1
|
Wang P, Wu Y, Zhang J, Si J, Wang X, Jiao Z, Meng X, Zhang L, Meng F, Li Y. TaMIR397-6A and -6B Homoeologs Encode Active miR397 Contributing to the Regulation of Grain Size in Hexaploid Wheat. Int J Mol Sci 2024; 25:7696. [PMID: 39062941 PMCID: PMC11276883 DOI: 10.3390/ijms25147696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Wheat is one of the most important food crops globally, and understanding the regulation of grain size is crucial for wheat breeding to achieve a higher grain yield. MicroRNAs (miRNAs) play vital roles in plant growth and development. However, the miRNA-mediated mechanism underlying grain size regulation remains largely elusive in wheat. Here, we report the characterization and functional validation of a miRNA, TamiR397a, associated with grain size regulation in wheat. The function of three TaMIR397 homoeologs was determined through histochemical β-glucuronidase-dependent assay. MiRNA expression was detected using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and the function of TamiR397a was validated through its transgenic overexpression and repression in wheat. It was found that TaMIR397-6A and TaMIR397-6B encode active TamiR397a. The expression profiling indicated that TamiR397a was differentially expressed in various tissues and gradually up-regulated during grain filling. The inhibition of TamiR397a perturbed grain development, leading to a decrease in grain size and weight. Conversely, the overexpression of TamiR397a resulted in increased grain size and weight by accelerating the grain filling process. Transcriptome analysis revealed that TamiR397a regulates a set of genes involved in hormone response, desiccation tolerance, regulation of cellular senescence, seed dormancy, and seed maturation biological processes, which are important for grain development. Among the down-regulated genes in the grains of the TamiR397a-overexpressing transgenic plants, 11 putative targets of the miRNA were identified. Taken together, our results demonstrate that TamiR397a is a positive regulator of grain size and weight, offering potential targets for breeding wheat with an increased grain yield.
Collapse
Affiliation(s)
- Putong Wang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Yujie Wu
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Junhui Zhang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiao Si
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoteng Wang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhongfa Jiao
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaodan Meng
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Li Zhang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Fanrong Meng
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yongchun Li
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| |
Collapse
|
2
|
Wang M, Wang L, Wang S, Zhang J, Fu Z, Wu P, Yang A, Wu D, Sun G, Wang C. Identification and Analysis of lncRNA and circRNA Related to Wheat Grain Development. Int J Mol Sci 2024; 25:5484. [PMID: 38791522 PMCID: PMC11122269 DOI: 10.3390/ijms25105484] [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: 04/14/2024] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The role of lncRNA and circRNA in wheat grain development is still unclear. The objectives of this study were to characterize the lncRNA and circRNA in the wheat grain development and to construct the interaction network among lncRNA, circRNA, and their target miRNA to propose a lncRNA-circRNA-miRNA module related to wheat grain development. Full transcriptome sequencing on two wheat varieties (Annong 0942 and Anke 2005) with significant differences in 1000-grain weight at 10 d (days after pollination), 20 d, and 30 d of grain development were conducted. We detected 650, 736, and 609 differentially expressed lncRNA genes, and 769, 1054, and 1062 differentially expressed circRNA genes in the grains of 10 days, 20 days and 30 days after pollination between Annong 0942 and Anke 2005, respectively. An analysis of the lncRNA-miRNA and circRNA-miRNA targeting networks reveals that circRNAs exhibit a more complex and extensive interaction network in the development of cereal grains and the formation of grain shape. Central to these interactions are tae-miR1177, tae-miR1128, and tae-miR1130b-3p. In contrast, lncRNA genes only form a singular network centered around tae-miR1133 and tae-miR5175-5p when comparing between varieties. Further analysis is conducted on the underlying genes of all target miRNAs, we identified TaNF-YB1 targeted by tae-miR1122a and TaTGW-7B targeted by miR1130a as two pivotal regulatory genes in the development of wheat grains. The quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays confirmed the target regulatory relationships between miR1130a-TaTGW-7B and miR1122a-TaNF-YB1. We propose a network of circRNA and miRNA-mediated gene regulation in the development of wheat grains.
Collapse
Affiliation(s)
- Meng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Lu Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Shuanghong Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Junli Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Zhe Fu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Panpan Wu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Anqi Yang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
| | - Chengyu Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| |
Collapse
|
3
|
Saroha M, Arya A, Singh G, Sharma P. Genome-wide expression analysis of novel heat-responsive microRNAs and their targets in contrasting wheat genotypes at reproductive stage under terminal heat stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1328114. [PMID: 38660446 PMCID: PMC11039868 DOI: 10.3389/fpls.2024.1328114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Introduction Heat stress at terminal stage of wheat is critical and leads to huge yield losses worldwide. microRNAs (miRNAs) play significant regulatory roles in gene expression associated with abiotic and biotic stress at the post-transcriptional level. Methods In the present study, we carried out a comparative analysis of miRNAs and their targets in flag leaves as well as developing seeds of heat tolerant (RAJ3765) and heat susceptible (HUW510) wheat genotypes under heat stress and normal conditions using small RNA and degradome sequencing. Results and discussion A total of 84 conserved miRNAs belonging to 35 miRNA families and 93 novel miRNAs were identified in the 8 libraries. Tae-miR9672a-3p, tae-miR9774, tae-miR9669-5p, and tae-miR5048-5p showed the highest expression under heat stress. Tae-miR9775, tae-miR9662b-3p, tae-miR1120a, tae-miR5084, tae-miR1122a, tae-miR5085, tae-miR1118, tae-miR1130a, tae-miR9678-3p, tae-miR7757-5p, tae-miR9668-5p, tae-miR5050, tae-miR9652-5p, and tae-miR9679-5p were expressed only in the tolerant genotype, indicating their role in heat tolerance. Comparison between heat-treated and control groups revealed that 146 known and 57 novel miRNAs were differentially expressed in the various tissues. Eight degradome libraries sequence identified 457 targets of the differentially expressed miRNAs. Functional analysis of the targets indicated their involvement in photosynthesis, spliceosome, biosynthesis of nucleotide sugars and protein processing in the endoplasmic reticulum, arginine and proline metabolism and endocytosis. Conclusion This study increases the number of identified and novel miRNAs along with their roles involved in heat stress response in contrasting genotypes at two developing stages of wheat.
Collapse
Affiliation(s)
- Monika Saroha
- Department of Biotechnology, ICAR Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Haryana, India
| | - Aditi Arya
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Haryana, India
| | - Gyanendra Singh
- Department of Biotechnology, ICAR Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Pradeep Sharma
- Department of Biotechnology, ICAR Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| |
Collapse
|
4
|
Yang F, Sun X, Wu G, He X, Liu W, Wang Y, Sun Q, Zhao Y, Xu D, Dai X, Ma W, Zeng J. Genome-Wide Identification and Expression Profiling of the ABF Transcription Factor Family in Wheat ( Triticum aestivum L.). Int J Mol Sci 2024; 25:3783. [PMID: 38612594 PMCID: PMC11011718 DOI: 10.3390/ijms25073783] [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: 02/18/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Members of the abscisic acid (ABA)-responsive element (ABRE) binding factor (ABF) and ABA-responsive element binding protein (AREB) families play essential roles in the regulation of ABA signaling pathway activity and shape the ability of plants to adapt to a range of stressful environmental conditions. To date, however, systematic genome-wide analyses focused on the ABF/AREB gene family in wheat are lacking. Here, we identified 35 ABF/AREB genes in the wheat genome, designated TaABF1-TaABF35 according to their chromosomal distribution. These genes were further classified, based on their phylogenetic relationships, into three groups (A-C), with the TaABF genes in a given group exhibiting similar motifs and similar numbers of introns/exons. Cis-element analyses of the promoter regions upstream of these TaABFs revealed large numbers of ABREs, with the other predominant elements that were identified differing across these three groups. Patterns of TaABF gene expansion were primarily characterized by allopolyploidization and fragment duplication, with purifying selection having played a significant role in the evolution of this gene family. Further expression profiling indicated that the majority of the TaABF genes from groups A and B were highly expressed in various tissues and upregulated following abiotic stress exposure such as drought, low temperature, low nitrogen, etc., while some of the TaABF genes in group C were specifically expressed in grain tissues. Regulatory network analyses revealed that four of the group A TaABFs (TaABF2, TaABF7, TaABF13, and TaABF19) were centrally located in protein-protein interaction networks, with 13 of these TaABF genes being regulated by 11 known miRNAs, which play important roles in abiotic stress resistance such as drought and salt stress. The two primary upstream transcription factor types found to regulate TaABF gene expression were BBR/BPC and ERF, which have previously been reported to be important in the context of plant abiotic stress responses. Together, these results offer insight into the role that the ABF/AREB genes play in the responses of wheat to abiotic stressors, providing a robust foundation for future functional studies of these genes.
Collapse
Affiliation(s)
- Fuhui Yang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuelian Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Gang Wu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyan He
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenxing Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongmei Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qingyi Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yan Zhao
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuehuan Dai
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wujun Ma
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
| | - Jianbin Zeng
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
| |
Collapse
|
5
|
Han S, Han X, Qi C, Guo F, Yin J, Liu Y, Zhu Y. Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale. Int J Mol Sci 2024; 25:929. [PMID: 38256002 PMCID: PMC10815606 DOI: 10.3390/ijms25020929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.
Collapse
Affiliation(s)
- Shuo Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Xiaowen Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Chuandong Qi
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Fengling Guo
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Junliang Yin
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yiqing Liu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yongxing Zhu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| |
Collapse
|
6
|
Abasi F, Raja NI, Mashwani ZUR, Ehsan M, Ali H, Shahbaz M. Heat and Wheat: Adaptation strategies with respect to heat shock proteins and antioxidant potential; an era of climate change. Int J Biol Macromol 2024; 256:128379. [PMID: 38000583 DOI: 10.1016/j.ijbiomac.2023.128379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
Extreme changes in weather including heat-wave and high-temperature fluctuations are predicted to increase in intensity and duration due to climate change. Wheat being a major staple crop is under severe threat of heat stress especially during the grain-filling stage. Widespread food insecurity underscores the critical need to comprehend crop responses to forthcoming climatic shifts, pivotal for devising adaptive strategies ensuring sustainable crop productivity. This review addresses insights concerning antioxidant, physiological, molecular impacts, tolerance mechanisms, and nanotechnology-based strategies and how wheat copes with heat stress at the reproductive stage. In this study stress resilience strategies were documented for sustainable grain production under heat stress at reproductive stage. Additionally, the mechanisms of heat resilience including gene expression, nanomaterials that trigger transcription factors, (HSPs) during stress, and physiological and antioxidant traits were explored. The most reliable method to improve plant resilience to heat stress must include nano-biotechnology-based strategies, such as the adoption of nano-fertilizers in climate-smart practices and the use of advanced molecular approaches. Notably, the novel resistance genes through advanced molecular approach and nanomaterials exhibit promise for incorporation into wheat cultivars, conferring resilience against imminent adverse environmental conditions. This review will help scientific communities in thermo-tolerance wheat cultivars and new emerging strategies to mitigate the deleterious impact of heat stress.
Collapse
Affiliation(s)
- Fozia Abasi
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan.
| | - Naveed Iqbal Raja
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan.
| | | | - Maria Ehsan
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Habib Ali
- Department of Agronomy, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Muhammad Shahbaz
- Institute for Tropical Biology and Conservation (ITBC), Universiti Malaysia Sabah, 88400 Kota Kinabalu, Malaysia
| |
Collapse
|
7
|
Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
Collapse
Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
| |
Collapse
|
8
|
Adavi B S, Pandesha PH, B J, Jha SK, Chinnusamy V, Sathee L. Nitrate supply regulates tissue calcium abundance and transcript level of Calcineurin B-like (CBL) gene family in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107724. [PMID: 37172401 DOI: 10.1016/j.plaphy.2023.107724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Calcium ion (Ca2+) is the most ubiquitous signalling molecule and is sensed by different classes of Ca2+ sensor proteins. Recent evidences underscore the role of calcium signalling in plant response to nitrogen/nitrate supply. Recently we found that under nitrate deficiency, a short-term supply of calcium could improve the plant biomass, nitrate assimilation, anthocyanin accumulation and expression of nitrate uptake and signalling genes. Long-term calcium supply, on the other hand, was not beneficial. Calcineurin B-like (CBL) proteins are one of the vital plant Ca2+ sensory protein family which is essential for stress perception and signaling. To understand the dynamics of CBL-mediated stress signalling in bread wheat, we identified CBL genes in bread wheat (Triticum aestivum) and its progenitors, namely Triticum dicoccoides, Triticum urartu and Aegilops tauschii with the aid of newly available whole-genome sequence. The expression of different CBLs and the changes in root Ca2+ localization in response to nitrate provision or deficiency were analysed. Expression of the CBLs were studied in two bread wheat genotypes with comparatively higher (B.T. Schomburgk, BTS) and lower (Gluyas early, GE) nitrate responsiveness and nitrogen use efficiency. High N promoted the expression of CBLs in seedling leaves while in roots the expression was promoted by N deficiency. At the 5 days after anthesis stage, nitrate starvation downregulated the expression of CBLs while nitrate supply enhanced the expression. At anthesis stage, expression of CBL6 was significantly promoted by HN in panicles of both the genotypes, the highest expression was recorded in BTS. Expression of CBL6 was significantly upregulated by short term nitrate treatment also suggesting its role in Primary nitrate response (PNR) in wheat. There was a significant down regulation of CBL6 expression post nitrate starvation, making it a probable regulator of nitrogen starvation response (NSR) as well. In seedling roots, the tissue localization of Ca2+ was increased both by high and low nitrate treatments, albeit at different magnitudes. Our results suggest that calcium signalling might be a major signalling pathway governing nitrogen responsiveness and CBL6 might be playing pivotal role in NSR and PNR in wheat.
Collapse
Affiliation(s)
- Sandeep Adavi B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pratheek H Pandesha
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jagadhesan B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra K Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| |
Collapse
|
9
|
Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses. Int J Mol Sci 2023; 24:ijms24032226. [PMID: 36768565 PMCID: PMC9917100 DOI: 10.3390/ijms24032226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/10/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs at a large scale. Wheat is among the leading food staples worldwide whose production is threatened by both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense against wheat stem sawfly, a devastating insect pest. We also analyzed and annotated lncRNAs from two bread wheat varieties, resistant and susceptible to another destructive pest, orange wheat blossom midge, with and without infestation. Several putative lncRNAs contained potential precursor sequences and/or target regions for microRNAs, another type of regulatory noncoding RNAs, which may indicate functional networks. Interestingly, in contrast to lncRNAs themselves, microRNAs with potential precursors within the lncRNA sequences appeared to be highly conserved at the sequence and family levels. We also observed a few putative lncRNAs that have perfect to near-perfect matches to organellar genomes, supporting the recent observations that organellar genomes may contribute to the noncoding transcript pool of the cell.
Collapse
|
10
|
Gómez-Martín C, Zhou H, Medina JM, Aparicio-Puerta E, Hackenberg M, Shi B. Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits. Funct Integr Genomics 2022; 23:15. [PMID: 36562829 DOI: 10.1007/s10142-022-00920-1] [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: 06/29/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Wheat is one of the most important food sources on Earth. MicroRNAs (miRNA) play important roles in wheat productivity. To identify wheat miRNAs, we constructed and sequenced sRNA libraries from leaves and roots of two wheat cultivars (RAC875 and Kukri) with many different traits. Given that available miRNA wheat complement in the plant-specific database PmiREN ( https://pmiren.com ) does not include root tissues and root-associated miRNAs might thus be missing, we performed first the prediction of novel miRNAs using the sRNAbench tool. We found a total of 150 putatively novel miRNA genes with expression of both arms from 289 unique mature sequences and nearly 30% of all miRNA reads in roots corresponded to novel miRNAs. In contrast, this figure in leaves dropped to under 3%, confirming the undersampling of roots in the complement of known miRNAs. By using 120 publicly available wheat datasets, 598 Zea mays small RNA libraries, 64 plant species genomes, wheat degradome library, and functional enrichment analysis, a subset of novel miRNAs were confirmed as bona-fide miRNAs. Of the total 605 miRNAs identified in this study inclusive of 316 known miRNAs, 528 miRNAs were shared by both cultivars, 429 miRNAs were shared by both root tissues and 329 miRNAs were shared by both leaf tissues. In addition, 32 miRNAs were specific to Kukri while 45 miRNAs were specific to RAC875. These miRNAs had diverse functions, such as regulation of gene transcription, protein translation, energy metabolism, and cell cycle progression. Our data provide a genome-wide miRNA expression profile in these two wheat cultivars and help functional studies of wheat genomics.
Collapse
Affiliation(s)
- Cristina Gómez-Martín
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Hui Zhou
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - José Maria Medina
- Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain.,Bioinformatics Laboratory, Centro de Investigación Biomédica, Biotechnology Institute, PTS, Avda. del Conocimiento S/N, 18100, Granada, Spain
| | - Ernesto Aparicio-Puerta
- Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain.,Bioinformatics Laboratory, Centro de Investigación Biomédica, Biotechnology Institute, PTS, Avda. del Conocimiento S/N, 18100, Granada, Spain.,Instituto de Investigación Biosanitaria Ibs.GRANADA, University of Granada, 18071, Granada, Spain.,Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071, Granada, Spain
| | - Michael Hackenberg
- Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain. .,Bioinformatics Laboratory, Centro de Investigación Biomédica, Biotechnology Institute, PTS, Avda. del Conocimiento S/N, 18100, Granada, Spain. .,Instituto de Investigación Biosanitaria Ibs.GRANADA, University of Granada, 18071, Granada, Spain. .,Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071, Granada, Spain.
| | - Bujun Shi
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia.
| |
Collapse
|
11
|
Wu B, Zhang X, Hu K, Zheng H, Zhang S, Liu X, Ma M, Zhao H. Two alternative splicing variants of a wheat gene TaNAK1, TaNAK1.1 and TaNAK1.2, differentially regulate flowering time and plant architecture leading to differences in seed yield of transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1014176. [PMID: 36531344 PMCID: PMC9751850 DOI: 10.3389/fpls.2022.1014176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
In wheat production, appropriate flowering time and ideal plant architecture are the prerequisites for high grain yield. Alternative splicing (AS) is a vital process that regulates gene expression at the post-transcriptional level, and AS events in wheat have been found to be closely related to grain-related traits and abiotic stress tolerance. However, AS events and their biological roles in regulating flowering time and plant architecture in wheat remain unclear. In this study, we report that TaNAK1 undergoes AS, producing three splicing variants. Molecular characterization of TaNAK1 and its splicing variants demonstrated that all three protein isoforms have a conserved NB-ARC domain and a protein kinase domain, but the positions of these two domains and the length of the protein kinase domains are different among them, implying that they may have different three-dimensional structures and therefore have different functions. Further investigations showed that the two splicing variants of TaNAK1, TaNAK1.1 and TaNAK1.2, exhibited different expression patterns during wheat growth and development, while the other one, TaNAK1.3, was not detected. Subcellular localization demonstrated that TaNAK1.1 was mainly localized in the cytoplasm, while TaNAK1.2 was localized in the nucleus and cytoplasm. Both TaNAK1.1 and TaNAK1.2 exhibit protein kinase activity in vitro. Ectopic expression of TaNAK1.1 and TaNAK1.2 in Arabidopsis demonstrated that these two splicing variants play opposite roles in regulating flowering time and plant architecture, resulting in different seed yields. TaNAK1.2 positive regulates the transition from vegetative to reproductive growth, plant height, branching number, seed size, and seed yield of Arabidopsis, while TaNAK1.1 negatively regulates these traits. Our findings provide new gene resource for regulating flowering time and plant architecture in crop breeding for high grain yield.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Meng Ma
- *Correspondence: Huixian Zhao, ; Meng Ma,
| | | |
Collapse
|
12
|
Mueth NA, Hulbert SH. Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction. Genomics 2022; 114:110526. [PMID: 36427746 DOI: 10.1016/j.ygeno.2022.110526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The wheat stripe rust fungus (Puccinia striiformis f.sp. tritici) threatens global wheat production. Small RNAs (sRNAs) modulate plant defense induction, and RNA exchange between host and microbe causes cross-kingdom gene silencing, but few examples are known in rust fungi. This study combined sRNA, parallel analysis of RNA ends, and gene expression data to discover sRNA-target pairs on each side of the interaction. Specific wheat 24 nt sRNAs were suppressed, while particular 35 nt fragments were strongly induced upon infection. Wheat sRNAs cleaved fungal transcripts coding for a ribosomal protein and a glycosyl hydrolase effector. Fungal microRNA-like and phased 21 nt sRNAs originated from long inverted repeats near protein coding genes. Fungal sRNAs targeted native transcripts: transposons and kinases; and cross-kingdom transcripts: a wheat nucleotide-binding domain leucine-rich repeat receptor (NLR) and multiple defense-related transcription factor families. This work sheds light on host-microbe coevolution and delivers prospects for developing pathogen control biotechnology.
Collapse
Affiliation(s)
- Nicholas A Mueth
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA.
| | - Scot H Hulbert
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
| |
Collapse
|
13
|
Identification of miRNAs Mediating Seed Storability of Maize during Germination Stage by High-Throughput Sequencing, Transcriptome and Degradome Sequencing. Int J Mol Sci 2022; 23:ijms232012339. [PMID: 36293196 PMCID: PMC9604548 DOI: 10.3390/ijms232012339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Seed storability is an important trait for improving grain quality and germplasm conservation, but little is known about the regulatory mechanisms and gene networks involved. MicroRNAs (miRNAs) are small non-coding RNAs regulating the translation and accumulation of their target mRNAs by means of sequence complementarity and have recently emerged as critical regulators of seed germination. Here, we used the germinating embryos of two maize inbred lines with significant differences in seed storability to identify the miRNAs and target genes involved. We identified a total of 218 previously known and 448 novel miRNAs by miRNA sequencing and degradome analysis, of which 27 known and 11 newly predicted miRNAs are differentially expressed in two maize inbred lines, as measured by Gene Ontology (GO) enrichment analysis. We then combined transcriptome sequencing and real-time quantitative polymerase chain reaction (RT-PCR) to screen and confirm six pairs of differentially expressed miRNAs associated with seed storability, along with their negative regulatory target genes. The enrichment analysis suggested that the miRNAs/target gene mediation of seed storability occurs via the ethylene activation signaling pathway, hormone synthesis and signal transduction, as well as plant organ morphogenesis. Our results should help elucidate the mechanisms through which miRNAs are involved in seed storability in maize.
Collapse
|
14
|
Badoni S, Parween S, Henry RJ, Sreenivasulu N. Systems seed biology to understand and manipulate rice grain quality and nutrition. Crit Rev Biotechnol 2022:1-18. [PMID: 35723584 DOI: 10.1080/07388551.2022.2058460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
Collapse
Affiliation(s)
- Saurabh Badoni
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Sabiha Parween
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Robert J Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| |
Collapse
|
15
|
Zhang L, Wang K, Han Y, Yan L, Zheng Y, Bi Z, Zhang X, Zhang X, Min D. Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.). BMC Genomics 2022; 23:292. [PMID: 35410124 PMCID: PMC8996428 DOI: 10.1186/s12864-022-08519-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND VQ motif-containing (VQ) proteins are cofactors of transcriptional regulation that are widely involved in plant growth and development and respond to various stresses. The VQ gene family has been identified and characterized for many plants, but there is little research on VQ gene family proteins in wheat (Triticum aestivum L.). RESULTS In this study, 113 TaVQ genes (40 homoeologous groups) were identified in the wheat genome. TaVQ proteins all contain the conserved motif FxxhVQxhTG, and most of the TaVQ genes do not contain introns. Phylogenetic analysis demonstrated that TaVQ proteins can be divided into 8 subgroups (I-VIII). The chromosomal location mapping analysis indicated that TaVQ genes are disproportionally distributed on 21 wheat chromosomes. Gene duplication analysis revealed that segmental duplication significantly contributes to the expansion of the TaVQ gene family. Gene expression analysis demonstrated that the expression pattern of TaVQ genes varies in different tissues. The results of quantitative real-time PCR (qRT-PCR) found that TaVQ genes displayed different expression levels under different phytohormones and abiotic stresses. The cis-elements analysis of the promoter region demonstrated that stress responses, hormone responses, growth and development, and WRKY binding elements are all widely distributed. Additionally, a potential regulatory network between TaVQ proteins and WRKY transcription factors was visualized. CONCLUSION This study systematically analyzed the wheat TaVQ gene family, providing a reference for further functional characterization of TaVQ genes in wheat.
Collapse
Affiliation(s)
- Lili Zhang
- College of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Shaanxi, Yangling, China
| | - Keke Wang
- College of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Shaanxi, Yangling, China
| | - Yuxuan Han
- College of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Shaanxi, Yangling, China
| | - Luyu Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yan Zheng
- College of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Shaanxi, Yangling, China
| | - Zhenzhen Bi
- College of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Shaanxi, Yangling, China
| | - Xin Zhang
- College of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Shaanxi, Yangling, China
| | - Xiaohong Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Donghong Min
- College of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Shaanxi, Yangling, China.
| |
Collapse
|
16
|
Identification of Sex Differentiation-Related microRNAs in Spinach Female and Male Flower. Int J Mol Sci 2022; 23:ijms23084090. [PMID: 35456907 PMCID: PMC9029227 DOI: 10.3390/ijms23084090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
Sex determination and differentiation is an important biological process for unisexual flower development. Spinach is a model plant to study the mechanism of sex determination and differentiation of dioecious plant. Till now, little is known about spinach sex determination and differentiation mechanism. MicroRNAs are key factors in flower development. Herein, small RNA sequencing was performed to explore the roles of microRNAs in spinach sex determination and differentiation. As a result, 92 known and 3402 novel microRNAs were identified in 18 spinach female and male flower samples. 74 differentially expressed microRNAs were identified between female and male flowers, including 20 female-biased and 48 male-biased expression microRNAs. Target prediction identified 22 sex-biased microRNA-target pairs, which may be involved in spinach sex determination or differentiation. Among the differentially expressed microRNAs between FNS and M03, 55 microRNAs were found to reside in sex chromosome; one of them, sol-miR2550n, was functionally studied via genetic transformation. Silencing of sol-miR2550n resulted in abnormal anther while overexpression of sol-miR2550n induced early flowering, indicating sol-miR2550n was a male-promoting factor and validating the reliability of our small RNA sequencing data. Conclusively, this work can supply valuable information for exploring spinach sex determination and differentiation and provide a new insight in studying unisexual flower development.
Collapse
|
17
|
Sánchez-Romo D, Hernández-Vásquez CI, Pereyra-Alférez B, García-García JH. Identification of potential target genes in Homo sapiens, by miRNA of Triticum aestivum: A cross kingdom computational approach. Noncoding RNA Res 2022; 7:89-97. [PMID: 35387280 PMCID: PMC8961073 DOI: 10.1016/j.ncrna.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
Plant-derived miRNAs can be found in the human body after dietary intake, and they can affect post-transcriptional gene regulation in human. It is important to identify targets to determine the possible effects in human genes by using computational approach. In this study, 787 possible mRNAs human targets were predicted by 84 miRNAs of wheat. A total of 14 miRNAs were identified with individual binding to 33 mRNAs associated with schizophrenia, epilepsy, neurodevelopmental disorders, and various cancers, located in the 3′UTR of the mRNA. A functional enrichment was carried out, where the results showed associations to pathways such as dopaminergic synapse (hsa04728), and signaling pathways, significantly associated with the target genes. The prediction of target mRNAs in humans by wheat miRNAs, offer candidates that could facilitate the search and verification, which could be of relevance for future projects and therefor contribute in the therapeutic treatment of various human diseases.
Collapse
|
18
|
Rathour M, Shumayla, Alok A, Upadhyay SK. Investigation of Roles of TaTALE Genes during Development and Stress Response in Bread Wheat. PLANTS (BASEL, SWITZERLAND) 2022; 11:587. [PMID: 35270056 PMCID: PMC8912380 DOI: 10.3390/plants11050587] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 08/27/2023]
Abstract
The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and performed a comprehensive investigation for gene and protein structural properties, phylogeny, expression patterns, and multilevel gene regulations. The identified TaTALE proteins were further classified into two groups, TaBLHs and TaKNOXs, which were tightly clustered into the phylogeny. The negative Ka/Ks ratio of duplicated genes suggested purifying selection pressure with confined functional divergence. Various signature domains and motifs were found conserved in both groups of proteins. The occurrence of diverse cis-regulatory elements and modulated expression during various developmental stages and in the presence of abiotic (heat, drought, salt) and two different fungal stresses suggested their roles in development and stress response, as well. The interaction of TaTALEs with the miRNAs and other development-related homeobox proteins also suggested their roles in growth and development and stress response. The present study revealed several important aspects of TaTALEs that will be useful in further functional validation of these genes in future studies.
Collapse
Affiliation(s)
- Meenakshi Rathour
- Department of Botany, Panjab University, Chandigarh 160014, India; (M.R.); (S.)
| | - Shumayla
- Department of Botany, Panjab University, Chandigarh 160014, India; (M.R.); (S.)
| | - Anshu Alok
- Department of Plant Pathology, University of Minnesota, Twin Cities, Saint Paul, MN 55108, USA;
| | | |
Collapse
|
19
|
Wang M, Yang C, Wei K, Zhao M, Shen L, Ji J, Wang L, Zhang D, Guo J, Zheng Y, Yu J, Zhu M, Liu H, Li YF. Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions. BMC Genomics 2021; 22:793. [PMID: 34736408 PMCID: PMC8567549 DOI: 10.1186/s12864-021-08048-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions. RESULTS In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs. CONCLUSIONS The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.
Collapse
Affiliation(s)
- Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.,Present address: National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenhui Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Liqiang Shen
- Jindal School of Management, University of Texas at Dallas, 800 W Campbell RD, Richardson, TX, 75080, USA
| | - Jie Ji
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Daijing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Junqiang Guo
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Mo Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China
| | - Haiying Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China. .,Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, 453007, China.
| |
Collapse
|
20
|
He X, Han Z, Yin H, Chen F, Dong Y, Zhang L, Lu X, Zeng J, Ma W, Mu P. High-Throughput Sequencing-Based Identification of miRNAs and Their Target mRNAs in Wheat Variety Qing Mai 6 Under Salt Stress Condition. Front Genet 2021; 12:724527. [PMID: 34456980 PMCID: PMC8385717 DOI: 10.3389/fgene.2021.724527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 07/20/2021] [Indexed: 12/04/2022] Open
Abstract
Soil salinization is one of the major abiotic stresses that adversely affect the yield and quality of crops such as wheat, a leading cereal crop worldwide. Excavating the salt-tolerant genes and exploring the salt tolerance mechanism can help breeding salt-tolerant wheat varieties. Thus, it is essential to identify salt-tolerant wheat germplasm resources. In this study, we carried out a salt stress experiment using Qing Mai 6 (QM6), a salt-tolerant wheat variety, and sequenced the miRNAs and mRNAs. The differentially expressed miRNAs and mRNAs in salt stress conditions were compared with the control. As results, a total of eight salt-tolerance-related miRNAs and their corresponding 11 target mRNAs were identified. Further analysis revealed that QM6 enhances salt tolerance through increasing the expression level of genes related to stress resistance, antioxidation, nutrient absorption, and lipid metabolism balance, and the expression of these genes was regulated by the identified miRNAs. The resulting data provides a theoretical basis for future research studies on miRNAs and novel genes related to salt tolerance in wheat in order to develop genetically improved salt-tolerant wheat varieties.
Collapse
Affiliation(s)
- Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Zhen Han
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Huayan Yin
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Fan Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Yihuan Dong
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Lufei Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Xiaoqing Lu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, China.,State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Ping Mu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
21
|
Niekerk LA, Carelse MF, Bakare OO, Mavumengwana V, Keyster M, Gokul A. The Relationship between Cadmium Toxicity and the Modulation of Epigenetic Traits in Plants. Int J Mol Sci 2021; 22:ijms22137046. [PMID: 34209014 PMCID: PMC8268939 DOI: 10.3390/ijms22137046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 01/17/2023] Open
Abstract
Elevated concentrations of heavy metals such as cadmium (Cd) have a negative impact on staple crop production due to their ability to elicit cytotoxic and genotoxic effects on plants. In order to understand the relationship between Cd stress and plants in an effort to improve Cd tolerance, studies have identified genetic mechanisms which could be important for conferring stress tolerance. In recent years epigenetic studies have garnered much attention and hold great potential in both improving the understanding of Cd stress in plants as well as revealing candidate mechanisms for future work. This review describes some of the main epigenetic mechanisms involved in Cd stress responses. We summarize recent literature and data pertaining to chromatin remodeling, DNA methylation, histone acetylation and miRNAs in order to understand the role these epigenetic traits play in cadmium tolerance. The review aims to provide the framework for future studies where these epigenetic traits may be used in plant breeding and molecular studies in order to improve Cd tolerance.
Collapse
Affiliation(s)
- Lee-Ann Niekerk
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Mogamat Fahiem Carelse
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Olalekan Olanrewaju Bakare
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Vuyo Mavumengwana
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Tygerberg Campus, Stellenbosch University, Cape Town 7505, South Africa;
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
- Correspondence: (M.K.); (A.G.); Tel.: +27-587185392 (M.K. & A.G.)
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of the Free State, Phuthadithjaba 9866, South Africa
- Correspondence: (M.K.); (A.G.); Tel.: +27-587185392 (M.K. & A.G.)
| |
Collapse
|
22
|
Xu X, Zhang L, Zhao W, Fu L, Han Y, Wang K, Yan L, Li Y, Zhang XH, Min DH. Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response. BMC Genomics 2021; 22:350. [PMID: 33992092 PMCID: PMC8126144 DOI: 10.1186/s12864-021-07647-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/21/2021] [Indexed: 12/17/2022] Open
Abstract
Background The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family members have not yet been performed in wheat. Results In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat. Conclusions We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07647-6.
Collapse
Affiliation(s)
- Xiaomin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Liang Fu
- Xinxiang Academy of Agricultural Sciences of He'nan Province, Xinxiang, China
| | - Yuxuan Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Keke Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Luyu Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ye Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao-Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Dong-Hong Min
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
| |
Collapse
|
23
|
Liu Y, Wang X, Yuan L, Liu Y, Shen T, Zhang Y. Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation. Front Genet 2021; 12:635599. [PMID: 33936166 PMCID: PMC8084923 DOI: 10.3389/fgene.2021.635599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Cadmium is a toxic metal widely found in workplaces and plant soil because of extensive industrialization. Wheat is an important source of food generated from plant soil. The different responses of wheat against different omic levels of cadmium have been observed and widely studied worldwide. With the development of high-throughput sequencing, micro-level biological research has extended to the microRNA level. In this study, high-cadmium-accumulating wheat cultivars (Annong9267) and low-cadmium-accumulating wheat cultivars (Qian 102032) were used as experimental models. The two cultivars were treated by Cd for 2 h to explore the microRNA profiles in root and leaf tissues through small RNA sequencing. Important small RNAs, such as tae-miR9663-5p and tae-miR6201, and potential small RNA-mediated mechanisms associated with cadmium accumulation were identified by summarizing specific microRNA profiling patterns and their respective target genes. At the wheat roots and leaves, differentially expressed small RNAs related to cadmium accumulation in different plant tissues (roots or leaves) were identified, and functional enrichment analyses on target genes of differentially expressed miRNAs in low- and high-cadmium-accumulating wheat cultivars in different plant tissues (roots or leaves) obtained some known mature miRNAs and new miRNAs. The identified miRNA will be regarded as a potential screening biomarker for low-cadmium-accumulating wheat.
Collapse
Affiliation(s)
- Yuqing Liu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Xudong Wang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Leyi Yuan
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Yuxiang Liu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Tong Shen
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Yunhua Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| |
Collapse
|
24
|
Deng K, Yin H, Xiong F, Feng L, Dong P, Ren M. Genome-wide miRNA expression profiling in potato ( Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway. PeerJ 2021; 9:e10704. [PMID: 33520467 PMCID: PMC7811781 DOI: 10.7717/peerj.10704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/14/2020] [Indexed: 12/29/2022] Open
Abstract
Target of rapamycin (TOR) operates as a hub of the signal transduction that integrates nutrient and energy signaling to promote cell proliferation and growth through mediating the transcriptional and post- transcriptional regulator networks in all eukaryotic species. MicroRNAs (miRNAs) are widespread classes of small, single-stranded, non-coding endogenous RNAs and are widely found in eukaryotes, which play a vital role in regulating gene expression by degrading targeted mRNAs or translational repression at post-transcriptional level. Recent studies found that there were necessarily close connections between miRNA and TOR pathways in mammals. However, there is little information about the interplay between the miRNA and TOR in plants. Thus, the aim of this study was to identify potential TOR-miRNA-mRNA regulatory networks in TOR signaling through global mRNA and microRNA expression profiling in potato. Based on the previous high-throughput transcriptome sequencing and filtering, a total of 2,899 genes were significantly differentially expressed in potato under TOR inhibitors treatment. Pathway analysis revealed that these genes were significantly enriched in multiple metabolic processes. Similarly, in the present study, suppression of TOR resulted in 41 miRNAs up-regulated and 45 down-regulated, revealing that TOR plays a crucial role in the regulation of miRNA regulatory network. Furthermore, integrated mRNA and miRNA expression profiling uncovered that these miRNAs participated in large-scale metabolic process in the TOR signal pathway in potato, such as regulation of autophagy and ubiquitination, and biosynthesis of secondary metabolites. Overall, the results shed new insight into TOR related post-transcriptional gene regulatory networks in potato and suggesting TOR-miRNA-targeting genes relevant networks as a potential genetic resource for potato improvement.
Collapse
Affiliation(s)
- Kexuan Deng
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huan Yin
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fangjie Xiong
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Li Feng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Pan Dong
- School of Life Sciences, Chongqing University, Chongqing, China.,Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing University, Chongqing, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| |
Collapse
|
25
|
Xie D, Yu Y, Dai Z, Sun J, Su J. Identification and characterization of miRNAs and target genes in developing flax seeds by multigroup analysis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1903337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Dongwei Xie
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Yue Yu
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Zhigang Dai
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Jian Sun
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Jianguang Su
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| |
Collapse
|
26
|
Yu Y, Sun F, Chen N, Sun G, Wang CY, Wu DX. MiR396 regulatory network and its expression during grain development in wheat. PROTOPLASMA 2021; 258:103-113. [PMID: 32929630 DOI: 10.1007/s00709-020-01556-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Wheat contains the largest number of miR396 family with 17 miR396 in Poaceae. MiR396 regulatory network underlying wheat grain development has not comprehensively been explored. Our results showed that precursor miR396 family in Poaceae exhibited not only conservativeness but also diversification especially in wheat. Five haplotypes were detected in Poaceae species, while 4 haplotypes in wheat with Hap-4 (miR396a) and Hap-5 (miR396n) unique to wheat. GO enrichment analysis of target genes showed that the first 20 enrichment functions of miR396a and miR396n are completely different from each other, and also completely different from miR396(b-g), miR396(h-m), and miR396(o-q). Functional annotation on the 18 target genes shared by miR396(b-g), miR396(h-m), and miR396(o-q) found that 11 of the 18 target genes are growth-regulating factor (GRF) genes. Our results indicated that, during the grain filling stage of wheat, miR396 is involved in the development of grains by regulating the expression of GRF genes (GRF1, GRF6, and GRF9). Although the enrichment function of miR396(b-g), miR396(h-m), and miR396(o-q) is the same, the gene functional networks they formed differ greatly. Our results indicated that polyploidization enriches not only the diversity of miR396 family and its target genes but also gene functional networks in wheat. These results laid foundation for further elucidating function of miR396 gene family underlying wheat grain development.
Collapse
Affiliation(s)
- Yi Yu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Fangyao Sun
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Ning Chen
- Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3, Canada
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3, Canada.
| | - Cheng-Yu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Hefei, 230036, China.
| | - De-Xiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| |
Collapse
|
27
|
Tang W, Zhao Y, Zeng J, Li Z, Fu Z, Yang M, Zeng D, Chen X, Lai Z, Wang-Pruski G, Guo R. Integration of Small RNA and Transcriptome Sequencing Reveal the Roles of miR395 and ATP Sulfurylase in Developing Seeds of Chinese Kale. FRONTIERS IN PLANT SCIENCE 2021; 12:778848. [PMID: 35185948 PMCID: PMC8851238 DOI: 10.3389/fpls.2021.778848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/22/2021] [Indexed: 05/23/2023]
Abstract
Seed development is closely related to plant production and reproduction, and MicroRNAs (miRNA) is widely involved in plant development including seed development. Chinese kale, as a Brassicaceae vegetable, mainly depends on seed for proper reproduction. In the present study, Chinese kale seed and silique at different stages were selected to establish small RNA (sRNA) libraries including silique wall sRNA libraries at torpedo-embryo stage (PC), silique wall sRNA libraries at cotyledonary-embryo stage (PD), seed sRNA libraries at torpedo-embryo stage (SC), and seed sRNA libraries at cotyledonary-embryo stage (SD). The results showed that miRNA expressed differentially in the seeds and corresponding siliques at different stages. To further clarify the functional mode of miRNA in the process of seed development, Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis was performed on target genes of the differentially expressed miRNAs, and these target genes were mainly enriched in plant hormone signal transduction, primary and secondary metabolic pathways. After joint analysis with the transcriptome change of the corresponding period, miR156-SPL10/SPL11, miR395-APS3, and miR397-LAC2/LAC11 modules were identified to be directly involved in the development of Chinese kale seeds. What's more, modified 5'RLM-RACE and Agrobacteria-mediated Chinese kale transient transformation suggest miR395b_2 is involved in sulfur metabolism during seed development by regulating its target gene APS3.
Collapse
Affiliation(s)
- Weiling Tang
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yijiao Zhao
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiajing Zeng
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zunwen Li
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenlin Fu
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengyu Yang
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Donglin Zeng
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodong Chen
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongxiong Lai
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gefu Wang-Pruski
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Rongfang Guo
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
28
|
Hajiahmadi Z, Abedi A, Wei H, Sun W, Ruan H, Zhuge Q, Movahedi A. Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.). BMC Genomics 2020; 21:778. [PMID: 33167859 PMCID: PMC7653692 DOI: 10.1186/s12864-020-07199-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/27/2020] [Indexed: 12/28/2022] Open
Abstract
Backgrounds Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs). Results 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07199-1.
Collapse
Affiliation(s)
- Zahra Hajiahmadi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, 4199613776, Iran
| | - Amin Abedi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, 4199613776, Iran
| | - Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.
| |
Collapse
|
29
|
Li H, Wei C, Meng Y, Fan R, Zhao W, Wang X, Yu X, Laroche A, Kang Z, Liu D. Identification and expression analysis of some wheat F-box subfamilies during plant development and infection by Puccinia triticina. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:535-548. [PMID: 32836199 DOI: 10.1016/j.plaphy.2020.06.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
As one of the largest protein families in plants, F-box proteins are involved in many important cellular processes. Until now, a limited number of investigations have been conducted on wheat F-box genes due to its variable structure and large and polyploid genome. Classification, identification, structural analysis, evolutionary relationship, and chromosomal distribution of some wheat F-box genes are described in the present study. A total number of 1013 potential F-box proteins which are encoded by 409 genes was identified in wheat, and classified into 12 subfamilies based on their C-terminal domain structures. Furthermore, proteins with identical or similar C-terminal domain were clustered together. Location of 409 F-box genes was identified on all 21 wheat chromosomes but showed an uneven distribution. Segmental duplication was the main reason for the increase in the number of wheat F-box genes. Gene expression analysis based on digital PCR showed that most of the F-box genes were highly expressed in the later development stages of wheat, including the formation of spike, grain, flag leaf, and participated in drought stress (DS), heat stress (HS), and their combination (HD). Of the nine F-box genes we investigated using quantitative PCR (qPCR) following fungal pathogen infection, five were involved in wheat resistance to the infection by leaf rust pathogen and one in the susceptible response. These results provide important information on wheat F-box proteins for further functional studies, especially the proteins that played roles in response to heat and drought stresses and leaf rust pathogen infection.
Collapse
Affiliation(s)
- Huying Li
- College of Life Sciences, Hebei Agricultural University/ Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Baoding, 071001, China; College of Forestry, Shandong Agricultural University, Taian, Shangdong, 271018, China
| | - Chunru Wei
- College of Life Sciences, Hebei Agricultural University/ Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Yuyu Meng
- College of Life Sciences, Hebei Agricultural University/ Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Runqiao Fan
- College of Life Sciences, Hebei Agricultural University/ Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Baoding, 071001, China
| | - Weiquan Zhao
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, 071001, China
| | - Xiaodong Wang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, 071001, China
| | - Xiumei Yu
- College of Life Sciences, Hebei Agricultural University/ Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Baoding, 071001, China; Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, 071001, China.
| | - André Laroche
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, T1J 4B1, Canada
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, NWAFU, Yangling, Shaanxi, 712100, China.
| | - Daqun Liu
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, 071001, China.
| |
Collapse
|
30
|
Hasrak S, Lohrasebi T, Bagheri A, Shariati V, Marashi H, Razavi K. A Study to Assess the Role of Gluten Encoded Genes and Their Regulatory Elements in Bread Making Quality of Wheat. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 17:e2164. [PMID: 32671123 PMCID: PMC7357697 DOI: 10.30498/ijb.2019.82861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background: Quality of bread baking is affected by gluten genes and balance between their expressions. Hence, it is necessary for a comprehensive
research to study and compare all gluten genes and their regulating elements simultaneously. Objectives: The aim of this study was to evaluate the molecular mechanism of bread quality at the level of coding genes and regulating elements via comparative
transcriptome analysis of two extreme wheat cultivars. Materials and Methods: RNAs were extracted from the grain of two wheat cultivars with high (Pishtaz) and low (Navid) bread making qualities, collected during endosperm
development at five stages. mRNAs were sequenced and gluten transcripts were assessed to find differentially expressed genes. Then, transcription
factors interacting with gluten genes were detected and evaluated for expression. Results: Results showed that Ɣ-gliadin and LMW-GS genes had a higher expression in Pishtaz and Navid, respectively. Most identified transcription
factors were active at the early stage of growth and it seemed that NAC and ERF transcription factors had significant roles in regulating genes
with different expressions. There was no significant difference in the expression level of NACs between two cultivars. It is proposed that
the ERF transcription factor which classified as BREB2C transcription factor could control the expression of LMW-GS genes in two cultivars and
functionally act as a repressor for their target genes. Conclusion: The priority of Pishtaz wheat cultivar in bread quality originated from high expression levels of Ɣ-gliadin gene and ERF transcription factor.
Collapse
Affiliation(s)
- Shabnam Hasrak
- Biotechnology and Plant Breeding Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Tahmineh Lohrasebi
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Abdolreza Bagheri
- Biotechnology and Plant Breeding Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Vahid Shariati
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hasan Marashi
- Biotechnology and Plant Breeding Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Khadijeh Razavi
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| |
Collapse
|
31
|
Smoczynska A, Pacak AM, Nuc P, Swida-Barteczka A, Kruszka K, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. A Functional Network of Novel Barley MicroRNAs and Their Targets in Response to Drought. Genes (Basel) 2020; 11:genes11050488. [PMID: 32365647 PMCID: PMC7290300 DOI: 10.3390/genes11050488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/27/2022] Open
Abstract
The regulation of mRNA (messenger RNA) levels by microRNA-mediated activity is especially important in plant responses to environmental stresses. In this work, we report six novel barley microRNAs, including two processed from the same precursor that are severely downregulated under drought conditions. For all analyzed microRNAs, we found target genes that were upregulated under drought conditions and that were known to be involved in a plethora of processes from disease resistance to chromatin–protein complex formation and the regulation of transcription in mitochondria. Targets for novel barley microRNAs were confirmed through degradome data analysis and RT-qPCR using primers flanking microRNA-recognition site. Our results show a broad transcriptional response of barley to water deficiency conditions through microRNA-mediated gene regulation and facilitate further research on drought tolerance in crops.
Collapse
Affiliation(s)
- Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Andrzej M. Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-712 Poznan, Poland;
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
- Correspondence: ; Tel.: +48-61-829-5950
| |
Collapse
|
32
|
Hou G, Du C, Gao H, Liu S, Sun W, Lu H, Kang J, Xie Y, Ma D, Wang C. Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels. BMC PLANT BIOLOGY 2020; 20:87. [PMID: 32103721 PMCID: PMC7045451 DOI: 10.1186/s12870-020-2296-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions. RESULTS A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns. CONCLUSIONS The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.
Collapse
Affiliation(s)
- Gege Hou
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyang Du
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Honghuan Gao
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Sujun Liu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wan Sun
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongfang Lu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan Kang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingxin Xie
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dongyun Ma
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Chenyang Wang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
33
|
Ramachandran SR, Mueth NA, Zheng P, Hulbert SH. Analysis of miRNAs in Two Wheat Cultivars Infected With Puccinia striiformis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2020; 10:1574. [PMID: 31998329 PMCID: PMC6965360 DOI: 10.3389/fpls.2019.01574] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/11/2019] [Indexed: 05/27/2023]
Abstract
MicroRNAs are small RNAs that regulate gene expression in eukaryotes. In this study, we analyzed the small RNA profiles of two cultivars that exhibit different reactions to stripe rust infection: one susceptible, the other partially resistant. Using small RNA libraries prepared from the two wheat cultivars infected with stripe rust fungus (Puccinia striiformis f. sp. tritici), we identified 182 previously known miRNAs, 91 variants of known miRNAs, and 163 candidate novel wheat miRNAs. Known miRNA loci were usually copied in all three wheat sub-genomes, whereas novel miRNA loci were often specific to a single sub-genome. DESeq2 analysis of differentially expressed microRNAs revealed 23 miRNAs that exhibit cultivar-specific differences. TA078/miR399b showed cultivar-specific differential regulation in response to infection. Using different target prediction algorithms, 145 miRNAs were predicted to target wheat genes, while 69 miRNAs were predicted to target fungal genes. We also confirmed reciprocal expression of TA078/miR399b and tae-miR9664 and their target genes in different treatments, providing evidence for miRNA-mediated regulation during infection. Both known and novel miRNAs were predicted to target fungal genes, suggesting trans-kingdom regulation of gene expression. Overall, this study contributes to the current repository of wheat miRNAs and provides novel information on the yet-uncharacterized roles for miRNAs in the wheat-stripe rust pathosystem.
Collapse
Affiliation(s)
| | - Nicholas A. Mueth
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| |
Collapse
|
34
|
Kumar A, Sharma M, Gahlaut V, Nagaraju M, Chaudhary S, Kumar A, Tyagi P, Gajula MP, Singh KP. Genome-wide identification, characterization, and expression profiling of SPX gene family in wheat. Int J Biol Macromol 2019; 140:17-32. [DOI: 10.1016/j.ijbiomac.2019.08.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 01/11/2023]
|
35
|
Li YF, Wei K, Wang M, Wang L, Cui J, Zhang D, Guo J, Zhao M, Zheng Y. Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field. Front Genet 2019; 10:779. [PMID: 31552091 PMCID: PMC6737308 DOI: 10.3389/fgene.2019.00779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022] Open
Abstract
Cold acclimation and vegetative/reproductive transition are two important evolutionary adaptive mechanisms for winter wheat surviving the freezing temperature in winter and successful seeds setting in the next year. MicroRNA (miRNA) is a class of regulatory small RNAs (sRNAs), which plays critical roles in the growth and development of plants. However, the regulation mechanism of miRNAs during cold acclimation and vegetative/reproductive transition of winter wheat is not much understood. In this study, four sRNA libraries from leaves of winter wheat grown in the field at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage were analyzed to identify known and novel miRNAs and to understand their potential roles in the growth and development of winter wheat. We examined miRNA expression using a high-throughput sequencing technique. A total of 373 known, 55 novel, and 27 putative novel miRNAs were identified. Ninety-one miRNAs were found to be differentially expressed at the four stages. Among them, the expression of six known and eight novel miRNAs was significantly suppressed at the winter dormancy stage, whereas the expression levels of seven known and eight novel miRNAs were induced at this stage; three known miRNAs and three novel miRNAs were significantly induced at the spring green-up stage; six known miRNAs were induced at the spring green-up stage and reached the highest expression level at the jointing stage; and 20 known miRNAs and 10 novel miRNAs were significantly induced at the jointing stage. Expression of a number of representative differentially expressed miRNAs was verified using quantitative real-time polymerase chain reaction (qRT-PCR). Potential target genes for known and novel miRNAs were predicted. Moreover, six novel target genes for four Pooideae species-specific miRNAs and two novel miRNAs were verified using the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5'RACE) technique. These results indicate that miRNAs are key non-coding regulatory factors modulating the growth and development of wheat. Our study provides valuable information for in-depth understanding of the regulatory mechanism of miRNAs in cold acclimation and vegetative/reproductive transition of winter wheat grown in the field.
Collapse
Affiliation(s)
- Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Junxia Cui
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Daijing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Junqiang Guo
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| |
Collapse
|
36
|
Comparative profiling of roots small RNA expression and corresponding gene ontology and pathway analyses for low- and high-cadmium-accumulating genotypes of wheat in response to cadmium stress. Funct Integr Genomics 2019; 20:177-190. [PMID: 31435847 DOI: 10.1007/s10142-019-00710-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
MicroRNAs (miRNAs) participate in multiple biological processes in plant. Cd accumulation ability differs among varieties in wheat, but little is known about miRNAs and their function in Cd accumulation of wheat under Cd stress. Therefore, the present study detected small RNAs responsible for differential Cd accumulation between two contrasting wheat genotypes (low-Cd accumulation one L17 and high-Cd accumulation one H17) to identify novel targets to further study Cd stress in wheat. Under normal conditions, 139 miRNAs were differentially expressed between L17 and H17, while this value reached 142 after Cd exposure. For Cd-induced DEMs, total 25 miRNAs were differentially expressed in L17 after Cd treatment, while, 70 Cd-induced DEMs were found in H17. Moreover, GO analysis revealed that target genes of DEMs related to lipid biosynthetic process and chlorophyll binding are uniquely enriched in L17, target genes of DEMs related to ribosome biogenesis and sucrose alpha-glucosidase activity are uniquely enriched in H17. By pathway analysis, target genes of DEMs related to PI3K-Akt signaling pathway was specifically enriched in L17, target genes of DEMs related to carbohydrate digestion and absorption pathway was uniquely enriched in H17. In addition, miRNA-gene co-expression showed that tae-miR9774 was uniquely expressed between L17Cd and L17CK, while tae-miR398 was specially expressed between H17Cd and H17CK. Our results suggested that Cd-accumulating ability of L17 and H17 varied from the expression of induced unique miRNA, such as expression of tae-miR-9774 and tae-miR-398. Our study not only provide the foundation for further exploring the miRNAs-induced molecular mechanisms of Cd accumulation in wheat but also supply novel strategies for improving phytoremediation ability of food plants through genetic engineering.
Collapse
|
37
|
Joint RNA-Seq and miRNA Profiling Analyses to Reveal Molecular Mechanisms in Regulating Thickness of Pod Canopy in Brassica napus. Genes (Basel) 2019; 10:genes10080591. [PMID: 31387302 PMCID: PMC6722711 DOI: 10.3390/genes10080591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 07/31/2019] [Indexed: 12/14/2022] Open
Abstract
Oilseed rape (Brassica napus) is the second largest oilseed crop worldwide. As an architecture component of B. napus, thickness of pod canopy (TPC) plays an important role in yield formation, especially under high-density cultivation conditions. However, the mechanisms underlying the regulation of TPC remain unclear. RNA and microRNA (miRNA) profiling of two groups of B. napus lines with significantly different TPC at the bolting with a tiny bud stage revealed differential expressions of numerous genes involved in nitrogen-related pathways. Expression of several nitrogen-related response genes, including ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15, was dramatically changed in the thick TPC lines compared to those in the thin TPC lines. Differentially expressed miRNAs also included many involved in nitrogen-related pathways. Expression of most target genes was negatively associated with corresponding miRNAs, such as miR159, miR6029, and miR827. In addition, 12 (including miR319, miR845, and miR158) differentially expressed miRNAs between two plant tissues sampled (stem apex and flower bud) were identified, implying that they might have roles in determining overall plant architecture. These results suggest that nitrogen signaling may play a pivotal role in regulating TPC in B. napus.
Collapse
|
38
|
Zhou M, Zheng S, Liu R, Lu L, Zhang C, Zhang L, Yant L, Wu Y. The genome-wide impact of cadmium on microRNA and mRNA expression in contrasting Cd responsive wheat genotypes. BMC Genomics 2019; 20:615. [PMID: 31357934 PMCID: PMC6664702 DOI: 10.1186/s12864-019-5939-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 06/26/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Heavy metal ATPases (HMAs) are responsible for Cd translocation and play a primary role in Cd detoxification in various plant species. However, the characteristics of HMAs and the regulatory mechanisms between HMAs and microRNAs in wheat (Triticum aestivum L) remain unknown. RESULTS By comparative microRNA and transcriptome analysis, a total three known and 19 novel differentially expressed microRNAs (DEMs) and 1561 differentially expressed genes (DEGs) were found in L17 after Cd treatment. In H17, by contrast, 12 known and 57 novel DEMs, and only 297 Cd-induced DEGs were found. Functional enrichments of DEMs and DEGs indicate how genotype-specific biological processes responded to Cd stress. Processes found to be involved in microRNAs-associated Cd response include: ubiquitin mediated proteolysis, tyrosine metabolism, and carbon fixation pathways and thiamine metabolism. For the mRNA response, categories including terpenoid backbone biosynthesis and phenylalanine metabolism, and photosynthesis - antenna proteins and ABC transporters were enriched. Moreover, we identified 32 TaHMA genes in wheat. Phylogenetic trees, chromosomal locations, conserved motifs and expression levels in different tissues and roots under Cd stress are presented. Finally, we infer a microRNA-TaHMAs expression network, indicating that miRNAs can regulate TaHMAs. CONCLUSION Our findings suggest that microRNAs play important role in wheat under Cd stress through regulation of targets such as TaHMA2;1. Identification of these targets will be useful for screening and breeding low-Cd accumulation wheat lines.
Collapse
Affiliation(s)
- Min Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Shigang Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Rong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lu Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Chihong Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Lei Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| |
Collapse
|
39
|
Fileccia V, Ingraffia R, Amato G, Giambalvo D, Martinelli F. Identification of microRNAS differentially regulated by water deficit in relation to mycorrhizal treatment in wheat. Mol Biol Rep 2019; 46:5163-5174. [PMID: 31327121 DOI: 10.1007/s11033-019-04974-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/09/2019] [Indexed: 11/29/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are soil microrganisms that establish symbiosis with plants positively influencing their resistance to abiotic stresses. The aim of this work was to identify wheat miRNAs differentially regulated by water deficit conditions in presence or absence of AMF treatment. Small RNA libraries were constructed for both leaf and root tissues considering four conditions: control (irrigated) or water deficit in presence/absence of mycorrhizal (AMF) treatment. A total of 12 miRNAs were significantly regulated by water deficit in leaves: five in absence and seven in presence of AMF treatment. In roots, three miRNAs were water deficit-modulated in absence of mycorrhizal treatment while six were regulated in presence of it. The most represented miRNA family was miR167 that was regulated by water deficit in both leaf and root tissues. Interestingly, miR827-5p was differentially regulated in leaves in the absence of mycorrhizal treatment while it was water deficit-modulated in roots irrespective of AMF treatment. In roots, water deficit repressed miR827-5p, miR394, miR6187, miR167e-3p, and miR9666b-3p affecting transcription, RNA synthesis, protein synthesis, and protein modifications. In leaves, mycorrhizae modulated miR5384-3p and miR156e-3p affecting trafficking and cell redox homeostasis. DNA replication and transcription regulation should be targeted by the repression of miR1432-5p and miR166h-3p. This work provided interesting insights into the post-transcriptional mechanisms of wheat responses to water deficit in relation to mycorrhizal symbiosis.
Collapse
Affiliation(s)
- Veronica Fileccia
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Rosolino Ingraffia
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Gaetano Amato
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Dario Giambalvo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | | |
Collapse
|
40
|
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
|
41
|
Wei J, Cao H, Liu JD, Zuo JH, Fang Y, Lin CT, Sun RZ, Li WL, Liu YX. Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq. Funct Integr Genomics 2019; 19:919-932. [PMID: 31168755 DOI: 10.1007/s10142-019-00693-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 03/21/2019] [Accepted: 05/17/2019] [Indexed: 11/28/2022]
Abstract
Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat.
Collapse
Affiliation(s)
- Jun Wei
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Dong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Hong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Fang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Run-Ze Sun
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wen-Long Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,Science and Technology Daily, Beijing, 100093, China
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| |
Collapse
|
42
|
Faraji S, Rasouli SH, Kazemitabar SK. Genome-wide exploration of C2H2 zinc finger family in durum wheat (Triticum turgidum ssp. Durum): insights into the roles in biological processes especially stress response. Biometals 2018; 31:1019-1042. [PMID: 30288657 DOI: 10.1007/s10534-018-0146-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/22/2018] [Indexed: 11/30/2022]
Abstract
C2H2 type of zinc finger transcription factors (C2H2-ZFP TFs) play crucial roles in plant developments and stress response. Regarding its importance, genome-wide study of C2H2-ZFs were performed in multiple important plant species, but any such investigation was not fulfilled in Triticum turgidum ssp. Durum (durum wheat) as an important nutritional crop. The present study identified 122 C2H2-ZFs in durum wheat and physically mapped them onto the genome. The phylogenetic analysis classified these TFs into six major groups. Genes structure and conserved motifs assay showed TtC2H2-ZF involvement in the important cellular functions. Comparative phylogeny between durum wheat TtC2H2-ZF genes and the orthologs in rice revealed the evolutionary relationships of C2H2-ZF proteins. The gene ontology and promoter cis-element analysis indicated that most of TtC2H2-ZF genes are involved in multiple molecular functions including metal ion-binding and various stimuli responses. Further, the miRNAs targeting TtC2H2-ZF transcripts, homology modeling and proteins interaction network were also demonstrated, suggesting the vital cellular functions of TtC2H2-ZFs during various circumstances. The expression heatmap demonstrated differential and tissue-specific expression patterns of these genes. Expression profiling of this gene family members in response to dehydration and heat stresses showed differential expression pattern of these genes at multiple time points of stresses. This study can prepare a comprehensive overview of the durum wheat C2H2-ZF gene family and may provide a new perspective on the evolution of them, which will form the basis for further investigation of the roles of this family members and future genetic engineering studies in crops.
Collapse
Affiliation(s)
- Sahar Faraji
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
| | - Seyyed Hamidreza Rasouli
- Department of Entrepreneurship Technology, Faculty of Management, Payame Noor University (PNU), Babol, Iran
| | - Seyyed Kamal Kazemitabar
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| |
Collapse
|
43
|
Wang Y, Shi C, Yang T, Zhao L, Chen J, Zhang N, Ren Y, Tang G, Cui D, Chen F. High-throughput sequencing revealed that microRNAs were involved in the development of superior and inferior grains in bread wheat. Sci Rep 2018; 8:13854. [PMID: 30218081 PMCID: PMC6138641 DOI: 10.1038/s41598-018-31870-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/28/2018] [Indexed: 01/09/2023] Open
Abstract
High-throughput sequencing was employed to investigate the expression of miRNAs and their target genes in superior and inferior seeds of Aikang 58. Small RNA sequencing revealed 620 conserved and 64 novel miRNAs in superior grains, and 623 conserved and 66 novel miRNAs in inferior grains. Among these, 97 known miRNAs, and eight novel miRNAs showed differential expression between the superior and inferior seeds. Degradome sequencing revealed at least 140 candidate target genes associated with 35 miRNA families during the development of superior and inferior seeds. GO and KEGG pathway analysis showed that the differentially expressed miRNAs, both conserved and novel, were likely involved in hormone production, carbohydrate metabolic pathways, and cell division. We validated eight known and four novel grain development-related miRNAs and their target genes by quantitative real-time polymerase chain reaction to ensure the reliability of small RNA and degradome-seq results. Of these, miR160 and miR165/166 were knocked down in Arabidopsis using short-tandem target mimic (STTM160 and STTM165/166) technology, which confirmed their roles in seed development. Specifically, STTM160 showed significantly smaller grain size, lower grain weight, shorter siliques length, shorter plant height, and more serrated leaves, whereas STTM165/166 showed decreased seed number, disabled siliques, and curled upward leaves.
Collapse
Affiliation(s)
- Yongyan Wang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
- Department of Biological Sciences, Life Science and Technology Instituted, Michigan Technological University, Houghton, MI, 49931, USA
| | - Chaonan Shi
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Tianxiao Yang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Lei Zhao
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Jianhui Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Ning Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Yan Ren
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Guiliang Tang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
- Department of Biological Sciences, Life Science and Technology Instituted, Michigan Technological University, Houghton, MI, 49931, USA
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China.
| |
Collapse
|
44
|
Hussain K, Mungikar K, Kulkarni A, Kamble A. Identification, characterization and expression analysis of pigeonpea miRNAs in response to Fusarium wilt. Gene 2018; 653:57-64. [DOI: 10.1016/j.gene.2018.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/25/2022]
|
45
|
Guo G, Liu X, Sun F, Cao J, Huo N, Wuda B, Xin M, Hu Z, Du J, Xia R, Rossi V, Peng H, Ni Z, Sun Q, Yao Y. Wheat miR9678 Affects Seed Germination by Generating Phased siRNAs and Modulating Abscisic Acid/Gibberellin Signaling. THE PLANT CELL 2018; 30:796-814. [PMID: 29567662 PMCID: PMC5969276 DOI: 10.1105/tpc.17.00842] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/23/2018] [Accepted: 03/13/2018] [Indexed: 05/19/2023]
Abstract
Seed germination is important for grain yield and quality and rapid, near-simultaneous germination helps in cultivation; however, cultivars that germinate too readily can undergo preharvest sprouting (PHS), which causes substantial losses in areas that tend to get rain around harvest time. Moreover, our knowledge of mechanisms regulating seed germination in wheat (Triticum aestivum) remains limited. In this study, we analyzed function of a wheat-specific microRNA 9678 (miR9678), which is specifically expressed in the scutellum of developing and germinating seeds. Overexpression of miR9678 delayed germination and improved resistance to PHS in wheat through reducing bioactive gibberellin (GA) levels; miR9678 silencing enhanced germination rates. We provide evidence that miR9678 targets a long noncoding RNA (WSGAR) and triggers the generation of phased small interfering RNAs that play a role in the delay of seed germination. Finally, we found that abscisic acid (ABA) signaling proteins bind the promoter of miR9678 precursor and activate its expression, indicating that miR9678 affects germination by modulating the GA/ABA signaling.
Collapse
Affiliation(s)
- Guanghui Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Fenglong Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Jie Cao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Na Huo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Bala Wuda
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Vincenzo Rossi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, I-24126 Bergamo, Italy
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R. China
| |
Collapse
|
46
|
López-Galiano MJ, González-Hernández AI, Crespo-Salvador O, Rausell C, Real MD, Escamilla M, Camañes G, García-Agustín P, González-Bosch C, García-Robles I. Epigenetic regulation of the expression of WRKY75 transcription factor in response to biotic and abiotic stresses in Solanaceae plants. PLANT CELL REPORTS 2018; 37:167-176. [PMID: 29079899 DOI: 10.1007/s00299-017-2219-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/05/2017] [Indexed: 05/12/2023]
Abstract
SlyWRKY75: gene expression was induced in response to biotic stresses, especially in Botrytis cinerea-infected tomato plants, in which Sly-miR1127-3p is a putative SlyWRKY75 regulator and epigenetic marks were detected. WRKY75 transcription factor involved in Pi homeostasis was recently found also induced in defense against necrotrophic pathogens. In this study, we analyzed by RT-qPCR the expression of SlyWRKY75 gene in tomato plants in response to abiotic stresses (drought or heat) and biotic stresses (Colorado potato beetle larvae infestation, Pseudomonas syringae or Botrytis cinerea infection) being only differentially expressed following biotic stresses, especially upon B. cinerea infection (55-fold induction). JA and JA-Ile levels were significantly increased in tomato plants under biotic stresses compared with control plants, indicating that SlyWRKY75 might be a transcriptional regulator of the JA pathway. The contribution of miRNAs and epigenetic molecular mechanisms to the regulation of this gene in B. cinerea-infected tomato plants was explored. We identified a putative Sly-miR1127-3p miRNA predicted to bind the intronic region of the SlyWRKY75 genomic sequence. Sly-miR1127-3p miRNA was repressed in infected plants (0.4-fold) supporting that it might act as an epigenetic regulation factor of SlyWRKY75 gene expression rather than via the post-transcriptional mechanisms of canonical miRNAs. It has been proposed that certain miRNAs can mediate DNA methylation in the plant nucleus broadening miRNA functions with transcriptional gene silencing by targeting intron-containing pre-mRNAs. Histone modifications analysis by chromatin immunoprecipitation (ChIP) demonstrated the presence of the activator histone modification H3K4me3 on SlyWRKY75 transcription start site and gene body. The induction of this gene in response to B. cinerea correlates with the presence of an activator mark. Thus, miRNAs and chromatin modifications might cooperate as epigenetic factors to modulate SlyWRKY75 gene expression.
Collapse
Affiliation(s)
- María José López-Galiano
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Ana I González-Hernández
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Oscar Crespo-Salvador
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - M Dolores Real
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Mónica Escamilla
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Gemma Camañes
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Pilar García-Agustín
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Carmen González-Bosch
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain.
| |
Collapse
|
47
|
Kiegle EA, Garden A, Lacchini E, Kater MM. A Genomic View of Alternative Splicing of Long Non-coding RNAs during Rice Seed Development Reveals Extensive Splicing and lncRNA Gene Families. FRONTIERS IN PLANT SCIENCE 2018; 9:115. [PMID: 29467783 PMCID: PMC5808331 DOI: 10.3389/fpls.2018.00115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/22/2018] [Indexed: 05/08/2023]
Abstract
Alternative splicing (AS) is a key modulator of development in many eukaryotic organisms. In plants, alternative splice forms of non-coding RNAs (ncRNAs) are known to modulate flowering time in Arabidopsis and fertility in rice. Here we demonstrate that alternative splicing of coding and long non-coding RNAs occurs during rice seed development by comparing AS in immature seeds vs. embryo and endosperm of mature seeds. Based on computational predictions of AS events determined from a Bayesian analysis of junction counts of RNA-seq datasets, differential splicing of protein-coding, and non-coding RNAs was determined. In contrast to roots, leaves, flowers, buds, and reproductive meristems, developing seeds had 5.8-57 times more predicted AS. Primers designed to span introns and exons were used to detect AS events predicted by rMATs in cDNA derived from early (milk) seed, embryo, and endosperm. Comparing milk seed vs. mature embryo and endosperm, AS of MORC7 (a gene implicated in epigenetic gene silencing), was markedly different. Long non-coding RNAs (lncRNAs) also underwent AS during the transition from milk seed to mature embryo and endosperm, with a complex gene structure, and were more extensively processed than predicted by current genome annotation. Exon retention of lncRNAs was enhanced in embryos. Searching all 5,515 lncRNAs in the NCBI genome annotation uncovered gene families based on highly conserved regions shared by groups of 3-35 lncRNAs. The homologies to other lncRNAs, as well as homologies to coding sequences, and the genomic context of lncRNAs provide inroads for functional analysis of multi-exonic lncRNAs that can be extensively processed during seed development.
Collapse
|
48
|
Bai B, Shi B, Hou N, Cao Y, Meng Y, Bian H, Zhu M, Han N. microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination. BMC PLANT BIOLOGY 2017; 17:150. [PMID: 28877679 PMCID: PMC5586051 DOI: 10.1186/s12870-017-1095-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/22/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Small RNA and degradome sequencing have identified a large number of miRNA-target pairs in plant seeds. However, detailed spatial and temporal studies of miRNA-mediated regulation, which can reflect links between seed development and germination are still lacking. RESULTS In this study, we extended our investigation on miRNAs-involved gene regulation by a combined analysis of seed maturation and germination in barley. Through bioinformatics analysis of small RNA sequencing data, a total of 1324 known miRNA families and 448 novel miRNA candidates were identified. Of those, 16 known miRNAs with 40 target genes, and three novel miRNAs with four target genes were confirmed based on degradome sequencing data. Conserved miRNA families such as miR156, miR168, miR166, miR167, and miR894 were highly expressed in embryos of developing and germinating seeds. A barley-specific miRNA, miR5071, which was predicted to target an OsMLA10-like gene, accumulated at a high level, suggesting its involvement in defence response during these two developmental stages. Based on target prediction and Kyoto Encyclopedia of Genes and Genomes analysis of putative targets, nine highly expressed miRNAs were found to be related to phytohormone signalling and hormone cross-talk. Northern blot and qRT-PCR analysis showed that these miRNAs displayed differential expression patterns during seed development and germination, indicating their different roles in hormone signalling pathways. In addition, we showed that miR393 affected seed development through targeting two genes encoding the auxin receptors TIR1/AFBs in barley, as over-expression of miR393 led to an increased length-width ratio of seeds, whereas target mimic (MIM393)-mediated inhibition of its activity decreased the 1000-grain weight of seeds. Furthermore, the expression of auxin-responsive genes, abscisic acid- and gibberellic acid-related genes was altered in miR393 misexpression lines during germination and early seedling growth. CONCLUSIONS Our work indicates that miRNA-target pairs participate in gene expression regulation and hormone interaction in barley embryo and provides evidence that miR393-mediated auxin response regulation affects grain development and influences gibberellic acid and abscisic acid homeostasis during germination.
Collapse
Affiliation(s)
- Bin Bai
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Bo Shi
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Ning Hou
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Yanli Cao
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou 310036 China
| | - Hongwu Bian
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Muyuan Zhu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| | - Ning Han
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou 310058 China
| |
Collapse
|
49
|
Bakhshi B, Fard EM, Gharechahi J, Safarzadeh M, Nikpay N, Fotovat R, Azimi MR, Salekdeh GH. The contrasting microRNA content of a drought tolerant and a drought susceptible wheat cultivar. JOURNAL OF PLANT PHYSIOLOGY 2017; 216:35-43. [PMID: 28575745 DOI: 10.1016/j.jplph.2017.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/14/2017] [Accepted: 05/17/2017] [Indexed: 05/08/2023]
Abstract
Drought stress represents one of the most common stresses affecting the productivity of crop plants. A rather recently discovered component of the plant response to drought is the cellular population of microRNAs. Here, the microRNA content was revealed of two bread wheat cultivars contrasting strongly with respect to the ability to withstand drought stress. A total of 1813 miRNAs was identified, grouped into 106 families. Some 104 of these miRNAs were predicted to match 212 novel miRNA precursors. In the drought tolerant cultivar (SM), 105 (33 known and 72 novel) miRNAs were altered in abundance by the imposition of drought stress, while the equivalent number in the more sensitive cultivar (SW) was 51 (20 and 31). An in silico analysis predicted that these miRNAs target at least 1959 genes in SM and 1111 in SW, suggesting their broad contribution to the drought stress response. Among the target genes were several known stress-related genes, encoding, for example, superoxide dismutase, various MYB transcription factors, various ABA signaling proteins and various MADS-box transcription factors. In many cases, the more susceptible cultivar SW behaved in a contrasting manner. The suggestion is that miRNAs represent an important aspect of the drought stress response, post-transcriptionally regulating a range of stress-related genes.
Collapse
Affiliation(s)
- Behnam Bakhshi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran
| | - Ehsan Mohseni Fard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahdieh Safarzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran
| | - Nava Nikpay
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran
| | - Reza Fotovat
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Mohammad Reza Azimi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran; Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| |
Collapse
|
50
|
Huang D, Feurtado JA, Smith MA, Flatman LK, Koh C, Cutler AJ. Long noncoding miRNA gene represses wheat β-diketone waxes. Proc Natl Acad Sci U S A 2017; 114:E3149-E3158. [PMID: 28351975 PMCID: PMC5393243 DOI: 10.1073/pnas.1617483114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The cuticle of terrestrial plants functions as a protective barrier against many biotic and abiotic stresses. In wheat and other Triticeae, β-diketone waxes are major components of the epicuticular layer leading to the bluish-white glaucous trait in reproductive-age plants. Glaucousness in durum wheat is controlled by a metabolic gene cluster at the WAX1 (W1) locus and a dominant suppressor INHIBITOR of WAX1 (Iw1) on chromosome 2B. The wheat D subgenome from progenitor Aegilops tauschii contains W2 and Iw2 paralogs on chromosome 2D. Here we identify the Iw1 gene from durum wheat and demonstrate the unique regulatory mechanism by which Iw1 acts to suppress a carboxylesterase-like protein gene, W1-COE, within the W1 multigene locus. Iw1 is a long noncoding RNA (lncRNA) containing an inverted repeat (IR) with >80% identity to W1-COE The Iw1 transcript forms a miRNA precursor-like long hairpin producing a 21-nt predominant miRNA, miRW1, and smaller numbers of related sRNAs associated with the nonglaucous phenotype. When Iw1 was introduced into glaucous bread wheat, miRW1 accumulated, W1-COE and its paralog W2-COE were down-regulated, and the phenotype was nonglaucous and β-diketone-depleted. The IR region of Iw1 has >94% identity to an IR region on chromosome 2 in Ae. tauschii that also produces miRW1 and lies within the marker-based location of Iw2 We propose the Iw loci arose from an inverted duplication of W1-COE and/or W2-COE in ancestral wheat to form evolutionarily young miRNA genes that act to repress the glaucous trait.
Collapse
Affiliation(s)
- Daiqing Huang
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - J Allan Feurtado
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Mark A Smith
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Leah K Flatman
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Chushin Koh
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Adrian J Cutler
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| |
Collapse
|