Zhang Q. Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume. FRONTIERS IN PLANT SCIENCE 2021; 12:690841. [PMID: 34335659 PMCID: PMC8319914 DOI: 10.3389/fpls.2021.690841] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/28/2021] [Indexed: 05/12/2023]
Abstract
Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.
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Affiliation(s)
- Man Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qingqing Yang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xi Yuan
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | | | - Jia Wang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- *Correspondence: Qixiang Zhang
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