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Liu X, Zhang H, Liu Z, Tang C, Lv S, Qian M, Zhang N, Zhang S, Wu J, Wang P. PbrMYB186 activation of PbrF3H increased flavonol biosynthesis and promoted pollen tube growth in Pyrus. MOLECULAR HORTICULTURE 2024; 4:30. [PMID: 39160606 PMCID: PMC11334369 DOI: 10.1186/s43897-024-00110-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 07/23/2024] [Indexed: 08/21/2024]
Affiliation(s)
- Xueying Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hao Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhuqin Liu
- Ningbo Key Laboratory of Characteristic Horticultural Crops in Quality Adjustment and Resistance Breeding, Ningbo Academy of Agricultural Science, Ningbo, 315040, Zhejiang, China
| | - Chao Tang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shouzheng Lv
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Ming Qian
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Ningyi Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
- Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu, 210014, China.
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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2
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Li ST, Ke Y, Zhu Y, Zhu TY, Huang H, Li L, Hou Z, Zhang X, Li Y, Liu C, Li X, Xie M, Zhou L, Meng C, Wang F, Gu X, Yang B, Yu H, Liang Z. Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N 6-methyladenosine. NATURE PLANTS 2024; 10:1201-1214. [PMID: 38997433 DOI: 10.1038/s41477-024-01745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome.
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Affiliation(s)
- Shang-Tong Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Glbizzia Biosciences, Beijing, China
| | - Yunzhuo Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunke Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tian-Yi Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Huanwei Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linxia Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyang Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuemin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaping Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaofan Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiulan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
| | - Faming Wang
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore.
| | - Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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3
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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4
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Zhang H, Liu X, Tang C, Lv S, Zhang S, Wu J, Wang P. PbRbohH/J mediates ROS generation to regulate the growth of pollen tube in pear. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108342. [PMID: 38219427 DOI: 10.1016/j.plaphy.2024.108342] [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: 10/08/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Respiratory burst oxidase homolog (Rboh) family genes play crucial functions in development and growth. However, comprehensive and systematic investigation of Rboh family members in Rosaceae and their specific functions during pear pollen development are still limited. In the study, 63 Rboh genes were identified from eight Rosaceae genomes (Malus domestica, Pyrus bretschneideri, Pyrus communis, Prunus persica, Rubus occidentalis, Fragaria vesca, Prunus mume and Prunus avium) and divided into seven main subfamilies (I-VII) according to phylogenetic and structural features. Different modes of gene duplication led to the expansion of Rboh family, with purifying selection playing a vital role in the evolution of Rboh genes. In addition, RNA sequencing and qRT-PCR results indicated that PbRbohH and PbRbohJ were specifically high-expressed in pear pollen. Subsequently, subcellular localization revealed that PbRbohH/J distributed at the plasma membrane. Furthermore, by pharmacological analysis and antisense oligodeoxynucleotide assay, PbRbohH/J were demonstrated to mediate the formation of reactive oxygen species (ROS) to manage pollen tube growth. In conclusion, our results provide useful insights into the functions, expression patterns, evolutionary history of the Rboh genes in pear and other Rosaceae species.
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Affiliation(s)
- Hao Zhang
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xueying Liu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chao Tang
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shouzheng Lv
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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5
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Song YC, Das D, Zhang Y, Chen MX, Fernie AR, Zhu FY, Han J. Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants. Trends Biotechnol 2023; 41:1532-1548. [PMID: 37365082 DOI: 10.1016/j.tibtech.2023.05.010] [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: 03/17/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.
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Affiliation(s)
- Yu-Chen Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri-Columbia, MO 65201, USA
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Mo-Xian Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.
| | - Fu-Yuan Zhu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Jiangang Han
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
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6
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Hu J, Huang B, Yin H, Qi K, Jia Y, Xie Z, Gao Y, Li H, Li Q, Wang Z, Zou Y, Zhang S, Qiao X. PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study. Database (Oxford) 2023; 2023:baad050. [PMID: 37410918 PMCID: PMC10325485 DOI: 10.1093/database/baad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing pear multiomics data. A variety of online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis and primer design. The information of DNA methylation sites and single-nucleotide polymorphisms can be retrieved through the custom JBrowse, providing an opportunity to explore the genetic polymorphisms linked to phenotype variation. Moreover, different gene families involving transcription factors, transcription regulators and disease resistance (nucleotide-binding site leucine-rich repeat) were identified and compiled for quick search. In particular, biosynthetic gene clusters (BGCs) were identified in pear genomes, and specialized webpages were set up to show detailed information of BGCs, laying a foundation for studying metabolic diversity among different pear varieties. Overall, PearMODB provides an important platform for pear genomics, genetics and breeding studies. Database URL http://pearomics.njau.edu.cn.
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Affiliation(s)
- Jian Hu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Baisha Huang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yin
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyuan Jia
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongxiang Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zewen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Zou
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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