1
|
Pang Y, Zheng K, Min Q, Wang Y, Xue X, Li W, Zhao H, Qiao F, Han S. Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots. Int J Mol Sci 2024; 25:6226. [PMID: 38892412 PMCID: PMC11172603 DOI: 10.3390/ijms25116226] [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: 05/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca2+]i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments.
Collapse
Affiliation(s)
- Yanrong Pang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Kaifeng Zheng
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Qinyue Min
- School of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Yinxing Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Xiuhua Xue
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Wanjie Li
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
| | - Feng Qiao
- School of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (Y.P.); (K.Z.); (Y.W.); (X.X.); (W.L.); (H.Z.)
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
| |
Collapse
|
2
|
Fan H, Wang X, Zhong H, Quan K, Yu R, Ma S, Song S, Lin M. Integrated analysis of miRNAs, transcriptome and phytohormones in the flowering time regulatory network of tea oil camellia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:945-956. [PMID: 38974357 PMCID: PMC11222345 DOI: 10.1007/s12298-024-01473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024]
Abstract
Camellia oleifera is a crucial cash crop in the southern region of China. Timely flowering is a crucial characteristic for maximizing crop productivity. Nevertheless, the cold temperature and wet weather throughout the fall and winter seasons in South China impact the timing of flowering and the yield produced by C. oleifera. This study examined the miRNAs, transcriptomes, and phytohormones that are part of the flowering time regulatory networks in distinct varieties of C. oleifera (Sep, Oct, and Nov). This study provides evidence that phytohormones significantly impact the timing of flowering in C. oleifera leaves. There is a positive correlation between the accumulation variations of zeatin (cZ), brassinolide (BL), salicylic acid (SA), 1-amino cyclopropane carboxylic acid (ACC), and jasmonic acid (JA) and flowering time. This means that blooming occurs earlier when the quantity of these substances in leaves increases. Abscisic acid (ABA), trans-zeatin-riboside (tZR), dihydrozeatin (dh-Z), and IP (N6-Isopentenyladenine) exhibit contrasting effects. Furthermore, both miR156 and miR172 play a crucial function in regulating flowering time in C. oleifera leaves by modulating the expression of SOC1, primarily through the miR156-SPL and miR172-AP2 pathways. These findings establish a strong basis for future research endeavors focused on examining the molecular network associated with the flowering period of C. oleifera and controlling flowering time management through external treatments. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01473-2.
Collapse
Affiliation(s)
- Haixiao Fan
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Xiaoling Wang
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Huiqi Zhong
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Kehui Quan
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Ruohan Yu
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Shiying Ma
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Siqiong Song
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Mengfei Lin
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| |
Collapse
|
3
|
Dai Y, Gao X, Zhang S, Li F, Zhang H, Li G, Sun R, Zhang S, Hou X. Exploring the Regulatory Dynamics of BrFLC-Associated lncRNA in Modulating the Flowering Response of Chinese Cabbage. Int J Mol Sci 2024; 25:1924. [PMID: 38339202 PMCID: PMC10856242 DOI: 10.3390/ijms25031924] [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: 01/08/2024] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Vernalization plays a crucial role in the flowering and yield of Chinese cabbage, a process intricately influenced by long non-coding RNAs (lncRNAs). Our research focused on lncFLC1, lncFLC2a, and lncFLC2b, which emerged as key players in this process. These lncRNAs exhibited an inverse expression pattern to the flowering repressor genes FLOWERING LOCUS C 1 (BrFLC1) and FLOWERING LOCUS C 2 (BrFLC2) during vernalization, suggesting a complex regulatory mechanism. Notably, their expression in the shoot apex and leaves was confirmed through in fluorescent in situ hybridization (FISH). Furthermore, when these lncRNAs were overexpressed in Arabidopsis, a noticeable acceleration in flowering was observed, unveiling functional similarities to Arabidopsis's COLD ASSISTED INTRONIC NONCODING RNA (COOLAIR). This resemblance suggests a potentially conserved regulatory mechanism across species. This study not only enhances our understanding of lncRNAs in flowering regulation, but also opens up new possibilities for their application in agricultural practices.
Collapse
Affiliation(s)
- Yun Dai
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xinyu Gao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shifan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Fei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Hui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Guoliang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Rifei Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shujiang Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xilin Hou
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
| |
Collapse
|
4
|
Kumar S, Sharma N, Sopory SK, Sanan-Mishra N. miRNAs and genes as molecular regulators of rice grain morphology and yield. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108363. [PMID: 38281341 DOI: 10.1016/j.plaphy.2024.108363] [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: 07/03/2023] [Revised: 12/07/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.
Collapse
Affiliation(s)
- Sudhir Kumar
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Sudhir K Sopory
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| |
Collapse
|
5
|
Wu H, Zhang Z, Liu Z, Meng Q, Xu Z, Zhang H, Qian W, She H. Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Bolting Periods in Spinacia oleracea. Genes (Basel) 2023; 15:36. [PMID: 38254926 PMCID: PMC10815260 DOI: 10.3390/genes15010036] [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: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting is relatively weak, with specific regulatory pathways and genes unclear. To clarify the regulatory characteristics and key genes related to bolting in spinach, we conducted a comparative transcriptome analysis. In this study, 18 samples from three periods of bolting-tolerant spinach material 12S3 and bolting-susceptible material 12S4 were analyzed using RNA-seq on, resulting in 10,693 differentially expressed genes (DEGs). Functional enrichment and co-expression trend analysis indicated that most DEGs were enriched in the photoperiod pathway, the hormone signaling pathway, and the cutin, suberin, and wax biosynthetic pathways. According to the weighted gene co-expression network analysis (WGCNA), SpFT (SOV4g003400), SOV4g040250, and SpGASA1 (SOV6g017600) were likely to regulate bolting through the gibberellin and photoperiod pathways, and SpELF4 (SOV1g028600) and SpPAT1 (SOV4g058860) caused differences in early and late bolting among different cultivars. These results provide important insights into the genetic control of bolting in spinach and will help elucidate the molecular mechanisms of bolting in leafy vegetables.
Collapse
Affiliation(s)
- Hao Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhilong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qing Meng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
6
|
Hidalgo M, Ramos C, Zolla G. Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response. Noncoding RNA 2023; 9:48. [PMID: 37736894 PMCID: PMC10514842 DOI: 10.3390/ncrna9050048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/23/2023] Open
Abstract
Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with -105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between L. mutabilis (S03) and S. lycopersicum (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of L. mutabilis. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions.
Collapse
Affiliation(s)
- Manuel Hidalgo
- Programa de Estudio de Medicina Humana, Universidad Privada Antenor Orrego, Av. América Sur 3145, Trujillo 13008, Peru; (M.H.); (C.R.)
| | - Cynthia Ramos
- Programa de Estudio de Medicina Humana, Universidad Privada Antenor Orrego, Av. América Sur 3145, Trujillo 13008, Peru; (M.H.); (C.R.)
| | - Gaston Zolla
- Laboratorio de Fisiología Molecular de Plantas del Programa de Cereales y Granos Nativos, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Lima 12, Peru
| |
Collapse
|
7
|
Wang X, Li Q, Zhu H, Song M, Zhang K, Ge W. Molecular mechanisms of miR172a and its target gene LbrTOE3 regulating maturation in Lilium. PLANTA 2023; 258:53. [PMID: 37515607 DOI: 10.1007/s00425-023-04208-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
MAIN CONCLUSION Lbr-miR172a could promote the growth phase transition and shorten maturation in Lilium, while LbrTOE3 inhibited this process and prolonged the growth period. Lilium is an ornamental flower with high economic value for both food and medicinal purposes. However, under natural conditions, Lilium bulbs take a long time and cost more to grow to commercial size. This research was conducted to shorten the maturation time by subjecting Lilium bulbs to alternating temperature treatment. To explore the molecular mechanism of the vegetative phase change (VPC) in Lilium after variable temperature treatment, the key module miR172a-TOE3 was selected based on a combined omics analysis. Gene cloning and transgene functional validation showed that overexpression of Lbr-mir172a promoted a phase change, while overexpression of LbrTOE3 inhibited this process. Subcellular localization and transcriptional activation assays indicated that LbrTOE3 was predominantly localized in the nucleus and showed transcriptional activity. In situ hybridization showed that LbrTOE3 expression was significantly downregulated after alternating temperature treatment. This study elucidates the molecular mechanisms of the phase transition of Lilium and provides a scientific basis for the phase transition in other plants.
Collapse
Affiliation(s)
- Xiaoshan Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Qing Li
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Haoran Zhu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Meiqi Song
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People's Republic of China.
| | - Wei Ge
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People's Republic of China.
| |
Collapse
|
8
|
Pavani G, Malhotra PK, Verma SK. Flowering in sugarcane-insights from the grasses. 3 Biotech 2023; 13:154. [PMID: 37138783 PMCID: PMC10149435 DOI: 10.1007/s13205-023-03573-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
Flowering is a crucial phase for angiosperms to continue their species propagation and is highly regulated. In the current review, flowering in sugarcane and the associated mechanisms are elaborately presented. In sugarcane, flowering has two effects, wherein it is a beneficial factor from the breeder's perspective and crucial for crop improvement, but commercially, it depletes the sucrose reserves from the stalks; hence, less value is assigned. Different species of Saccharum genus are spread across geographical latitudes, thereby proving their ability to grow in multiple inductive daylengths of different locations according in the habituated zone. In general, sugarcane is termed an intermediate daylength plant with quantitative short-day behaviour as it requires reduction in daylength from 12 h 55 min to 12 h or 12 h 30 min. The prime concern in sugarcane flowering is its erratic flowering nature. The transition to reproductive stage which reverts to vegetative stage if there is any deviation from ambient temperature and light is also an issue. Spatial and temporal gene expression patterns during vegetative to reproductive stage transition and after reverting to vegetative state could possibly reveal how the genetic circuits are being governed. This review will also shed a light on potential roles of genes and/or miRNAs in flowering in sugarcane. Knowledge of transcriptomic background of circadian, photoperiod, and gibberellin pathways in sugarcane will enable us to better understand of variable response in floral development.
Collapse
Affiliation(s)
- Gongati Pavani
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Pawan Kumar Malhotra
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Sandeep Kumar Verma
- Institute of Biological Science, SAGE University, Bypass Road, Kailod Kartal, Indore, Madhya Pradesh 452020 India
| |
Collapse
|
9
|
Cui J, Qiu T, Li L, Cui S. De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments. BMC Genomics 2023; 24:180. [PMID: 37020272 PMCID: PMC10077656 DOI: 10.1186/s12864-023-09271-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/23/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies. RESULTS In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments. CONCLUSIONS Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.
Collapse
Affiliation(s)
- Jipeng Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Tianhang Qiu
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Li Li
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Suxia Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China.
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China.
| |
Collapse
|
10
|
Wang X, Fan H, Wang B, Yuan F. Research progress on the roles of lncRNAs in plant development and stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1138901. [PMID: 36959944 PMCID: PMC10028117 DOI: 10.3389/fpls.2023.1138901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) are RNAs of more than 200 nucleotides in length that are not (or very rarely) translated into proteins. In eukaryotes, lncRNAs regulate gene expression at the transcriptional, post-transcriptional, and epigenetic levels. lncRNAs are categorized according to their genomic position and molecular mechanism. This review summarized the characteristics and mechanisms of plant lncRNAs involved in vegetative growth, reproduction, and stress responses. Our discussion and model provide a theoretical basis for further studies of lncRNAs in plant breeding.
Collapse
Affiliation(s)
| | | | | | - Fang Yuan
- *Correspondence: Baoshan Wang, ; Fang Yuan,
| |
Collapse
|
11
|
Lee S, Singh MB, Bhalla PL. Functional analysis of soybean miR156 and miR172 in tobacco highlights their role in plant morphology and floral transition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:393-401. [PMID: 36753825 DOI: 10.1016/j.plaphy.2023.01.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Soybean (Glycine max), a significant oilseed and protein source for humans and livestock feed, needs short day photoperiod for floral induction. Further, soybean has a paleopolyploid genome with multiple copies of flowering genes adding to the complexity of genetic regulation of flowering, and seed set, especially in investigating the role of the noncoding genome. microRNAs, a class of noncoding RNA, play a regulatory role in plant development. miR156 and miR172 are major components of the essential regulatory hub controlling juvenile and vegetative developments and initiation of reproductive phase change leading to flowering. These microRNAs have been originally isolated and studied from model plant, Arabidopsis. However, a study on soybean microRNAs is lacking. We investigated the temporal expression patterns of gma-miR156a and gma-miR172a and found inversely related - gma-miR156a expression was higher in the vegetative stage, and gma-miR172a expression was elevated under inductive flowering conditions. The functions of gma-miR156a and gma-miR172a were evaluated via heterologous expressions in transgenic tobacco plants (Nicotiana tabacum L.). The analysis of overexpression transgenic lines highlighted that gma-miR156a plays a role in juvenile development via repression of the SPL transcription factor family. In contrast, gma-miR172a plays a pivotal role in the reproductive development phase by down-regulating its target genes, AP2. In addition, ectopic expression of gma-miR156a and gma-miR172a affected plant morphology and physiology during plant growth. Collectively, our results suggest that gma-miR156a and gma-miR172a regulate multiple morpho-physiological traits that could be used to enhance crop yield under changing climate conditions.
Collapse
Affiliation(s)
- Sangil Lee
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| |
Collapse
|
12
|
Li Y, Tan Z, Zeng C, Xiao M, Lin S, Yao W, Li Q, Guo L, Lu S. Regulation of seed oil accumulation by lncRNAs in Brassica napus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:22. [PMID: 36765368 PMCID: PMC9921586 DOI: 10.1186/s13068-022-02256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/28/2022] [Indexed: 02/12/2023]
Abstract
BACKGROUND Studies have indicated that long non-coding RNAs (lncRNAs) play important regulatory roles in many biological processes. However, the regulation of seed oil biosynthesis by lncRNAs remains largely unknown. RESULTS We comprehensively identified and characterized the lncRNAs from seeds in three developing stages in two accessions of Brassica napus (B. napus), ZS11 (high oil content) and WH5557 (low oil content). Finally, 8094 expressed lncRNAs were identified. LncRNAs MSTRG.22563 and MSTRG.86004 were predicted to be related to seed oil accumulation. Experimental results show that the seed oil content is decreased by 3.1-3.9% in MSTRG.22563 overexpression plants, while increased about 2% in MSTRG.86004, compared to WT. Further study showed that most genes related to lipid metabolism had much lower expression, and the content of some metabolites in the processes of respiration and TCA (tricarboxylic acid) cycle was reduced in MSTRG.22563 transgenic seeds. The expression of genes involved in fatty acid synthesis and seed embryonic development (e.g., LEC1) was increased, but genes related to TAG assembly was decreased in MSTRG.86004 transgenic seeds. CONCLUSION Our results suggest that MSTRG.22563 might impact seed oil content by affecting the respiration and TCA cycle, while MSTRG.86004 plays a role in prolonging the seed developmental time to increase seed oil accumulation.
Collapse
Affiliation(s)
- Yuqing Li
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Zengdong Tan
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Chenghao Zeng
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Mengying Xiao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Shengli Lin
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Wei Yao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Qing Li
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Liang Guo
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070 China ,grid.410727.70000 0001 0526 1937Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Genome Analysis Laboratory of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
| |
Collapse
|
13
|
Liu Y, Yang N, Yuan H, Chen P, Gu R, Zhang Y. BraVRG, a novel protein of Brassica rapa, is induced by vernalization and promotes flowering in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111544. [PMID: 36462681 DOI: 10.1016/j.plantsci.2022.111544] [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: 07/27/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Plant flowering is an important economical characteristic for the transformation from vegetative growth to reproductive growth, especially for biennial crops. Additionally, bolting or flowering time is more important for vegetable plants due to their different harvest organs, such as flower for cauliflower and broccoli and leafy heads for cabbage and Chinese cabbage. The flowering time of Arabidopsis thaliana has six classical regulated pathways, and some key regulated genes are identified in Brassicaceae crops. However, the regulatory mechanism needs further exploration. Here, we reported an novel protein BraVRG (Vernalization Related Gene) of Chinese cabbage induced by vernalization. The expression of BraVRG increased rapidly at 14 day of vernalization in the semi-winter type of Brassica rapa and 21 days for the winter types. Meanwhile the modifications of H3K4me3 deposited on BraVRG increased but H3K27me3 decreased. Moreover, BraVRG promoted flowering in transgenic A. thaliana compared with the wild types accompanied the downregulated expression of FLC caused by the decrease of H3K4me3 enrichment and the increase of H3K27me3 on FLC with or without vernalization conditions.
Collapse
Affiliation(s)
- Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region) Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150000, China; College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
| | - Na Yang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region) Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150000, China; College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
| | - Hongkun Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region) Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150000, China; College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
| | - Peng Chen
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region) Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150000, China; College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region) Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150000, China; College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region) Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150000, China; College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
| |
Collapse
|
14
|
Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
Collapse
Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
| |
Collapse
|
15
|
Babaei S, Singh MB, Bhalla PL. Role of long non-coding RNAs in rice reproductive development. FRONTIERS IN PLANT SCIENCE 2022; 13:1040366. [PMID: 36457537 PMCID: PMC9705774 DOI: 10.3389/fpls.2022.1040366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/28/2022] [Indexed: 05/13/2023]
Abstract
Rice is a staple crop, feeding over half of the global population. The future demand of population growth and climate change requires substantial rice improvement. Recent advances in rice genomics have highlighted the vital role of the non-coding part of the genome. The protein-coding regions account for only a tiny portion of the eukaryotic genome, and most of the genomic regions transcribe copious amounts of non-coding RNAs. Of these, the long non-coding RNAs, including linear non-coding RNAs (lncRNAs) and circular non-coding RNAs (circRNAs), have been shown to play critical roles in various developmental processes by regulating the expression of genes and functions of proteins at transcriptional, post-transcriptional and post-translational levels. With the advances in next-generation sequencing technologies, a substantial number of long non-coding RNAs have been found to be expressed in plant reproductive organs in a cell- and tissue-specific manner suggesting their reproductive development-related functions. Accumulating evidence points towards the critical role of these non-coding RNAs in flowering, anther, and pollen development, ovule and seed development and photoperiod and temperature regulation of male fertility. In this mini review, we provide a brief overview of the role of the linear and circular long non-coding RNAs in rice reproductive development and control of fertility and crop yield.
Collapse
Affiliation(s)
| | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
16
|
Yao W, Li C, Fu H, Yang M, Wu H, Ding Y, Li L, Lin S. Genome-Wide Analysis of SQUAMOSA-Promoter-Binding Protein-like Family in Flowering Pleioblastus pygmaeus. Int J Mol Sci 2022; 23:ijms232214035. [PMID: 36430513 PMCID: PMC9695801 DOI: 10.3390/ijms232214035] [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: 10/14/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL genes in reproductive growth are undisclosed in bamboo plants. In the study, a total of 28 SPLs were screened from an ornamental dwarf bamboo species, Pleioblastus pygmaeus. Phylogenetic analysis indicates that 183 SPLs from eight plant species can be classified into nine subfamilies, and the 28 PpSPLs are distributed among eight subfamilies. Homologous analysis shows that as many as 32 pairs of homologous genes were found between P. pygmaeus and rice, and 83 pairs were found between P. pygmaeus and Moso bamboo, whose Ka/Ks values are all <1. MiRNA target prediction reveals that 13 out of the 28 PpSPLs have recognition sites complementary to miRNA156. To screen the SPLs involved in the reproductive growth of bamboo plants, the mRNA abundance of the 28 PpSPLs was profiled in the different tissues of flowering P. pygmaeus and non-flowering plants by RNA-Seq. Moreover, the relative expression level of eight PpSPLs is significantly higher in flowering P. pygmaeus than that in non-flowering plants, which was also validated by RT-qPCR. Combined with phylogenetic analysis and homologous analysis, the eight significant, differentially expressed PpSPLs were identified to be associated with the reproductive process and flower organ development. Among them, there are four potential miRNA156-targeting PpSPLs involved in the flowering process. Of significant interest in the study is the identification of 28 SPLs and the exploration of four key flowering-related SPLs from P. pygmaeus, which provides a theoretic basis for revealing the underlying functions of SPLs in the reproductive growth of bamboo plants.
Collapse
Affiliation(s)
- Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Chuanzhe Li
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region, Jiangsu Academy of Agricultural Sciences, Huaian 223001, China
| | - Huajun Fu
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Meng Yang
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (L.L.); (S.L.)
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (L.L.); (S.L.)
| |
Collapse
|
17
|
Khemka N, Rajkumar MS, Garg R, Jain M. Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea. PLANTA 2022; 256:79. [PMID: 36094579 DOI: 10.1007/s00425-022-03986-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The integrated transcriptome data analyses suggested the plausible roles of lncRNAs during seed development in chickpea. The candidate lncRNAs associated with QTLs and those involved in miRNA-mediated seed size/weight determination in chickpea have been identified. Long non-coding RNAs (lncRNAs) are important regulators of various biological processes. Here, we identified lncRNAs at seven successive stages of seed development in small-seeded and large-seeded chickpea cultivars. In total, 4751 lncRNAs implicated in diverse biological processes were identified. Most of lncRNAs were conserved between the two cultivars, whereas only a few of them were conserved in other plants, suggesting their species-specificity. A large number of lncRNAs differentially expressed between the two chickpea cultivars associated with seed development-related processes were identified. The lncRNAs acting as precursors of miRNAs and those mimicking target protein-coding genes of miRNAs involved in seed size/weight determination, including HAIKU1, BIG SEEDS1, and SHB1, were also revealed. Further, lncRNAs located within seed size/weight associated quantitative trait loci were also detected. Overall, we present a comprehensive resource and identified candidate lncRNAs that may play important roles during seed development and seed size/weight determination in chickpea.
Collapse
Affiliation(s)
- Niraj Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
18
|
Tu Z, Yu L, Wen S, Zhai X, Li W, Li H. Identification and analysis of HD-Zip genes involved in the leaf development of Liriodendron chinense using multidimensional analysis. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:874-886. [PMID: 35491433 DOI: 10.1111/plb.13431] [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: 01/30/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Homeodomain-leucine zipper (HD-Zip) proteins are plant-specific transcription factors that play important roles in different biological processes, especially leaf development. However, no studies to date have identified the HD-Zip genes in Liriodendron chinense nor characterized their functions. We identified the HD-Zip genes in L. chinense by analysing the phylogeny, chromosome location, structure, conserved motif, cis-regulatory elements, synteny, post-transcriptional regulation and expression patterns of these genes during leaf development. A total of 36 LcHD-Zip genes were identified and divided into four subfamilies (HD-Zip I to IV). Synteny analysis revealed that segmental duplication was the main force driving the expansion of LcHD-Zip genes. These 36 LcHD-Zip genes exhibited 11 different expression patterns. Pattern 1, 2, 3, 4, 6, 7, 8 and 9 genes may play important roles in leaf development, such as leaf initiation, leaf polarity establishment, leaf shape development, phytohormone-mediated leaf growth and leaf epidermal structure formation. Four HD-Zip III genes were targeted by microRNAs (miRNAs), and the miR165/166a-HD-Zip regulatory module formed regulated leaf initiation and leaf polarity establishment. Overall, LcHD-Zip genes play key roles in leaf development of L. chinense. This work provides a foundation for the functional verification of HD-Zip genes identified in this study.
Collapse
Affiliation(s)
- Z Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - L Yu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - S Wen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - X Zhai
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - W Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - H Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
19
|
Ye J, Ge L, Geng X, He M, Yang X, Zhang L, Song X. Identification and validation of TCONS_00093333 for regulating fertility conversion of thermo-sensitive cytoplasmic male-sterility wheat with Aegilops kotschyi cytoplasm. Gene X 2022; 838:146707. [DOI: 10.1016/j.gene.2022.146707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/01/2022] [Accepted: 06/24/2022] [Indexed: 11/04/2022] Open
|
20
|
A survey of transcriptome complexity using full-length isoform sequencing in the tea plant Camellia sinensis. Mol Genet Genomics 2022; 297:1243-1255. [PMID: 35763065 DOI: 10.1007/s00438-022-01913-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/29/2022] [Indexed: 10/17/2022]
Abstract
Tea is one of the most popular beverages and its leaves are rich in catechins, contributing to the diverse flavor as well as beneficial for human health. However, the study of the post-transcriptional regulatory mechanism affecting the synthesis of catechins remains insufficient. Here, we sequenced the transcriptome using PacBio sequencing technology and obtained 63,111 full-length high-quality isoforms, including 1302 potential novel genes and 583 highly reliable fusion transcripts. We also identified 1204 lncRNAs with high quality, containing 188 known and 1016 novel lncRNAs. In addition, 311 mis-annotated genes were corrected based on the high-quality Isoseq reads. A large number of alternative splicing (AS) events (3784) and alternative polyadenylation (APA) genes (18,714) were analyzed, accounting for 8.84% and 43.7% of the total annotated genes, respectively. We also found that 2884 genes containing AS and APA features exhibited higher expression levels than other genes. These genes are mainly involved in amino acid biosynthesis, carbon fixation in photosynthetic organisms, phenylalanine, tyrosine, tryptophan biosynthesis, and pyruvate metabolism, suggesting that they play an essential role in the catechins content of tea polyphenols. Our results further improved the level of genome annotation and indicated that post-transcriptional regulation plays a crucial part in synthesizing catechins.
Collapse
|
21
|
Single trait versus principal component based association analysis for flowering related traits in pigeonpea. Sci Rep 2022; 12:10453. [PMID: 35729192 PMCID: PMC9211048 DOI: 10.1038/s41598-022-14568-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 03/18/2022] [Indexed: 11/08/2022] Open
Abstract
Pigeonpea, a tropical photosensitive crop, harbors significant diversity for days to flowering, but little is known about the genes that govern these differences. Our goal in the current study was to use genome wide association strategy to discover the loci that regulate days to flowering in pigeonpea. A single trait as well as a principal component based association study was conducted on a diverse collection of 142 pigeonpea lines for days to first and fifty percent of flowering over 3 years, besides plant height and number of seeds per pod. The analysis used seven association mapping models (GLM, MLM, MLMM, CMLM, EMLM, FarmCPU and SUPER) and further comparison revealed that FarmCPU is more robust in controlling both false positives and negatives as it incorporates multiple markers as covariates to eliminate confounding between testing marker and kinship. Cumulatively, a set of 22 SNPs were found to be associated with either days to first flowering (DOF), days to fifty percent flowering (DFF) or both, of which 15 were unique to trait based, 4 to PC based GWAS while 3 were shared by both. Because PC1 represents DOF, DFF and plant height (PH), four SNPs found associated to PC1 can be inferred as pleiotropic. A window of ± 2 kb of associated SNPs was aligned with available transcriptome data generated for transition from vegetative to reproductive phase in pigeonpea. Annotation analysis of these regions revealed presence of genes which might be involved in floral induction like Cytochrome p450 like Tata box binding protein, Auxin response factors, Pin like genes, F box protein, U box domain protein, chromatin remodelling complex protein, RNA methyltransferase. In summary, it appears that auxin responsive genes could be involved in regulating DOF and DFF as majority of the associated loci contained genes which are component of auxin signaling pathways in their vicinity. Overall, our findings indicates that the use of principal component analysis in GWAS is statistically more robust in terms of identifying genes and FarmCPU is a better choice compared to the other aforementioned models in dealing with both false positive and negative associations and thus can be used for traits with complex inheritance.
Collapse
|
22
|
Liang F, Zhang Y, Wang X, Yang S, Fang T, Zheng S, Zeng L. Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan ( Dimocarpus longan Lour.). FRONTIERS IN PLANT SCIENCE 2022; 13:923183. [PMID: 35774802 PMCID: PMC9237614 DOI: 10.3389/fpls.2022.923183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 05/27/2023]
Abstract
Longan (Dimocarpus longan Lour.) is a tropical/subtropical fruit tree of significant economic importance. Floral induction is an essential process for longan flowering and plays decisive effects on the longan yield. Due to the instability of flowering, it is necessary to understand the molecular mechanisms of floral induction in longan. In this study, mRNA and long noncoding RNA (lncRNA) transcriptome sequencing were performed using the apical buds of fruiting branches as materials. A total of 7,221 differential expressions of mRNAs (DEmRNAs) and 3,238 differential expressions of lncRNAs (DElncRNAs) were identified, respectively. KEGG enrichment analysis of DEmRNAs highlighted the importance of starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways during floral induction. Combining the analysis of weighted gene co-expression network (WGCNA) and expression pattern of DEmRNAs in the three pathways, specific transcriptional characteristics at each stage during floral induction and regulatory network involving co-expressed genes were investigated. The results showed that sucrose metabolism and auxin signal transduction may be crucial for the growth and maturity of autumn shoots in September and October (B1-B2 stage); starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways participated in the regulation of floral bud physiological differentiation together in November and December (B3-B4 stage) and the crosstalk among three pathways was also found. Hub genes in the co-expression network and key DEmRNAs in three pathways were identified. The circadian rhythm genes FKF1 and GI were found to activate SOC1gene through the photoperiod core factor COL genes, and they were co-expressed with auxin, gibberellin, abscisic acid, ethylene signaling genes, and sucrose biosynthesis genes at B4 stage. A total of 12 hub-DElncRNAs had potential for positively affecting their distant target genes in three putative key pathways, predominantly in a co-transcriptional manner. A hypothetical model of regulatory pathways and key genes and lncRNAs during floral bud induction in longan was proposed finally. Our studies will provide valuable clues and information to help elucidate the potential molecular mechanisms of floral initiation in longan and woody fruit trees.
Collapse
Affiliation(s)
- Fan Liang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yiyong Zhang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodan Wang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuo Yang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Fang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoquan Zheng
- Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzho, China
| | - Lihui Zeng
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
23
|
Bernardi Y, Ponso MA, Belén F, Vegetti AC, Dotto MC. MicroRNA miR394 regulates flowering time in Arabidopsis thaliana. PLANT CELL REPORTS 2022; 41:1375-1388. [PMID: 35333960 DOI: 10.1007/s00299-022-02863-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
miR394 regulates Arabidopsis flowering time in a LCR-independent manner. Arabidopsis plants harboring mutations in theMIR394 genes exhibit early flowering, lower expression of floral repressor FLC and higher expression of floral integrators FT and SOC1. Plant development occurs throughout its entire life cycle and involves a phase transition between vegetative and reproductive phases, leading to the flowering process, fruit formation and ultimately seed production. It has been shown that the microRNA394 (miR394) regulates the accumulation of the transcript coding for LEAF CURLING RESPONSIVENESS, a member of a family of F-Box proteins. The miR394 pathway regulates several processes including leaf morphology and development of the shoot apical meristem during embryogenesis, as well as having been assigned a role in the response to biotic and abiotic stress in Arabidopsis thaliana and other species. Here, we characterized plants harboring mutations in MIR394 precursor genes and demonstrate that mir394a mir394b double mutants display an early flowering phenotype which correlates with a lower expression of FLOWERING LOCUS C earlier in development and higher expression of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Consequently, mutant plants produce fewer branches and exhibit lower seed production. Our work reveals previously unknown developmental aspects regulated by the miR394 pathway, in an LCR-independent manner, contributing to the characterization of the multiple roles of this versatile plant regulatory miRNA.
Collapse
Affiliation(s)
- Yanel Bernardi
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
- Instituto Tecnológico de Chascomús (INTECH, CONICET-UNSAM), Chascomús, Argentina
| | - María Agustina Ponso
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB, UNVM-CONICET). Instituto de Ciencias Básicas, Villa María, Córdoba, Argentina
| | - Federico Belén
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
| | - Abelardo C Vegetti
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
| | - Marcela C Dotto
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina.
| |
Collapse
|
24
|
The Genetic and Hormonal Inducers of Continuous Flowering in Orchids: An Emerging View. Cells 2022; 11:cells11040657. [PMID: 35203310 PMCID: PMC8870070 DOI: 10.3390/cells11040657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/07/2023] Open
Abstract
Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time regulation is the key to studies about orchid flower development. Although there are some rare orchids with a continuous flowering pattern, the molecular regulatory mechanisms are yet to be elucidated to find applicable solutions to other orchid species. Multiple regulatory pathways, such as photoperiod, vernalization, circadian clock, temperature and hormonal pathways are thought to signalize flower timing using a group of floral integrators. This mini review, thus, organizes the current knowledge of floral time regulators to suggest future perspectives on the continuous flowering mechanism that may help to plan functional studies to induce flowering revolution in precious orchid species.
Collapse
|
25
|
Wang L, Gao J, Wang C, Xu Y, Li X, Yang J, Chen K, Kang Y, Wang Y, Cao P, Xie X. Comprehensive Analysis of Long Non-coding RNA Modulates Axillary Bud Development in Tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:809435. [PMID: 35237286 PMCID: PMC8884251 DOI: 10.3389/fpls.2022.809435] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression and are crucial for plant growth and development. However, the mechanisms underlying the effects of activated lncRNAs on axillary bud development remain largely unknown. By lncRNA transcriptomes of axillary buds in topped and untopped tobacco plants, we identified a total of 13,694 lncRNAs. LncRNA analysis indicated that the promoted growth of axillary bud by topping might be partially ascribed to the genes related to hormone signal transduction and glycometabolism, trans-regulated by differentially expressed lncRNAs, such as MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1. Metabolite profiling indicated that auxin, abscisic acid and gibberellin were decreased in axillary buds of topped tobacco lines, while cytokinin was increased, consistent with the expression levels of related lncRNAs. MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1 were shown to be influenced by hormones and sucrose treatments, and were associated with changes of axillary bud growth in the overexpression of NtCCD8 plants (with reduced axillary buds) and RNA interference of NtTB1 plants (with increased axillary buds). Moreover, MSTRG.28151.1 was identified as the antisense lncRNA of NtTB1. Silencing of MSTRG.28151.1 in tobacco significantly attenuated the expression of NtTB1 and resulted in larger axillary buds, suggesting the vital function of MSTRG.28151.1 axillary bud developmen by NtTB1. Our findings shed light on lncRNA-mRNA interactions and their functional roles in axillary bud growth, which would improve our understanding of lncRNAs as important regulators of axillary bud development and plant architecture.
Collapse
Affiliation(s)
- Lin Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Junping Gao
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Chen Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaoxu Li
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Kai Chen
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Yile Kang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yaofu Wang
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| |
Collapse
|
26
|
Tu Z, Xia H, Yang L, Zhai X, Shen Y, Li H. The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2022; 13:816875. [PMID: 35154228 PMCID: PMC8829146 DOI: 10.3389/fpls.2022.816875] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/04/2022] [Indexed: 05/27/2023]
Abstract
The leaf and the flower are vital plant organs owing to their roles in photosynthesis and reproduction. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and transcription factors (TFs) are very important to the development of these organs. Liriodendron chinense is a common ornamental tree species in southern China with an unusual leaf shape and tulip-like flowers. The genetic mechanisms underlying leaf and flower development in L. chinense and the miRNA-lncRNA-TF regulatory networks are poorly studied. Through the integration and analysis of different types of sequencing data, we identified the miRNA-lncRNA-TF regulatory networks that were related to leaf and flower development. These networks contained 105 miRNAs, 258 lncRNAs, 393 TFs, and 22 endogenous target mimics. Notably, lch-lnc7374-miR156h-SPL3 and lch-lnc7374-miR156j-SPL9 were potential regulators of stamen and pistil development in L. chinense, respectively. miRNA-lncRNA-mRNA regulatory networks were shown to impact anther development, male and female fertility, and petal color by regulating the biosynthesis of phenylpropanoid metabolites. Phenylpropanoid metabolite biosynthesis genes and TFs that were targeted by miRNAs and lncRNAs were differentially expressed in the leaf and flower. Moreover, RT-qPCR analysis confirmed 22 differentially expressed miRNAs, among which most of them showed obvious leaf or flower specificity; miR157a-SPL and miR160a-ARF module were verified by using RLM-RACE, and these two modules were related to leaf and flower development. These findings provide insight into the roles of miRNA-lncRNA-mRNA regulatory networks in organ development and function in L. chinense, and will facilitate further investigation into the regulatory mechanisms of leaf and flower development in L. chinense.
Collapse
Affiliation(s)
- Zhonghua Tu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Hui Xia
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lichun Yang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinyu Zhai
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yufang Shen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
27
|
Lebedeva M, Azarakhsh M, Sadikova D, Lutova L. At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia. PLANTS (BASEL, SWITZERLAND) 2021; 10:2654. [PMID: 34961125 PMCID: PMC8705049 DOI: 10.3390/plants10122654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 05/13/2023]
Abstract
The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.
Collapse
Affiliation(s)
- Maria Lebedeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Mahboobeh Azarakhsh
- Cell and Molecular Biology Department, Kosar University of Bojnord, 9415615458 Bojnord, Iran;
| | - Darina Sadikova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Lyudmila Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| |
Collapse
|
28
|
Osadchuk K, Cheng CL, Irish EE. The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111035. [PMID: 34620439 DOI: 10.1016/j.plantsci.2021.111035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.
Collapse
Affiliation(s)
- Krista Osadchuk
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Chi-Lien Cheng
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Erin E Irish
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
29
|
Malovichko YV, Shikov AE, Nizhnikov AA, Antonets KS. Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications. Int J Mol Sci 2021; 22:ijms22179252. [PMID: 34502157 PMCID: PMC8430901 DOI: 10.3390/ijms22179252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022] Open
Abstract
In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.
Collapse
Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence:
| |
Collapse
|
30
|
Gioppato HA, Dornelas MC. Plant design gets its details: Modulating plant architecture by phase transitions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:1-14. [PMID: 33799013 DOI: 10.1016/j.plaphy.2021.03.046] [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: 07/28/2020] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Plants evolved different strategies to better adapt to the environmental conditions in which they live: the control of their body architecture and the timing of phase change are two important processes that can improve their fitness. As they age, plants undergo two major phase changes (juvenile to adult and adult to reproductive) that are a response to environmental and endogenous signals. These phase transitions are accompanied by alterations in plant morphology and also by changes in physiology and the behavior of gene regulatory networks. Six main pathways involving environmental and endogenous cues that crosstalk with each other have been described as responsible for the control of plant phase transitions: the photoperiod pathway, the autonomous pathway, the vernalization pathway, the temperature pathway, the GA pathway, and the age pathway. However, studies have revealed that sugar is also involved in phase change and the control of branching behavior. In this review, we discuss recent advances in plant biology concerning the genetic and molecular mechanisms that allow plants to regulate phase transitions in response to the environment. We also propose connections between phase transition and plant architecture control.
Collapse
Affiliation(s)
- Helena Augusto Gioppato
- University of Campinas (UNICAMP), Biology Institute, Plant Biology Department, Rua Monteiro Lobato, 255 CEP 13, 083-862, Campinas, SP, Brazil
| | - Marcelo Carnier Dornelas
- University of Campinas (UNICAMP), Biology Institute, Plant Biology Department, Rua Monteiro Lobato, 255 CEP 13, 083-862, Campinas, SP, Brazil.
| |
Collapse
|
31
|
Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22115716. [PMID: 34071961 PMCID: PMC8198774 DOI: 10.3390/ijms22115716] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.
Collapse
|
32
|
Manechini JRV, Santos PHDS, Romanel E, Brito MDS, Scarpari MS, Jackson S, Pinto LR, Vicentini R. Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:635784. [PMID: 34211482 PMCID: PMC8239368 DOI: 10.3389/fpls.2021.635784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/12/2021] [Indexed: 05/11/2023]
Abstract
Flowering is of utmost relevance for the agricultural productivity of the sugarcane bioeconomy, but data and knowledge of the genetic mechanisms underlying its photoperiodic induction are still scarce. An understanding of the molecular mechanisms that regulate the transition from vegetative to reproductive growth in sugarcane could provide better control of flowering for breeding. This study aimed to investigate the transcriptome of +1 mature leaves of a sugarcane cultivar subjected to florally inductive and non-inductive photoperiodic treatments to identify gene expression patterns and molecular regulatory modules. We identified 7,083 differentially expressed (DE) genes, of which 5,623 showed significant identity to other plant genes. Functional group analysis showed differential regulation of important metabolic pathways involved in plant development, such as plant hormones (i.e., cytokinin, gibberellin, and abscisic acid), light reactions, and photorespiration. Gene ontology enrichment analysis revealed evidence of upregulated processes and functions related to the response to abiotic stress, photoprotection, photosynthesis, light harvesting, and pigment biosynthesis, whereas important categories related to growth and vegetative development of plants, such as plant organ morphogenesis, shoot system development, macromolecule metabolic process, and lignin biosynthesis, were downregulated. Also, out of 76 sugarcane transcripts considered putative orthologs to flowering genes from other plants (such as Arabidopsis thaliana, Oryza sativa, and Sorghum bicolor), 21 transcripts were DE. Nine DE genes related to flowering and response to photoperiod were analyzed either at mature or spindle leaves at two development stages corresponding to the early stage of induction and inflorescence primordia formation. Finally, we report a set of flowering-induced long non-coding RNAs and describe their level of conservation to other crops, many of which showed expression patterns correlated against those in the functionally grouped gene network.
Collapse
Affiliation(s)
- João Ricardo Vieira Manechini
- Laboratório de Biologia de Sistemas, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Paulo Henrique da Silva Santos
- Departamento de Genética e Melhoramento de Plantas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo (UNESP), Jaboticabal, Brazil
| | - Elisson Romanel
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, Brazil
| | - Michael dos Santos Brito
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, Brazil
| | | | - Stephen Jackson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Luciana Rossini Pinto
- Departamento de Genética e Melhoramento de Plantas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo (UNESP), Jaboticabal, Brazil
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, Brazil
| | - Renato Vicentini
- Laboratório de Biologia de Sistemas, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Renato Vicentini,
| |
Collapse
|
33
|
Jerome Jeyakumar JM, Ali A, Wang WM, Thiruvengadam M. Characterizing the Role of the miR156-SPL Network in Plant Development and Stress Response. PLANTS 2020; 9:plants9091206. [PMID: 32942558 PMCID: PMC7570127 DOI: 10.3390/plants9091206] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/27/2020] [Accepted: 09/11/2020] [Indexed: 01/22/2023]
Abstract
MicroRNA (miRNA) is a short, single-stranded, non-coding RNA found in eukaryotic cells that can regulate the expression of many genes at the post-transcriptional level. Among various plant miRNAs with diverse functions, miR156 plays a key role in biological processes, including developmental regulation, immune response, metabolic regulation, and abiotic stress. MiRNAs have become the regulatory center for plant growth and development. MicroRNA156 (miR156) is a highly conserved and emerging tool for the improvement of plant traits, including crop productivity and stress tolerance. Fine-tuning of squamosa promoter biding-like (SPL) gene expression might be a useful strategy for crop improvement. Here, we studied the regulation of the miR156 module and its interaction with SPL factors to understand the developmental transition of various plant species. Furthermore, this review provides a strong background for plant biotechnology and is an important source of information for further molecular breeding to optimize farming productivity.
Collapse
Affiliation(s)
- John Martin Jerome Jeyakumar
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Asif Ali
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
- Correspondence:
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, Seoul 05029, Korea;
| |
Collapse
|
34
|
Hamid R, Jacob F, Marashi H, Rathod V, Tomar RS. Uncloaking lncRNA-meditated gene expression as a potential regulator of CMS in cotton (Gossypium hirsutum L.). Genomics 2020; 112:3354-3364. [PMID: 32574832 DOI: 10.1016/j.ygeno.2020.06.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/03/2020] [Accepted: 06/17/2020] [Indexed: 02/01/2023]
Abstract
Cytoplasmic male sterility is a well-proven mechanism for cotton hybrid production. Long non-coding RNAs belong to a class of transcriptional regulators that function in multiple biological processes. The cDNA libraries from the flower buds of the cotton CGMS, it's restorer (Rf) and maintainer lines were sequenced using high throughput NGS technique. A total of 1531 lncRNAs showed significant differential expression patterns between these three lines. Functional analysis of the co-expression network of lncRNA-mRNA using gene ontology vouchsafes that, lncRNAs play a crucial role in cytoplasmic male sterility and fertility restoration through pollen development, INO80 complex, development of anther wall tapetum, chromatin remodeling, and histone modification. Additionally, 94 lncRNAs were identified as putative precursors of 49 miRNAs. qRT-PCR affirms the concordance of expression pattern to RNA-seq data. These findings divulge the lncRNA driven miRNA-mediated regulation of gene expression profiling superintended for a better understanding of the CMS mechanisms of cotton.
Collapse
Affiliation(s)
- Rasmieh Hamid
- Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Iran.
| | - Feba Jacob
- Centre for plant biotechnology and molecular biology, Kerala agricultural university, Thrissur, India
| | - Hassan Marashi
- Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Iran
| | - Visha Rathod
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Rukam S Tomar
- Department of Biotechnology and Biochemistry, Junagadh Agricultural University, Junagadh, Gujarat, India
| |
Collapse
|
35
|
Li F, Shi T, He A, Huang X, Gong J, Yi Y, Zhang J. Bacillus amyloliquefaciens LZ04 improves the resistance of Arabidopsis thaliana to high calcium stress and the potential role of lncRNA-miRNA-mRNA regulatory network in the resistance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:166-180. [PMID: 32222680 DOI: 10.1016/j.plaphy.2020.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/05/2020] [Accepted: 03/17/2020] [Indexed: 05/22/2023]
Abstract
Bacillus amyloliquefaciens is a non-pathogenic and plant growth-promoting rhizobacterium that enhances plant resistance to drought and diseases. Arabidopsis thaliana is a multipurpose model plant for exploring microorganism-plant interactions and a crucial vegetal tool for molecular research. Non-coding RNAs are RNA molecules involved in the regulation of various biological functions and constitute a research hotspot in the field of plant biology. In this study, the effect of B. amyloliquefaciens treatment on the resistance of A. thaliana to high calcium stress was analyzed. The transcriptome sequencing of A. thaliana roots under four treatment conditions was performed to screen differentially expressed lncRNAs, mRNAs and miRNAs. Functional analysis was also performed to understand the potential mechanism by which B. amyloliquefaciens-regulated lncRNAs, miRNAs and mRNAs affect the resistance of A. thaliana to high calcium stress. The results indicated that B. amyloliquefaciens treatment increased the resistance of A. thaliana to high calcium stress. A set of differentially expressed lncRNAs, mRNAs and miRNAs were screened between the high calcium and control group on one hand, and high calcium and high calcium + B. amyloliquefaciens groups on the other hand. Functional analysis indicated that the differentially expressed mRNAs and miRNA were involved in various biological functions and that transcriptional dysregulation caused by high calcium stress involves metabolic processes rather than defense responses. Conclusively, B. amyloliquefaciens may improve the resistance of A. thaliana to high calcium stress via a lncRNA-miRNA-mRNA regulatory network. These findings will contribute to the development of agriculture in karst regions with high calcium content.
Collapse
Affiliation(s)
- Fei Li
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China; Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China
| | - Tianlong Shi
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China; Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China
| | - Aolei He
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Xiaolong Huang
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China; Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China
| | - Jiyi Gong
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China; Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China
| | - Yin Yi
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China; Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, 550001, China.
| | - Jinlin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China.
| |
Collapse
|
36
|
Fan T, Zhang Q, Hu Y, Wang Z, Huang Y. Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering. Funct Integr Genomics 2020; 20:591-607. [PMID: 32215772 DOI: 10.1007/s10142-020-00737-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/04/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022]
Abstract
Non-coding RNAs with lengths greater than 200 bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in which three samples (H0311PF, H0318PF, and H0402PF) represent pre-flowering, flowering, and post-flowering, respectively, while eight male samples collected from May 8th to June 13th as this time course are the key stage for male floral bud differentiation. We identified 2163 lncRNAs in hickory during flowering, containing 213 intronic, 1488 intergenic, and 462 antisense lncRNAs. We noticed that 510 and 648 lncRNAs were differentially expressed corresponding to female and male floral buds, respectively. And some of the lncRNAs were in a tightly tissue-specific or stage-specific manner. To further understand the roles of the lncRNAs, we predicted the function of the lncRNAs in cis- and trans-acting modes. The results showed that 924 lncRNAs were cis-correlated with 1536 protein-coding genes, while 1207 lncRNAs co-expressed (trans-acting) with 7432 protein-coding genes (R > 0.95 or R < - 0.95). These lncRNAs were all enriched in flower development-associated biological processes, i.e., circadian rhythm, vernalization response, response to gibberellin, inflorescence development, floral organ development, etc. To further understand the relationships between lncRNAs and floral-core genes, we build a co-expressing lncRNA-mRNA flowering network. We classified these floral genes into different pathway (photoperiod, vernalization, gibberellin, autonomous, and sucrose pathway) according to their particular functions. We found a set of lncRNAs that preferentially expressed in these pathways. The network showed that some lncRNAs (i.e., XLOC_038669, XLOC_017938) functioned in a particular flowering time pathway, while others (i.e., XLOC_011251, XLOC_04110) were involved in multiple pathway. Furthermore, some lncRNAs (i.e., XLOC_038669, XLOC_009597, and XLOC_049539) played roles in single or multiple pathways via interaction with each other. This study provides a genome-wide survey of hickory flower-related lncRNAs and will contribute to further understanding of the molecular mechanism underpinning flowering in hickory.
Collapse
Affiliation(s)
- Tongqiang Fan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Qixiang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Yuanyuan Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, People's Republic of China.
| | - Youjun Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, People's Republic of China.
| |
Collapse
|
37
|
Waheed S, Zeng L. The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development. Genes (Basel) 2020; 11:genes11030319. [PMID: 32192095 PMCID: PMC7140873 DOI: 10.3390/genes11030319] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/02/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) are non-coding RNAs known as master modulators of gene expression at the post-transcriptional level. Many different miRNA families are involved in flowering-related processes such as the induction of floral competence, floral patterning, and the development of floral organs. This review highlights the diverse roles of miRNAs in controlling the flowering process and flower development, in combination with potential biotechnological applications for miRNAs implicated in flower regulation.
Collapse
Affiliation(s)
- Saquib Waheed
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China;
- Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: or
| |
Collapse
|
38
|
Budak H, Kaya SB, Cagirici HB. Long Non-coding RNA in Plants in the Era of Reference Sequences. FRONTIERS IN PLANT SCIENCE 2020; 11:276. [PMID: 32226437 PMCID: PMC7080850 DOI: 10.3389/fpls.2020.00276] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/21/2020] [Indexed: 05/04/2023]
Abstract
The discovery of non-coding RNAs (ncRNAs), and the subsequent elucidation of their functional roles, was largely delayed due to the misidentification of non-protein-coding parts of DNA as "junk DNA," which forced ncRNAs into the shadows of their protein-coding counterparts. However, over the past decade, insight into the important regulatory roles of ncRNAs has led to rapid progress in their identification and characterization. Of the different types of ncRNAs, long non-coding RNAs (lncRNAs), has attracted considerable attention due to their mRNA-like structures and gene regulatory functions in plant stress responses. While RNA sequencing has been commonly used for mining lncRNAs, a lack of widespread conservation at the sequence level in addition to relatively low and highly tissue-specific expression patterns challenges high-throughput in silico identification approaches. The complex folding characteristics of lncRNA molecules also complicate target predictions, as the knowledge about the interaction interfaces between lncRNAs and potential targets is insufficient. Progress in characterizing lncRNAs and their targets from different species may hold the key to efficient identification of this class of ncRNAs from transcriptomic and potentially genomic resources. In wheat and barley, two of the most important crops, the knowledge about lncRNAs is very limited. However, recently published high-quality genomes of these crops are considered as promising resources for the identification of not only lncRNAs, but any class of molecules. Considering the increasing demand for food, these resources should be used efficiently to discover molecular mechanisms lying behind development and a/biotic stress responses. As our understanding of lncRNAs expands, interactions among ncRNA classes, as well as interactions with the coding sequences, will likely define novel functional networks that may be modulated for crop improvement.
Collapse
Affiliation(s)
- Hikmet Budak
- Montana BioAgriculture, Inc., Bozeman, MT, United States
- *Correspondence: Hikmet Budak,
| | - Sezgi Biyiklioglu Kaya
- Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabancı University, Istanbul, Turkey
| | - Halise Busra Cagirici
- Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabancı University, Istanbul, Turkey
| |
Collapse
|
39
|
Wu Y, Guo J, Wang T, Cao F, Wang G. Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L. BMC PLANT BIOLOGY 2019; 19:527. [PMID: 31783794 PMCID: PMC6884798 DOI: 10.1186/s12870-019-2141-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/15/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood. RESULTS In this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks. CONCLUSIONS This study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.
Collapse
Affiliation(s)
- Yaqiong Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 China
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Jing Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 China
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Tongli Wang
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 China
| |
Collapse
|
40
|
Li D, Zhang H, Mou M, Chen Y, Xiang S, Chen L, Yu D. Arabidopsis Class II TCP Transcription Factors Integrate with the FT-FD Module to Control Flowering. PLANT PHYSIOLOGY 2019; 181:97-111. [PMID: 31235561 PMCID: PMC6716235 DOI: 10.1104/pp.19.00252] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/08/2019] [Indexed: 05/04/2023]
Abstract
The appropriate timing of flowering is critical for plant reproductive success. Although the FLOWERING LOCUS T (FT)-FD module plays crucial roles in the photoperiodic flowering pathway, the underlying mechanisms and signaling pathways involved still remain elusive. Here, we demonstrate that class II TCP transcription factors (TFs) integrate into the FT-FD complex to control floral initiation in Arabidopsis (Arabidopsis thaliana). Class II CINCINNATA (CIN) TCP TFs function as transcriptional activators by directly binding to the promoters of downstream floral meristem identity genes, such as APETALA1 (AP1). In addition, these TCPs directly interact with FD, a basic Leu zipper TF that plays a critical role in photoperiodic flowering, which further activates AP1 expression. Genetic analyses indicated that class II CIN TCP TFs function synergistically with FT and FD, to positively regulate flowering in an AP1-dependent manner. Thus, our results provide compelling evidence that class II CIN TCP TFs act directly at the AP1 promoter to enhance its transcription, thus further elucidating the molecular mechanisms underlying the regulation of photoperiodic flowering in Arabidopsis.
Collapse
Affiliation(s)
- Daibo Li
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Zhang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghui Mou
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanli Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengyuan Xiang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ligang Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| |
Collapse
|
41
|
Hou J, Lu D, Mason AS, Li B, Xiao M, An S, Fu D. Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses. PLANTA 2019; 250:23-40. [PMID: 30993403 DOI: 10.1007/s00425-019-03166-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.
Collapse
Affiliation(s)
- Jinna Hou
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Dandan Lu
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Baoquan Li
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sufang An
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
42
|
Emamjomeh A, Zahiri J, Asadian M, Behmanesh M, Fakheri BA, Mahdevar G. Identification, Prediction and Data Analysis of Noncoding RNAs: A Review. Med Chem 2019; 15:216-230. [PMID: 30484409 DOI: 10.2174/1573406414666181015151610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 06/03/2018] [Accepted: 09/30/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs. OBJECTIVE The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA's roles in cellular processes and drugs design, briefly. METHOD In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases. RESULTS The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs. CONCLUSION ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.
Collapse
Affiliation(s)
- Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Asadian
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Barat A Fakheri
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Ghasem Mahdevar
- Department of Mathematics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| |
Collapse
|
43
|
Li XY, Guo F, Ma SY, Zhu MY, Pan WH, Bian HW. Regulation of flowering time via miR172-mediated APETALA2-like expression in ornamental gloxinia (Sinningia speciosa). J Zhejiang Univ Sci B 2019; 20:322-331. [PMID: 30932377 PMCID: PMC6454313 DOI: 10.1631/jzus.b1800003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/19/2018] [Indexed: 01/14/2023]
Abstract
We investigated the microRNA172 (miR172)-mediated regulatory network for the perception of changes in external and endogenous signals to identify a universally applicable floral regulation system in ornamental plants, manipulation of which could be economically beneficial. Transgenic gloxinia plants, in which miR172 was either overexpressed or suppressed, were generated using Agrobacterium-mediated transformation. They were used to study the effect of altering the expression of this miRNA on time of flowering and to identify its mRNA target. Early or late flowering was observed in transgenic plants in which miR172 was overexpressed or suppressed, respectively. A full-length complementary DNA (cDNA) of gloxinia (Sinningia speciosa) APETALA2-like (SsAP2-like) was identified as a target of miR172. The altered expression levels of miR172 caused up- or down-regulation of SsAP2-like during flower development, which affected the time of flowering. Quantitative real-time reverse transcription PCR analysis of different gloxinia tissues revealed that the accumulation of SsAP2-like was negatively correlated with the expression of miR172a, whereas the expression pattern of miR172a was negatively correlated with that of miR156a. Our results suggest that transgenic manipulation of miR172 could be used as a universal strategy for regulating time of flowering in ornamental plants.
Collapse
Affiliation(s)
- Xiao-yan Li
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sheng-yun Ma
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mu-yuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei-huai Pan
- College of Life Sciences, Shaoxing University, Shaoxing 312000, China
| | - Hong-wu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
44
|
Zhang W, Abdelrahman M, Jiu S, Guan L, Han J, Zheng T, Jia H, Song C, Fang J, Wang C. VvmiR160s/VvARFs interaction and their spatio-temporal expression/cleavage products during GA-induced grape parthenocarpy. BMC PLANT BIOLOGY 2019; 19:111. [PMID: 30898085 PMCID: PMC6429806 DOI: 10.1186/s12870-019-1719-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/14/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Grape (Vitis vinifera) is highly sensitive to gibberellin (GA), which effectively induce grape parthenocarpy. Studies showed that miR160s and their target AUXIN RESPONSIVE FACTOR (ARF) responding hormones are indispensable for various aspects of plant growth and development, but their functions in GA-induced grape parthenocarpy remain elusive. RESULTS In this study, the morphological changes during flower development in response to GA treatments were examined in the 'Rosario Bianco' cultivar. The precise sequences of VvmiR160a/b/c/d/e and their VvARF10/16/17 target genes were cloned, sequenced and characterized. The phylogenetic relationship and intron-exon structure of VvARFs and other ARF family members derived from different species were investigated. All VvmiR160s (except VvmiR160b) and VvARF10/16/17 had the common cis-elements responsive to GA, which support their function in GA-mediated grape parthenocarpy. The cleavage role of VvmiR160s-mediated VvARF10/16/17 was verified in grape flowers. Moreover, spatio-temporal expression analysis demonstrated that among VvmiR160 family, VvmiR160a/b/c highly expressed at late stage of flower/berry development, while VvARF10/16/17showed a reverse expression trend. Interestingly, GA exhibited a long-term effect through inducing the expression of VvmiR160a/b/c/e to increase their cleavage product accumulations from 5 to 9 days after treatment, but GA enhanced the expressions of VvARF10/16/17 only at short term. Pearson correlation analysis based on expression data revealed a negative correlation between VvmiR160a/b/c and VvARF10/16/17 in flowers not berries during GA-induced grape parthenocarpy. CONCLUSIONS This work demonstrated that the negative regulation of VvARF10/16/17 expression by VvmiR160a/b/c as key regulatory factors is critical for GA-mediated grape parthenocarpy, and provide significant implications for molecular breeding of high-quality seedless berry.
Collapse
Affiliation(s)
- Wenying Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Mostafa Abdelrahman
- Department of Botany, Faculty of Sciences, Aswan University, Aswan, 81528 Egypt
- Arid Land Research Center, Tottori University, Tottori, 680-001 Japan
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Le Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jian Han
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ting Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Haifeng Jia
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Changnian Song
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
45
|
Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine. Sci Rep 2019; 9:3552. [PMID: 30837504 PMCID: PMC6401051 DOI: 10.1038/s41598-019-38989-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes–i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like ‘photosynthesis’ and ‘oxidative phosphorylation’. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.
Collapse
|
46
|
Ortuño-Miquel S, Rodríguez-Cazorla E, Zavala-Gonzalez EA, Martínez-Laborda A, Vera A. Arabidopsis HUA ENHANCER 4 delays flowering by upregulating the MADS-box repressor genes FLC and MAF4. Sci Rep 2019; 9:1478. [PMID: 30728422 PMCID: PMC6365585 DOI: 10.1038/s41598-018-38327-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022] Open
Abstract
The adaptive success of flowering plants is largely due to their ability to align floral production with optimal conditions. In Arabidopsis thaliana, MADS-box repressors of the FLC/MAF-clade prevent flowering under non-inductive conditions, although the role of some members is not yet clearly defined. Using a genetic strategy, we identified the KH-domain gene HEN4, previously shown to be involved in MADS-box floral homeotic gene regulation, as a modulator of flowering time. Loss-of-function hen4 mutants are early-flowering, and their response to low growth-temperature (16 °C) and day-length is altered. Interestingly, hen4 plants showed dramatic reduction of FLC and MAF4 transcripts, whereas other flowering repressors of the same clade (FLM, MAF2, MAF3, MAF5) remained unaltered. We also determined that hen4, partly due to loss of FLC, accelerates the vegetative phase-change. This report provides insight into flowering time control and highlights the potential of versatile regulators such as HEN4 to coordinate the juvenile-to-adult transition and floral timing.
Collapse
Affiliation(s)
- Samanta Ortuño-Miquel
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain
| | | | | | | | - Antonio Vera
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain.
| |
Collapse
|
47
|
Gahlaut V, Baranwal VK, Khurana P. miRNomes involved in imparting thermotolerance to crop plants. 3 Biotech 2018; 8:497. [PMID: 30498670 DOI: 10.1007/s13205-018-1521-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/17/2018] [Indexed: 12/20/2022] Open
Abstract
Thermal stress is one of the challenges to crop plants that negatively impacts crop yield. To overcome this ever-growing problem, utilization of regulatory mechanisms, especially microRNAs (miRNAs), that provide efficient and precise regulation in a targeted manner have been found to play determining roles. Besides their roles in plant growth and development, many recent studies have shown differential regulation of several miRNAs during abiotic stresses including heat stress (HS). Thus, understanding the underlying mechanism of miRNA-mediated gene expression during HS will enable researchers to exploit this regulatory mechanism to address HS responses. This review focuses on the miRNAs and regulatory networks that were involved in physiological, metabolic and morphological adaptations during HS in plant, specifically in crops. Illustrated examples including, the miR156-SPL, miR169-NF-YA5, miR395-APS/AST, miR396-WRKY, etc., have been discussed in specific relation to the crop plants. Further, we have also discussed the available plant miRNA databases and bioinformatics tools useful for miRNA identification and study of their regulatory role in response to HS. Finally, we have briefly discussed the future prospects about the miRNA-related mechanisms of HS for improving thermotolerance in crop plants.
Collapse
Affiliation(s)
- Vijay Gahlaut
- 1Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Vinay Kumar Baranwal
- 1Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- Department of Botany, Swami Devanand Post Graduate College, Math-lar, Lar, Deoria, Uttar Pradesh 274502 India
| | - Paramjit Khurana
- 1Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| |
Collapse
|
48
|
Chen Y, Li X, Su L, Chen X, Zhang S, Xu X, Zhang Z, Chen Y, XuHan X, Lin Y, Lai Z. Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour. BMC Genomics 2018; 19:805. [PMID: 30400813 PMCID: PMC6219066 DOI: 10.1186/s12864-018-5158-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 10/11/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development. RESULTS In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a). CONCLUSION Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE.
Collapse
Affiliation(s)
- Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xue Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Liyao Su
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| |
Collapse
|
49
|
Cardoso TCDS, Alves TC, Caneschi CM, Santana DDRG, Fernandes-Brum CN, Reis GLD, Daude MM, Ribeiro THC, Gómez MMD, Lima AA, Gomes LAA, Gomes MDS, Gandolfi PE, Amaral LRD, Chalfun-Júnior A, Maluf WR, de Souza Gomes M. New insights into tomato microRNAs. Sci Rep 2018; 8:16069. [PMID: 30375421 PMCID: PMC6207730 DOI: 10.1038/s41598-018-34202-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.
Collapse
Affiliation(s)
- Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Tamires Caixeta Alves
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Carolina Milagres Caneschi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Douglas Dos Reis Gomes Santana
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | | | - Gabriel Lasmar Dos Reis
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus Martins Daude
- Laboratory of Molecular Analysis, Federal University of Tocantins (UFT), Gurupi, 77402-970, Brazil
| | | | - Miguel Maurício Díaz Gómez
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - André Almeida Lima
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | | | - Marcos de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Peterson Elizandro Gandolfi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Antonio Chalfun-Júnior
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | - Wilson Roberto Maluf
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil.
| |
Collapse
|
50
|
Huang F, Wu X, Hou X, Shao S, Liu T. Vernalization can regulate flowering time through microRNA mechanism in Brassica rapa. PHYSIOLOGIA PLANTARUM 2018; 164:204-215. [PMID: 29345323 DOI: 10.1111/ppl.12692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 06/07/2023]
Abstract
Vernalization is an important process that regulates the floral transition in plants. MicroRNAs (miRNAs) are endogenous non-coding small RNA (sRNA) molecules that function in plant growth and development. Despite that miRNAs related to flowering have previously been characterized, their roles in response to vernalization in pak-choi (Brassica rapa ssp. chinensis) has never been studied. Here, two sRNA libraries from B. rapa leaves (vernalized and non-vernalized plants) were constructed and sequenced. Two hundred eight known and 535 novel miRNAs were obtained, of which 20 known and 66 new miRNAs were significantly differentially expressed and considered as vernalization-related miRNAs. The corresponding targets were predicted on the basic of sequence homology search. In addition, 11 miRNAs and eight targets were selected for real-time quantitative PCR to confirm their expression profiles. Functional annotation of targets using gene ontology and Kyoto encyclopedia of genes and genomes results suggested that most targets were significantly enriched in the hormone signaling pathway. Moreover, a decreased indole-3-acetic acid (IAA) and an increased GA3 hormone were detected after vernalization, indicating that the IAA and GA3 might response to vernalization. These results indicated that vernalization regulates flowering through microRNA mechanism by affecting endogenous hormone level in B. rapa. This study provides useful insights of promising miRNAs candidates involved in vernalization in B. rapa, and facilitates further investigation of the miRNA-mediated molecular mechanisms of vernalization in B. rapa.
Collapse
Affiliation(s)
- Feiyi Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoting Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuaixu Shao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|