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Paganová V, Hus M, Lichtnerová H, Žiarovská J, Moravčíková D, Kučka M, Ražná K, Abbas A. Physiological and Molecular Responses of Pyrus pyraster Seedlings to Salt Treatment Analyzed by miRNA and Cytochrome P450 Gene-Based Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:261. [PMID: 38256814 PMCID: PMC10820964 DOI: 10.3390/plants13020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Physiological and molecular marker-based changes were studied in the tissues of two-year-old Pyrus pyraster (L.) Burgsd. seedlings under salt treatment. For 60 days, 5 mL of 100 mM NaCl solution was applied to each plant per day to a cumulative volume of 300 mL in the substrate. In response to osmotic stress, the seedlings increased their water use efficiency (WUE) on day 20 of regular NaCl application and maintained a stable net photosynthetic rate (An) per unit area. Under conditions of increasing salinity, the young plants maintained a balanced water regime of the leaf tissues (Ψwl). The seedlings invested mass to their root growth (R/S), retained a substantial portion (72%) of Na+ ions in the roots, and protected their leaves against intoxication and damage. A significant decrease in the leaf gas exchange parameters (gs, E, An) was manifested on day 60 of the experiment when the cumulative NaCl intake was 300 mL per plant. The variability in the reactions of the seedlings to salinity is related to the use of open-pollinated progeny (54 genotypes) in the experiment. Lus-miR168 showed tissue- and genotype-specific genome responses to the applied stress. Polymorphic miRNA-based loci were mostly detected in the root samples on the 20th and 35th days of the experiment. The cumulative effect of the salt treatment was reflected in the predominance of polymorphic loci in the leaves. We can confirm that miRNA-based markers represent a sensitive detection tool for plant stress response on an individual level. The screening and selection of the optimal type of miRNA for this type of research is crucial. The cytochrome P450-Based Analog (PBA) techniques were unable to detect polymorphism among the control and treated seedlings, except for the primer pair CYP2BF+R, where, in the roots of the stressed plant, insertions in the amplicons were obtained. The expression ratios of cytochrome P450 in the salt-stressed plants were higher in the roots in the case of 20/100 mL and in the leaves with higher doses. The observed physiological and molecular responses to salinity reflect the potential of P. pyraster seedlings in adaptation to osmotic and ionic stress.
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Affiliation(s)
- Viera Paganová
- Institute of Landscape Architecture, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (M.H.); (H.L.)
| | - Marek Hus
- Institute of Landscape Architecture, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (M.H.); (H.L.)
| | - Helena Lichtnerová
- Institute of Landscape Architecture, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (M.H.); (H.L.)
| | - Jana Žiarovská
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Dagmar Moravčíková
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Matúš Kučka
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
| | - Aqsa Abbas
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia; (J.Ž.); (D.M.); (M.K.); (K.R.); (A.A.)
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Li J, Zhang M, Li X, Khan A, Kumar S, Allan AC, Lin-Wang K, Espley RV, Wang C, Wang R, Xue C, Yao G, Qin M, Sun M, Tegtmeier R, Liu H, Wei W, Ming M, Zhang S, Zhao K, Song B, Ni J, An J, Korban SS, Wu J. Pear genetics: Recent advances, new prospects, and a roadmap for the future. HORTICULTURE RESEARCH 2022; 9:uhab040. [PMID: 35031796 PMCID: PMC8778596 DOI: 10.1093/hr/uhab040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".
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Affiliation(s)
- Jiaming Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyue Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xiaolong Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Awais Khan
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Satish Kumar
- Hawke’s Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4157, New Zealand
| | - Andrew Charles Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Richard Victor Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Runze Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Mengfan Qin
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Manyi Sun
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Tegtmeier
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Hainan Liu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weilin Wei
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Meiling Ming
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kejiao Zhao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Bobo Song
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiangping Ni
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianping An
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Schuyler S Korban
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jun Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Jiang X, Chen P, Zhang X, Liu Q, Li H. Comparative analysis of the SPL gene family in five Rosaceae species: Fragaria vesca, Malus domestica, Prunus persica, Rubus occidentalis, and Pyrus pyrifolia. Open Life Sci 2021; 16:160-171. [PMID: 33817308 PMCID: PMC7968543 DOI: 10.1515/biol-2021-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
SQUAMOSA promoter-binding protein-like (SPL) transcription factors are very important for the plant growth and development. Here 15 RoSPLs were identified in Rubus occidentalis. The conserved domains and motifs, phylogenetic relationships, posttranscriptional regulation, and physiological function of the 92 SPL family genes in Fragaria vesca, Malus domestica, Prunus persica, R. occidentalis, and Pyrus pyrifolia were analyzed. Sequence alignment and phylogenetic analysis showed the SPL proteins had sequence conservation, some FvSPLs could be lost or developed, and there was a closer relationship between M. domestica and P. pyrifolia, F. vesca and R. occidentalis, respectively. Genes with similar motifs clustering together in the same group had their functional redundancy. Based on the function of SPLs in Arabidopsis thaliana, these SPLs could be involved in vegetative transition from juvenile to adult, morphological change in the reproductive phase, anthocyanin biosynthesis, and defense stress. Forty-eight SPLs had complementary sequences of miR156, of which nine PrpSPLs in P. persica and eight RoSPLs in R. occidentalis as the potential targets of miR156 were reported for the first time, suggesting the conservative regulatory effects of miR156 and indicating the roles of miR156-SPL modules in plant growth, development, and defense response. It provides a basic understanding of SPLs in Rosaceae plants.
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Affiliation(s)
- Xuwen Jiang
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
| | - Peng Chen
- Department of Entomology, College of plant protection, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China.,Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Gongye North Road No. 202, Jinan, 250100, China
| | - Xiaowen Zhang
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
| | - Qizhi Liu
- Department of Entomology, College of plant protection, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Heqin Li
- Dryland Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao, 266109, Shandong, China
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An N, Fan S, Yang Y, Chen X, Dong F, Wang Y, Xing L, Zhao C, Han M. Identification and Characterization of miRNAs in Self-Rooted and Grafted Malus Reveals Critical Networks Associated with Flowering. Int J Mol Sci 2018; 19:E2384. [PMID: 30104536 PMCID: PMC6121270 DOI: 10.3390/ijms19082384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/03/2018] [Accepted: 08/09/2018] [Indexed: 11/24/2022] Open
Abstract
Grafting can improve the agricultural traits of crop plants, especially fruit trees. However, the regulatory networks and differentially expressed microRNAs (miRNAs) related to grafting in apple remain unclear. Herein, we conducted high-throughput sequencing and identified differentially expressed miRNAs among self-rooted Fuji, self-rooted M9, and grafted Fuji/M9. We analyzed the flowering rate, leaf morphology, and nutrient and carbohydrate contents in the three materials. The flowering rate, element and carbohydrate contents, and expression levels of flowering genes were higher in Fuji/M9 than in Fuji. We detected 206 known miRNAs and 976 novel miRNAs in the three materials, and identified those that were up- or downregulated in response to grafting. miR156 was most abundant in Fuji, followed by Fuji/M9, and then self-rooted M9, while miR172 was most abundant in M9, followed by Fuji/M9, and then Fuji. These expression patterns suggest that that these miRNAs were related to grafting. A Gene Ontology (GO) analysis showed that the differentially expressed miRNAs controlled genes involved in various biological processes, including cellular biosynthesis and metabolism. The expression of differentially expressed miRNAs and flowering-related genes was verified by qRT-PCR. Altogether, this comprehensive analysis of miRNAs related to grafting provides valuable information for breeding and grafting of apple and other fruit trees.
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Affiliation(s)
- Na An
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
- College of Life Science, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
| | - Yang Yang
- Innovation Experimental College, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xilong Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
| | - Feng Dong
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
| | - Yibin Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
| | - Libo Xing
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, China.
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Qian M, Ni J, Niu Q, Bai S, Bao L, Li J, Sun Y, Zhang D, Teng Y. Response of miR156- SPL Module during the Red Peel Coloration of Bagging-Treated Chinese Sand Pear ( Pyrus pyrifolia Nakai). Front Physiol 2017; 8:550. [PMID: 28824447 PMCID: PMC5545762 DOI: 10.3389/fphys.2017.00550] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 07/14/2017] [Indexed: 11/18/2022] Open
Abstract
MicroRNA156 is an evolutionarily highly conserved plant micro-RNA (miRNA) that controls an age-dependent flowering pathway. miR156 and its target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes regulate anthocyanin accumulation in plants, but it is unknown whether this process is affected by light. Red Chinese sand pear (Pyrus pyrifolia) fruits exhibit a unique coloration pattern in response to bagging treatments, which makes them appropriate for studying the molecular mechanism underlying light-induced anthocyanin accumulation in fruit. Based on high-throughput miRNA and degradome sequencing data, we determined that miR156 was expressed in pear fruit peels, and targeted four SPL genes. Light-responsive elements were detected in the promoter regions of the miR156a and miR156ba precursors. We identified 19 SPL genes using the “Suli” pear (Pyrus pyrifolia Chinese White Pear Group) genome database, of which seven members were putative miR156 targets. The upregulated expression of anthocyanin biosynthetic and regulatory genes and downregulated expression of PpSPL2, PpSPL5, PpSPL7, PpSPL9, PpSPL10, PpSPL13, PpSPL16, PpSPL17, and PpSPL18 were observed in pear fruits after bags were removed from plants during the anthocyanin accumulation period. Additionally, miR156a/ba/g/s/sa abundance increased after bags were removed. Yeast two-hybrid results suggested that PpMYB10, PpbHLH, and PpWD40 could form a protein complex, probably involved in anthocyanin biosynthesis. Additionally, PpSPL10 and PpSPL13 interacted with PpMYB10. The results obtained in this study are helpful in understanding the possible role of miR156 and its target PpSPL genes in regulating light-induced red peel coloration and anthocyanin accumulation in pear.
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Affiliation(s)
- Minjie Qian
- Department of Horticulture, Zhejiang UniversityHangzhou, China.,The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of ChinaHangzhou, China.,Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural PlantsHangzhou, China
| | - Junbei Ni
- Department of Horticulture, Zhejiang UniversityHangzhou, China.,The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of ChinaHangzhou, China.,Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural PlantsHangzhou, China
| | - Qingfeng Niu
- Department of Horticulture, Zhejiang UniversityHangzhou, China.,The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of ChinaHangzhou, China.,Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural PlantsHangzhou, China
| | - Songling Bai
- Department of Horticulture, Zhejiang UniversityHangzhou, China.,The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of ChinaHangzhou, China.,Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural PlantsHangzhou, China
| | - Lu Bao
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Jianzhao Li
- Department of Horticulture, Zhejiang UniversityHangzhou, China.,The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of ChinaHangzhou, China.,Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural PlantsHangzhou, China
| | - Yongwang Sun
- Department of Horticulture, Zhejiang UniversityHangzhou, China.,The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of ChinaHangzhou, China.,Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural PlantsHangzhou, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang UniversityHangzhou, China.,The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of ChinaHangzhou, China.,Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural PlantsHangzhou, China
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The Effect of Different Pollination on the Expression of Dangshan Su Pear MicroRNA. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2794040. [PMID: 28497043 PMCID: PMC5402243 DOI: 10.1155/2017/2794040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 11/18/2016] [Accepted: 01/11/2017] [Indexed: 12/22/2022]
Abstract
The high-throughput sequencing of pear “Dangshan Su” × “Yali” (whose fruits lignin and stone cell content are high and quality is poor) and pear “Dangshan Su” × “Wonhwang” (whose fruits with low content of lignin and stone cell and the quality are better ) found that the expressions of these two miRNAs (pyr-1809 and pyr-novel-miR-144-3p) were significantly different; their corresponding target genes encode two kinds of laccase (Pbr018935.1 and Pbr003857.1). qRT-PCR results showed that these two enzymes are involved in the formation of lignin and stone cells and the existence of these two miRNAs has a negative effect on them. It was concluded that the effect of pollination on the development of stone cells may affect the synthesis of lignin, through the regulation of laccase controlled by miRNAs, and ultimately affect the formation of stone cell and fruit quality.
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Wang Y, Sun LE. Knockdown of LMP1-induced miR-155 sensitizes nasopharyngeal carcinoma cells to radiotherapy in vitro. Oncol Lett 2016; 11:3451-3456. [PMID: 27123134 DOI: 10.3892/ol.2016.4400] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 12/10/2015] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to confirm the promotion of microRNA (miR)-155 expression by latent membrane protein 1 (LMP1), and to recognize the oncogenic role of LMP1 and LMP1-promoted miR-155 in nasopharyngeal carcinoma (NPC), particularly the influence of miR-155 knockdown on the radiosensitivity of CNE-2 cells. Following the regulation of the levels of LMP1 or miR-155 and/or subsequent to radiation treatment, the proliferation ability of CNE-2 cells was examined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, colony formation and Cell Counting Kit-8 assays. The results demonstrated that miR-155 was upregulated by overexpression of LMP1 in CNE-2 cells, and LMP1 overexpression and miR-155 mimic transfection increased CNE-2 cell proliferation, whereas miR-155 knockdown attenuated the promotion of CNE-2 cell growth induced by LMP1 overexpression. Furthermore, knockdown of miR-155 enhanced the radiosensitivity of CNE-2 cells. In conclusion, the present study confirmed the oncogenic role of miR-155 in NPC, and demonstrated that knockdown of miR-155 inhibited the growth of NPC cells and sensitized NPC cells to radiotherapy.
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Affiliation(s)
- Yusheng Wang
- Department of Otolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - L E Sun
- Department of Otolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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Bai S, Saito T, Ito A, Tuan PA, Xu Y, Teng Y, Moriguchi T. Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui'). BMC Genomics 2016; 17:230. [PMID: 26976036 PMCID: PMC4791883 DOI: 10.1186/s12864-016-2514-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/23/2016] [Indexed: 01/12/2023] Open
Abstract
Background In woody perennial plants, including deciduous fruit trees, such as pear, endodormancy is a strategy for surviving the cold winter. A better understanding of the mechanism underlying the endodormancy phase transition is necessary for developing countermeasures against the effects of global warming. In this study, we analyzed the sRNAome of Japanese pear flower buds in endodormant and ecodormant stages over two seasons by implementing of RNA-seq and degradome-sequencing. Results We identified 137 conserved or less conserved miRNAs and 50 pear-specific miRNAs. However, none of the conserved microRNAs or pear-specific miRNAs was differentially expressed between endodormancy and ecodormancy stages. On the contrast, 1540 of 218,050 loci that produced sRNAs were differentially expressed between endodormancy and ecodormancy, suggesting their potential roles on the phase transition from endodormancy to ecodomancy. We also characterized a multifunctional miRNA precursor MIR168, which produces two functional miR168 transcripts, namely miR168.1 and miR168.2; cleavage events were predominantly mediated by the non-conserved variant miR168.2 rather than the conserved variant miR168.1. Finally, we showed that a TAS3 trans-acting siRNA triggered phased siRNA within the ORF of one of its target genes, AUXIN RESPONSE FACTOR 4, via the analysis of phased siRNA loci, indicating that siRNAs are able to trigger phased siRNAs in pear. Conclusion We analyzed the sRNAome of pear flower bud during dormant phase transition. Our work described the sRNA profiles of pear winter buds during dormant phase transition, showing that dormancy release is a highly coordinated physiological process involving the regulation of sRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2514-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Songling Bai
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan. .,Department of Horticulture, The State Agricultural Ministry's Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China.
| | - Takanori Saito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan.,Present address: Graduate School of Horticulture, Chiba University, Matsudo-shi, Chiba, 271-8510, Japan
| | - Akiko Ito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan
| | - Pham Anh Tuan
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan
| | - Ying Xu
- Department of Horticulture, The State Agricultural Ministry's Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yuanwen Teng
- Department of Horticulture, The State Agricultural Ministry's Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Takaya Moriguchi
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan.
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9
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Niu Q, Li J, Cai D, Qian M, Jia H, Bai S, Hussain S, Liu G, Teng Y, Zheng X. Dormancy-associated MADS-box genes and microRNAs jointly control dormancy transition in pear (Pyrus pyrifolia white pear group) flower bud. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:239-57. [PMID: 26466664 PMCID: PMC4682432 DOI: 10.1093/jxb/erv454] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Bud dormancy in perennial plants is indispensable to survival over winter and to regrowth and development in the following year. However, the molecular pathways of endo-dormancy induction, maintenance, and release are still unclear, especially in fruit crops. To identify genes with roles in regulating endo-dormancy, 30 MIKC(C)-type MADS-box genes were identified in the pear genome and characterized. The 30 genes were analysed to determine their phylogenetic relationships with homologous genes, genome locations, gene structure, tissue-specific transcript profiles, and transcriptional patterns during flower bud dormancy in 'Suli' pear (Pyrus pyrifolia white pear group). The roles in regulating bud dormancy varied among the MIKC gene family members. Yeast one-hybrid and transient assays showed that PpCBF enhanced PpDAM1 and PpDAM3 transcriptional activity during the induction of dormancy, probably by binding to the C-repeat/DRE binding site, while DAM proteins inhibited the transcriptional activity of PpFT2 during dormancy release. In the small RNA-seq analysis, 185 conserved, 24 less-conserved, and 32 pear-specific miRNAs with distinct expression patterns during bud dormancy were identified. Joint analyses of miRNAs and MIKC genes together with degradome data showed that miR6390 targeted PpDAM transcripts and degraded them to release PpFT2. Our data show that cross-talk among PpCBF, PpDAM, PpFT2, and miR6390 played important roles in regulating endo-dormancy. A model for the molecular mechanism of dormancy transition is proposed: short-term chilling in autumn activates the accumulation of CBF, which directly promotes DAM expression; DAM subsequently inhibits FT expression to induce endo-dormancy, and miR6390 degrades DAM genes to release endo-dormancy.
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Affiliation(s)
- Qingfeng Niu
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Jianzhao Li
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Danying Cai
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province 310021, China
| | - Minjie Qian
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Huimin Jia
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Songling Bai
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Sayed Hussain
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Guoqin Liu
- College of Agriculture, Guizhou University, Guiyang, Guizhou Province 550025, China
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Xiaoyan Zheng
- Institute of Horticulture and Landscape, College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
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Wu J, Wang D, Liu Y, Wang L, Qiao X, Zhang S. Identification of miRNAs involved in pear fruit development and quality. BMC Genomics 2014; 15:953. [PMID: 25366381 PMCID: PMC4233070 DOI: 10.1186/1471-2164-15-953] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/23/2014] [Indexed: 01/16/2023] Open
Abstract
Background MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs. Results Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor. Conclusion Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-953) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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11
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Apple ring rot-responsive putative microRNAs revealed by high-throughput sequencing in Malus × domestica Borkh. Mol Biol Rep 2014; 41:5273-86. [DOI: 10.1007/s11033-014-3399-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
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