1
|
Li Y, Zhang X, Ye J, Xu F, Zhang W, Liao Y, Yang X. The long noncoding RNAs lnc10 and lnc11 regulating flavonoid biosynthesis in Ginkgo biloba. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111948. [PMID: 38097046 DOI: 10.1016/j.plantsci.2023.111948] [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: 09/01/2023] [Revised: 10/27/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Although long non-coding RNAs have been recognized to play important roles in plant, their possible functions and potential mechanism in Ginkgo biloba flavonoid biosynthesis are poorly understood. Flavonoids are important secondary metabolites and healthy components of Ginkgo biloba. They have been widely used in food, medicine, and natural health products. Most previous studies have focused on the molecular mechanisms of structural genes and transcription factors that regulate flavonoid biosynthesis. Few reports have examined the biological functions of flavonoid biosynthesis by long non-coding RNAs in G. biloba. Long noncoding RNAs associated with flavonoid biosynthesis in G. biloba have been identified through RNA sequencing, but the function of lncRNAs has not been reported. In this study, the expression levels of lnc10 and lnc11 were identified. Quantitative real-time polymerase chain reaction analysis revealed that lnc10 and lnc11 were expressed in all detected organs, and they showed significantly higher levels in immature and mature leaves than in other organs. In addition, to fully identify the function of lnc10 and lnc11 in flavonoid biosynthesis in G. biloba, lnc10 and lnc11 were cloned from G. biloba, and were transformed into Arabidopsis and overexpressed. Compared with the wild type, the flavonoid content was increased in transgenic plants. Moreover, the RNA-sequencing analysis of wild-type, lnc10-overexpression, and lnc11-overexpression plants screened out 2019 and 2552 differentially expressed genes, and the transcript levels of structural genes and transcription factors associated with flavonoid biosynthesis were higher in transgenic Arabidopsis than in the wild type, indicating that lnc10 and lnc11 activated flavonoid biosynthesis in the transgenic lines. Overall, these results suggest that lnc10 and lnc11 positively regulate flavonoid biosynthesis in G. biloba.
Collapse
Affiliation(s)
- Yuting Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xiaoxi Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| |
Collapse
|
2
|
Chu X, Wang M, Fan Z, Li J, Yin H. Molecular Mechanisms of Seasonal Gene Expression in Trees. Int J Mol Sci 2024; 25:1666. [PMID: 38338945 PMCID: PMC10855862 DOI: 10.3390/ijms25031666] [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: 12/27/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond to day length or temperature can lead to the establishment of conserved periodic gene expression patterns. In recent years, it has been shown in many woody plants that change in annual rhythmic patterns of gene expression may underpin the adaptive evolution in forest trees. In this review, we summarize the progress on the molecular mechanisms of seasonal regulation on the processes of shoot growth, bud dormancy, and bud break in response to day length and temperature factors. We focus on seasonal expression patterns of genes involved in dormancy and their associated epigenetic modifications; the seasonal changes in the extent of modifications, such as DNA methylation, histone acetylation, and histone methylation, at dormancy-associated loci have been revealed for their actions on gene regulation. In addition, we provide an outlook on the direction of research on the annual cycle of tree growth under climate change.
Collapse
Affiliation(s)
- Xian Chu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Minyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Zhengqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.C.); (M.W.); (Z.F.); (J.L.)
| |
Collapse
|
3
|
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.
Collapse
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.)
| |
Collapse
|
4
|
Jin X, Wang Z, Li X, Ai Q, Wong DCJ, Zhang F, Yang J, Zhang N, Si H. Current perspectives of lncRNAs in abiotic and biotic stress tolerance in plants. FRONTIERS IN PLANT SCIENCE 2024; 14:1334620. [PMID: 38259924 PMCID: PMC10800568 DOI: 10.3389/fpls.2023.1334620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Abiotic/biotic stresses pose a major threat to agriculture and food security by impacting plant growth, productivity and quality. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long non-coding RNAs (lncRNAs) with sizes larger than 200 nucleotides in length, provides an important new perspective on the centrality of RNA in gene regulation. In plants, lncRNAs are widespread and fulfill multiple biological functions in stress response. In this paper, the research advances on the biological function of lncRNA in plant stress response were summarized, like as Natural Antisense Transcripts (NATs), Competing Endogenous RNAs (ceRNAs) and Chromatin Modification etc. And in plants, lncRNAs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid (ABA), jasmonate (JA), salicylic acid (SA) and redox signaling in response to many abiotic/biotic stresses. Moreover, conserved sequence motifs and structural motifs enriched within stress-responsive lncRNAs may also be responsible for the stress-responsive functions of lncRNAs, it will provide a new focus and strategy for lncRNA research. Taken together, we highlight the unique role of lncRNAs in integrating plant response to adverse environmental conditions with different aspects of plant growth and development. We envisage that an improved understanding of the mechanisms by which lncRNAs regulate plant stress response may further promote the development of unconventional approaches for breeding stress-resistant crops.
Collapse
Affiliation(s)
- Xin Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zemin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuan Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qianyi Ai
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Darren Chern Jan Wong
- Division of Ecology and Evolution, Research School Research of Biology, The Australian National University, Acton, ACT, Australia
| | - Feiyan Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
5
|
Li Z, Zhou H, Xu G, Zhang P, Zhai N, Zheng Q, Liu P, Jin L, Bai G, Zhang H. Genome-wide analysis of long noncoding RNAs in response to salt stress in Nicotiana tabacum. BMC PLANT BIOLOGY 2023; 23:646. [PMID: 38097981 PMCID: PMC10722832 DOI: 10.1186/s12870-023-04659-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have been shown to play important roles in the response of plants to various abiotic stresses, including drought, heat and salt stress. However, the identification and characterization of genome-wide salt-responsive lncRNAs in tobacco (Nicotiana tabacum L.) have been limited. Therefore, this study aimed to identify tobacco lncRNAs in roots and leaves in response to different durations of salt stress treatment. RESULTS A total of 5,831 lncRNAs were discovered, with 2,428 classified as differentially expressed lncRNAs (DElncRNAs) in response to salt stress. Among these, only 214 DElncRNAs were shared between the 2,147 DElncRNAs in roots and the 495 DElncRNAs in leaves. KEGG pathway enrichment analysis revealed that these DElncRNAs were primarily associated with pathways involved in starch and sucrose metabolism in roots and cysteine and methionine metabolism pathway in leaves. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 15 co-expression modules, with four modules strongly linked to salt stress across different treatment durations (MEsalmon, MElightgreen, MEgreenyellow and MEdarkred). Additionally, an lncRNA-miRNA-mRNA network was constructed, incorporating several known salt-associated miRNAs such as miR156, miR169 and miR396. CONCLUSIONS This study enhances our understanding of the role of lncRNAs in the response of tobacco to salt stress. It provides valuable information on co-expression networks of lncRNA and mRNAs, as well as networks of lncRNAs-miRNAs-mRNAs. These findings identify important candidate lncRNAs that warrant further investigation in the study of plant-environment interactions.
Collapse
Affiliation(s)
- Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
- Beijing Life Science Academy (BLSA), Beijing, China
| | - Huina Zhou
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
- Beijing Life Science Academy (BLSA), Beijing, China
| | - Guoyun Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
- Beijing Life Science Academy (BLSA), Beijing, China
| | - Peipei Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
| | - Niu Zhai
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
- Beijing Life Science Academy (BLSA), Beijing, China
| | - Qingxia Zheng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
- Beijing Life Science Academy (BLSA), Beijing, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
- Beijing Life Science Academy (BLSA), Beijing, China
| | - Lifeng Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China
- Beijing Life Science Academy (BLSA), Beijing, China
| | - Ge Bai
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China.
| | - Hui Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 45000, China.
- Beijing Life Science Academy (BLSA), Beijing, China.
| |
Collapse
|
6
|
Jha UC, Nayyar H, Roychowdhury R, Prasad PVV, Parida SK, Siddique KHM. Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108164. [PMID: 38008006 DOI: 10.1016/j.plaphy.2023.108164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/28/2023]
Abstract
Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.
Collapse
Affiliation(s)
- Uday Chand Jha
- Sustainable Intensification Innovation Lab, Kansas State University, Department of Agronomy, Manhattan, KS 66506, USA; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh 208024, India.
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, 160014, India.
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - The Volcani Institute, Rishon Lezion 7505101, Israel
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Department of Agronomy, Manhattan, KS 66506, USA
| | - Swarup K Parida
- National Institute of Plant Genomic Research, New Delhi, 110067, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| |
Collapse
|
7
|
Gou N, Chen C, Huang M, Zhang Y, Bai H, Li H, Wang L, Wuyun T. Transcriptome and Metabolome Analyses Reveal Sugar and Acid Accumulation during Apricot Fruit Development. Int J Mol Sci 2023; 24:16992. [PMID: 38069317 PMCID: PMC10707722 DOI: 10.3390/ijms242316992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The apricot (Prunus armeniaca L.) is a fruit that belongs to the Rosaceae family; it has a unique flavor and is of important economic and nutritional value. The composition and content of soluble sugars and organic acids in fruit are key factors in determining the flavor quality. However, the molecular mechanism of sugar and acid accumulation in apricots remains unclear. We measured sucrose, fructose, glucose, sorbitol, starch, malate, citric acid, titratable acid, and pH, and investigated the transcriptome profiles of three apricots (the high-sugar cultivar 'Shushanggan', common-sugar cultivar 'Sungold', and low-sugar cultivar 'F43') at three distinct developmental phases. The findings indicated that 'Shushanggan' accumulates a greater amount of sucrose, glucose, fructose, and sorbitol, and less citric acid and titratable acid, resulting in a better flavor; 'Sungold' mainly accumulates more sucrose and less citric acid and starch for the second flavor; and 'F43' mainly accumulates more titratable acid, citric acid, and starch for a lesser degree of sweetness. We investigated the DEGs associated with the starch and sucrose metabolism pathways, citrate cycle pathway, glycolysis pathway, and a handful of sugar transporter proteins, which were considered to be important regulators of sugar and acid accumulation. Additionally, an analysis of the co-expression network of weighted genes unveiled a robust correlation between the brown module and sucrose, glucose, and fructose, with VIP being identified as a hub gene that interacted with four sugar transporter proteins (SLC35B3, SLC32A, SLC2A8, and SLC2A13), as well as three structural genes for sugar and acid metabolism (MUR3, E3.2.1.67, and CSLD). Furthermore, we found some lncRNAs and miRNAs that regulate these genes. Our findings provide clues to the functional genes related to sugar metabolism, and lay the foundation for the selection and cultivation of high-sugar apricots in the future.
Collapse
Affiliation(s)
- Ningning Gou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Chen Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Mengzhen Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Yujing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Haikun Bai
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Tana Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| |
Collapse
|
8
|
Zhang D, Wang L, Wang W, Liu D. The Role of lncRNAs in Pig Muscle in Response to Cold Exposure. Genes (Basel) 2023; 14:1901. [PMID: 37895249 PMCID: PMC10606478 DOI: 10.3390/genes14101901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Cold exposure is an essential factor affecting breeding efforts in cold regions. Muscle, as an important tissue for homeothermic animals, can produce heat through shivering thermogenesis (ST) and non-shivering thermogenesis (NST) under cold exposure. Long non-coding RNAs (lncRNAs) play important roles in regulating gene expression. However, the regulatory mechanisms of lncRNAs and their role in the thermogenesis of pigs are unclear. We examined lncRNAs in the skeletal muscle of an indigenous pig breed, the Enshi black pig, when the pigs were exposed to acute or chronic cold. Three pigs were maintained inside a pig house (control group), three pigs were maintained outside the pig house for 55 d (chronic cold group), and three pigs were suddenly exposed to the conditions outside the pig house for 3 days (acute cold group). After the experiment, the longissimus dorsi of each pig were collected, and their lncRNA profiles were sequenced and analyzed. Each sample obtained nearly 12.56 Gb of clean data. A total of 11,605 non-coding RNAs were obtained, including 10,802 novel lncRNAs. The number of differentially expressed lncRNAs (DElncRNAs) was identified under acute cold (427) and cold acclimation (376), with 215 and 192 upregulated lncRNAs, respectively. However, only 113 lncRNAs were commonly upregulated by acute cold and cold acclimation. In addition, 65% of the target genes were trans-regulated by DElncRNAs. The target genes were enriched in signal transduction, immune system, cell growth and death pathways, and amino acid and carbohydrate metabolism. Compared to cold acclimation, acute cold stress-induced more DElncRNAs and response pathways. In conclusion, low temperatures altered the expression levels of lncRNAs and their target genes in muscle tissue. Some potential mechanisms were revealed, including ion migration and the metabolism of amino acids and carbohydrates.
Collapse
Affiliation(s)
| | | | | | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (D.Z.); (L.W.); (W.W.)
| |
Collapse
|
9
|
Sun N, Bu Y, Wu X, Ma X, Yang H, Du L, Li X, Xiao J, Lin J, Jing Y. Comprehensive analysis of lncRNA-mRNA regulatory network in Populus associated with xylem development. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154055. [PMID: 37506405 DOI: 10.1016/j.jplph.2023.154055] [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: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) play essential roles in numerous biological processes in plants, such as regulating the gene expression. However, only a few studies have looked into their potential functions in xylem development. High-throughput sequencing of P. euramericana 'Zhonglin46' developing and mature xylem was performed in this study. Through sequencing analysis, 14,028 putative lncRNA transcripts were identified, including 4525 differentially expressed lncRNAs (DELs). Additional research revealed that in mature xylem, a total of 2320 DELs were upregulated and 2205 were downregulated compared to developing xylem. Meanwhile, there were a total of 8122 differentially expressed mRNAs (DEMs) that were upregulated and 16,424 that were downregulated in mature xylem compared with developing xylem. The cis- and trans-target genes of DELs were analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, which indicated that these DELs participate in controlling the phenylpropanoid and lignin biosynthesis pathway as well as the starch and sucrose metabolism pathway. Among the cis-regulated DELs, LNC_006291, LNC_006292, and LNC_006532 all participate in regulating multiple HCT gene family membranes. As targets, POPTR_001G045900v3 (CCR2) and POPTR_018G063500v3 (SUS) both have only one cis-regulatory lncRNA, referred to as LNC_000057 and LNC_006212, respectively. Moreover, LNC_004484 and two DELs named LNC_008014 and LNC_010781 were revealed to be important nodes in the co-expression network of trans-lncRNAs and mRNAs associated to the lignin biosynthesis pathway and cellulose and xylan biosynthetic pathways, respectively. Finally, quantitative real-time PCR (qRT-PCR) was used to confirme 34 pairs of lncRNA-mRNA. Taken together, these findings may help to clarify the regulatory role that lncRNAs play in xylem development and wood formation.
Collapse
Affiliation(s)
- Na Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yufen Bu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xinyuan Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaocen Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Haobo Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaojuan Li
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jianwei Xiao
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jinxing Lin
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yanping Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| |
Collapse
|
10
|
Bai Y, Liu M, Zhou R, Jiang F, Li P, Li M, Zhang M, Wei H, Wu Z. Construction of ceRNA Networks at Different Stages of Somatic Embryogenesis in Garlic. Int J Mol Sci 2023; 24:ijms24065311. [PMID: 36982386 PMCID: PMC10049443 DOI: 10.3390/ijms24065311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
LncRNA (long non-coding RNA) and mRNA form a competitive endogenous RNA (ceRNA) network by competitively binding to common miRNAs. This network regulates various processes of plant growth and development at the post-transcriptional level. Somatic embryogenesis is an effective means of plant virus-free rapid propagation, germplasm conservation, and genetic improvement, which is also a typical process to study the ceRNA regulatory network during cell development. Garlic is a typical asexual reproductive vegetable. Somatic cell culture is an effective means of virus-free rapid propagation in garlic. However, the ceRNA regulatory network of somatic embryogenesis remains unclear in garlic. In order to clarify the regulatory role of the ceRNA network in garlic somatic embryogenesis, we constructed lncRNA and miRNA libraries of four important stages (explant stage: EX; callus stage: AC; embryogenic callus stage: EC; globular embryo stage: GE) in the somatic embryogenesis of garlic. It was found that 44 lncRNAs could be used as precursors of 34 miRNAs, 1511 lncRNAs were predicted to be potential targets of 144 miRNAs, and 45 lncRNAs could be used as eTMs of 29 miRNAs. By constructing a ceRNA network with miRNA as the core, 144 miRNAs may bind to 1511 lncRNAs and 12,208 mRNAs. In the DE lncRNA-DE miRNA-DE mRNA network of adjacent stages of somatic embryo development (EX-VS-CA, CA-VS-EC, EC-VS-GE), by KEGG enrichment of adjacent stage DE mRNA, plant hormone signal transduction, butyric acid metabolism, and C5-branched dibasic acid metabolism were significantly enriched during somatic embryogenesis. Since plant hormones play an important role in somatic embryogenesis, further analysis of plant hormone signal transduction pathways revealed that the auxin pathway-related ceRNA network (lncRNAs-miR393s-TIR) may play a role in the whole stage of somatic embryogenesis. Further verification by RT-qPCR revealed that the lncRNA125175-miR393h-TIR2 network plays a major role in the network and may affect the occurrence of somatic embryos by regulating the auxin signaling pathway and changing the sensitivity of cells to auxin. Our results lay the foundation for studying the role of the ceRNA network in the somatic embryogenesis of garlic.
Collapse
Affiliation(s)
- Yunhe Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
| | - Min Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
| | - Rong Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
- Department of Food Science, Aarhus University, Agro Food Park 48, 8200 Aarhus, Denmark
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
| | - Ping Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
| | - Mengqian Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
| | - Meng Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
| | - Hanyu Wei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing 210095, China
- Correspondence:
| |
Collapse
|
11
|
Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption. Cells 2023; 12:cells12050729. [PMID: 36899864 PMCID: PMC10001313 DOI: 10.3390/cells12050729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Abiotic stresses triggered by climate change and human activity cause substantial agricultural and environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, and regulation of transcription and translation. Over the past decade, a large body of literature has revealed the various regulatory roles of long non-coding RNAs (lncRNAs) in the plant response to abiotic stresses and their irreplaceable functions in environmental adaptation. LncRNAs are recognized as a class of ncRNAs that are longer than 200 nucleotides, influencing a variety of biological processes. In this review, we mainly focused on the recent progress of plant lncRNAs, outlining their features, evolution, and functions of plant lncRNAs in response to drought, low or high temperature, salt, and heavy metal stress. The approaches to characterize the function of lncRNAs and the mechanisms of how they regulate plant responses to abiotic stresses were further reviewed. Moreover, we discuss the accumulating discoveries regarding the biological functions of lncRNAs on plant stress memory as well. The present review provides updated information and directions for us to characterize the potential functions of lncRNAs in abiotic stresses in the future.
Collapse
|
12
|
Wang Y, Zhao Y, Wu Y, Zhao X, Hao Z, Luo H, Yuan Z. Transcriptional profiling of long non-coding RNAs regulating fruit cracking in Punica granatum L. under bagging. FRONTIERS IN PLANT SCIENCE 2022; 13:943547. [PMID: 36304394 PMCID: PMC9592827 DOI: 10.3389/fpls.2022.943547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Fruit cracking tremendously damages the appearance of fruit, easily leads to pathogen invasion, greatly reduces the marketability and causes immense economic losses. The pivotal role of long non-coding RNAs (lncRNAs) in diverse biological processes has been confirmed, while the roles of lncRNAs underlying fruit cracking remain poorly understood. In this study, the incidence of fruit cracking was 7.26% under the bagging treatment, the control group was 38.11%, indicating that bagging considerably diminished the fruit cracking rate. LncRNA libraries for fruit cracking (FC), fruit non-cracking (FNC) and fruit non-cracking under bagging (FB) in pomegranate (Punica granatum L.) were performed and analysed via high-throughput transcriptome sequencing. A total of 3194 lncRNAs were obtained with a total length of 4898846 nt and an average length of 1533.77 nt in pomegranate. We identified 42 differentially expressed lncRNAs (DELs) and 137 differentially expressed mRNAs (DEGs) in FC vs FNC and 35 DELs and 160 DEGs in FB vs FC that formed co-expression networks respectively, suggesting that there are involved in phytohormone signaling pathway, lignin catabolic process, lipid transport/binding, cutin biosynthetic process and cell wall organization. We also found that 18 cis-acting DELs regulated 18 target genes, and 10 trans-acting DELs regulated 24 target genes in FC vs FNC, 23 DELs regulate 23 target genes for the cis-acting lncRNAs and 12 DELs regulated 36 target genes in FB vs FC, which provides an understanding for the regulation of the fruit cracking. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results demonstrated that DELs participated in calcium ion binding, glycerophospholipid metabolism, flavonoid biosynthetic process, cell wall biogenesis, xyloglucan metabolic process, hormone signal transduction and starch and sucrose metabolism. Our findings provide new insights into the roles of lncRNAs in regulating the fruit cracking and lay the foundation for further improvement of pomegranate quality.
Collapse
Affiliation(s)
- Yuying Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yujie Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhaoxiang Hao
- Zaozhuang Pomegranate Research Center, Institute of Botany, Zaozhuang, China
| | - Hua Luo
- Zaozhuang Pomegranate Research Center, Institute of Botany, Zaozhuang, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
13
|
Xiao Q, Lin Y, Li H, Chen Y, Wei W, Li P, Chen L. Transcriptome sequencing reveals the differentially expressed lncRNAs and mRNAs in response to cold acclimation and cold stress in Pomacea canaliculata. BMC Genomics 2022; 23:382. [PMID: 35590244 PMCID: PMC9121591 DOI: 10.1186/s12864-022-08622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background Tolerance of low temperature has a significant impact on survival and expansion of invasive snail Pomacea canalicuata. Cold acclimation can enhance cold tolerance of Pomacea canalicuata. To elucidate the molecular mechanism of P. canaliculata’s responses to cold acclimation and cold stress, a high-throughput transcriptome analysis of P. canaliculata was performed, and gene expression following artificial cold acclimation and then cold stress at 0 °C for 24 h was compared using RNA sequencing. Results Using the Illumina platform, we obtained 151.59 G subreads. A total of 5,416 novel lncRNAs were identified, and 3166 differentially expressed mRNAs and 211 differentially expressed lncRNAs were screened with stringent thresholds. The potential antisense, cis and trans targets of lncRNAs were predicted. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that many target genes were involved in proteasome, linoleic acid metabolism and retinol metabolism under cold acclimation. The lncRNA of P. canaliculata could participate in cold acclimation by regulating the expression of E3 ubiquitin protein ligase, 26S proteasome non-ATPase dependent regulation subunit, glutathione S-transferase, sodium/glucose cotransporter and cytochrome P450. Conclusions These results broaden our understanding of cold acclimation and cold stress associated lncRNAs and mRNAs, and provide new insights into lncRNA mediated regulation of P. canaliculata cold acclimation and cold stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08622-5.
Collapse
Affiliation(s)
- Qi Xiao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Youfu Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yu Chen
- College of Life Sciences, Chemistry and Chemical Engineering, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Wei Wei
- College of Life Sciences, Chemistry and Chemical Engineering, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Lian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| |
Collapse
|
14
|
Yin J, Yan J, Hou L, Jiang L, Xian W, Guo Q. Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici. BMC Genomics 2021; 22:868. [PMID: 34856924 PMCID: PMC8638555 DOI: 10.1186/s12864-021-08183-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. RESULTS In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. CONCLUSIONS This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.
Collapse
Affiliation(s)
- Junliang Yin
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, 434000 Jingzhou, Hubei China
| | - Jiahui Yan
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Liling Jiang
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Wenrong Xian
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Qingyun Guo
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Qinghai Academy of Agriculture and Forestry Science, Qinghai University, 810016 Xining, China
| |
Collapse
|
15
|
Li L, Liu J, Liang Q, Feng Y, Wang C, Wu S, Li Y. Downregulation of lncRNA PpL-T31511 and Pp-miRn182 Promotes Hydrogen Cyanamide-Induced Endodormancy Release through the PP2C-H 2O 2 Pathway in Pear ( Pyrus pyrifolia). Int J Mol Sci 2021; 22:ijms222111842. [PMID: 34769273 PMCID: PMC8584160 DOI: 10.3390/ijms222111842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Bud endodormancy is an important, complex process subject to both genetic and epigenetic control, the mechanism of which is still unclear. The endogenous hormone abscisic acid (ABA) and its signaling pathway play important roles in the endodormancy process, in which the type 2C protein phosphatases (PP2Cs) is key to the ABA signal pathway. Due to its excellent effect on endodormancy release, hydrogen cyanamide (HC) treatment is considered an effective measure to study the mechanism of endodormancy release. In this study, RNA-Seq analysis was conducted on endodormant floral buds of pear (Pyrus pyrifolia) with HC treatment, and the HC-induced PP2C gene PpPP2C1 was identified. Next, software prediction, expression tests and transient assays revealed that lncRNA PpL-T31511-derived Pp-miRn182 targets PpPP2C1. The expression analysis showed that HC treatment upregulated the expression of PpPP2C1 and downregulated the expression of PpL-T31511 and Pp-miRn182. Moreover, HC treatment inhibited the accumulation of ABA signaling pathway-related genes and hydrogen peroxide (H2O2). Furthermore, overexpression of Pp-miRn182 reduced the inhibitory effect of PpPP2C1 on the H2O2 content. In summary, our study suggests that downregulation of PpL-T31511-derived Pp-miRn182 promotes HC-induced endodormancy release in pear plants through the PP2C-H2O2 pathway.
Collapse
Affiliation(s)
- Liang Li
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Jinan District, Fuzhou 350013, China
| | - Jinhang Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Qin Liang
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Yu Feng
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Chao Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Shaohua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
| | - Yongyu Li
- College of Horticulture, Fujian Agriculture and Forestry University, Cangshan District, Fuzhou 350002, China; (L.L.); (J.L.); (Q.L.); (Y.F.); (C.W.); (S.W.)
- Correspondence:
| |
Collapse
|
16
|
Pan W, Liang J, Sui J, Li J, Liu C, Xin Y, Zhang Y, Wang S, Zhao Y, Zhang J, Yi M, Gazzarrini S, Wu J. ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective. Genes (Basel) 2021; 12:genes12101635. [PMID: 34681029 PMCID: PMC8536057 DOI: 10.3390/genes12101635] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential mechanisms in this physiological process, including epigenetic regulation.
Collapse
Affiliation(s)
- Wenqiang Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Jiahui Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Juanjuan Sui
- Biology and Food Engineering College, Fuyang Normal University, Fuyang 236037, China;
| | - Jingru Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Chang Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Yin Xin
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Yanmin Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Shaokun Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Yajie Zhao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Jie Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350001, China
| | - Mingfang Yi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto, Toronto, ON M1C 1A4, Canada;
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.P.); (J.L.); (J.L.); (C.L.); (Y.X.); (Y.Z.); (S.W.); (Y.Z.); (J.Z.); (M.Y.)
- Correspondence:
| |
Collapse
|
17
|
Chen Q, Liu K, Yu R, Zhou B, Huang P, Cao Z, Zhou Y, Wang J. From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs. FRONTIERS IN PLANT SCIENCE 2021; 12:650926. [PMID: 34163498 PMCID: PMC8215657 DOI: 10.3389/fpls.2021.650926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA-molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.
Collapse
Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Pingping Huang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| |
Collapse
|