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Wang J, Wang X, Wang L, Nazir MF, Fu G, Peng Z, Chen B, Xing A, Zhu M, Ma X, Wang X, Jia Y, Pan Z, Wang L, Xia Y, He S, Du X. Exploring the regulatory role of non-coding RNAs in fiber development and direct regulation of GhKCR2 in the fatty acid metabolic pathway in upland cotton. Int J Biol Macromol 2024; 266:131345. [PMID: 38574935 DOI: 10.1016/j.ijbiomac.2024.131345] [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: 01/10/2024] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Cotton fiber holds immense importance as the primary raw material for the textile industry. Consequently, comprehending the regulatory mechanisms governing fiber development is pivotal for enhancing fiber quality. Our study aimed to construct a regulatory network of competing endogenous RNAs (ceRNAs) and assess the impact of non-coding RNAs on gene expression throughout fiber development. Through whole transcriptome data analysis, we identified differentially expressed genes (DEGs) regulated by non-coding RNA (ncRNA) that were predominantly enriched in phenylpropanoid biosynthesis and the fatty acid elongation pathway. This analysis involved two contrasting phenotypic materials (J02-508 and ZRI015) at five stages of fiber development. Additionally, we conducted a detailed analysis of genes involved in fatty acid elongation, including KCS, KCR, HACD, ECR, and ACOT, to unveil the factors contributing to the variation in fatty acid elongation between J02-508 and ZRI015. Through the integration of histochemical GUS staining, dual luciferase assay experiments, and correlation analysis of expression levels during fiber development stages for lncRNA MSTRG.44818.23 (MST23) and GhKCR2, we elucidated that MST23 positively regulates GhKCR2 expression in the fatty acid elongation pathway. This identification provides valuable insights into the molecular mechanisms underlying fiber development, emphasizing the intricate interplay between non-coding RNAs and protein-coding genes.
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Affiliation(s)
- Jingjing Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyang Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liyuan Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Mian Faisal Nazir
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Guoyong Fu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhen Peng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Baojun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Aishuang Xing
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Mengchen Zhu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xinli Ma
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Xiuxiu Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yinhua Jia
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Zhaoe Pan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liru Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yingying Xia
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou 455001, China
| | - Shoupu He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Xiongming Du
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China.
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2
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Wang B, Ji M, Fang H, Gu H, Mehari TG, Han J, Feng W, Huo X, Zhang J, Chen Y, Zhang J, Ditta A, Khan MKR, Paterson AH, Chee PW, Wang K. An analysis of lncRNAs related to fiber quality and the discovery of their target genes in a Gossypium hirsutum line with Gossypium mustelinum introgression. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:40. [PMID: 38296887 DOI: 10.1007/s00122-024-04541-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
KEY MESSAGE Analysis of fiber quality lncRNAs and their target genes from a pair of Gossypium mustelinum near-isogenic lines provide new prospects for improving the fiber quality of Upland cotton. Long noncoding RNAs (lncRNAs) are an important part of genome transcription and play roles in a wide range of biological processes in plants. In this research, a pair of near-isogenic cotton lines, namely, a Gossypium mustelinum introgression line (IL9) with outstanding fiber quality and its recurrent Upland cotton parent (PD94042), were used as the experimental materials. Cotton fibers were selected for lncRNA sequencing at 17 and 21 days post-anthesis. A total of 2693 differentially expressed genes were identified. In total, 5841 lncRNAs were ultimately screened, from which 163 differentially expressed lncRNAs were identified. Target genes of the lncRNAs were predicted by two different methods: cis and trans. Some of the target genes were related to cell components, membrane components, plant hormone signal transduction and catalytic metabolism, and the results indicated that there might also be important effects on the development of fiber. Four differentially expressed target genes related to fiber quality (Gomus.D05G015100, Gomus.A05G281300, Gomus.A12G023400 and Gomus.A10G226800) were screened through gene function annotation, and the functions of these four genes were verified through virus-induced gene silencing (VIGS). Compared to the negative controls, plants in which any of these four genes were silenced showed significant reductions in fiber strength. In addition, the plants in which the Gomus.A12G023400 gene was silenced showed a significant reduction in fiber uniformity, whereas the plants in which Gomus.A05G281300 was silenced showed a significant increase in fiber fineness as measured via micronaire. Our results showed that these genes play different roles during fiber development, impacting fiber quality.
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Affiliation(s)
- Baohua Wang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
| | - Meijun Ji
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Haijing Gu
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | | | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Wenxiang Feng
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Allah Ditta
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - Muhammad K R Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.
| | - Peng W Chee
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31793, USA.
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
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3
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Weng M, Zhang D, Wang H, Yang C, Lin H, Pan Y, Lin Y. Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage. Sci Rep 2024; 14:747. [PMID: 38185662 PMCID: PMC10772075 DOI: 10.1038/s41598-023-46744-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/04/2023] [Indexed: 01/09/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play crucial roles in response to aging processes. However, how lncRNAs regulate postharvest senescence of Sparassis latifolia (S. latifolia) with oriented polypropylene (OPP) film packing during cold storage remains unclear. In this study, we performed RNA-seq using the fruiting bodies of S. latifolia stored at 4 ℃ for 0, 8, 16 and 24 days after harvest, and profiled the lncRNA and mRNA transcriptome, respectively. In total, 1003 putative lncRNAs were identified, and there were 495, 483 and 162 differentially expressed (DE) lncRNAs, and 3680, 3941 and 1870 differentially expressed mRNAs after 8, 16 and 24 days of storage, respectively, compared to 0 day of storage. Target genes of differentially expressed lncRNAs were found to significantly associate with carbon and energy metabolism, response to abiotic stimulus, amino acid biosynthesis and metabolism, and protein synthesis and transcription. In addition, DE-lncRNA-mRNA co-expression networks in response to aging stress were also constructed. Taken together, these results confirm the regulatory role of lncRNAs in postharvest senescence of S. latifolia and will facilitate for improving preservation method.
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Affiliation(s)
- Mengting Weng
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Di Zhang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyu Wang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Chi Yang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyi Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Yanfang Pan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yanquan Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
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4
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Thatai AKS, Ammankallu S, Devasahayam Arokia Balaya R, Soman SP, Nisar M, Babu S, John L, George A, Anto CK, Sanjeev D, Kandiyil MK, Raj SS, Awasthi K, Vinodchandra SS, Prasad TSK, Raju R. VirhostlncR: A comprehensive database to explore lncRNAs and their targets in viral infections. Comput Biol Med 2023; 164:107279. [PMID: 37572440 DOI: 10.1016/j.compbiomed.2023.107279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 08/14/2023]
Abstract
Long non-coding-RNAs (lncRNAs) are an expanding set of cis-/trans-regulatory RNA genes that outnumber the protein-coding genes. Although being increasingly discovered, the functional role of the majority of lncRNAs in diverse biological conditions is undefined. Increasing evidence supports the critical role of lncRNAs in the emergence, regulation, and progression of various viral infections including influenza, hepatitis, coronavirus, and human immunodeficiency virus. Hence, the identification of signature lncRNAs would facilitate focused analysis of their functional roles accounting for their targets and regulatory mechanisms associated with infections. Towards this, we compiled 2803 lncRNAs identified to be modulated by 33 viral strains in various mammalian cell types and are provided through the resource named VirhostlncR (http://ciods.in/VirhostlncR/). The information on each of the viral strains, their multiplicity of infection, duration of infection, host cell name and cell types, fold change of lncRNA expression, and their specific identification methods are integrated into VirhostlncR. Based on the current datasets, we report 150 lncRNAs including differentiation antagonizing non-protein coding RNA (DANCR), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), maternally expressed gene 3 (MEG3), nuclear paraspeckle assembly transcript 1 (NEAT1), and plasmacytoma variant translocation 1 (PVT1) to be perturbed by two or more viruses. Analysis of viral protein interactions with human transcription factors (TFs) or TF-containing protein complexes identified that distinct viruses can transcriptionally regulate many of these lncRNAs through multiple protein complexes. Together, we believe that the current dataset will enable priority selection of lncRNAs for identification of their targets and serve as an effective platform for the analysis of noncoding RNA-mediated regulations in viral infections.
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Affiliation(s)
- Arun Kumar Sumaithangi Thatai
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Shruthi Ammankallu
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Rex Devasahayam Arokia Balaya
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Sreelakshmi Pathappillil Soman
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Sreeranjini Babu
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Anju George
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Christy Kallely Anto
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Mrudula Kinarulla Kandiyil
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Sini S Raj
- Department of Computer Science, University of Kerala, Thiruvananthapuram, 695 581, Kerala, India.
| | - Kriti Awasthi
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - S S Vinodchandra
- Department of Computer Science, University of Kerala, Thiruvananthapuram, 695 581, Kerala, India.
| | - Thottethodi Subrahmanya Keshava Prasad
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Omics Analytics Pvt. Ltd., Yenepoya Incubator, Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Rajesh Raju
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India; Omics Analytics Pvt. Ltd., Yenepoya Incubator, Deralakatte, Mangalore, 575 018, Karnataka, India.
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5
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Singh A, AT V, Gupta K, Sharma S, Kumar S. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J 2023; 21:3032-3044. [PMID: 37266406 PMCID: PMC10229759 DOI: 10.1016/j.csbj.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Allotetraploid cotton plants Gossypium hirsutum and Gossypium barbadense have been widely cultivated for their natural, renewable textile fibres. Even though ncRNAs in domesticated cotton species have been extensively studied, systematic identification and annotation of lncRNAs and miRNAs expressed in various tissues and developmental stages under various biological contexts are limited. This influences the comprehension of their functions and future research on these cotton species. Here, we report high confidence lncRNAs and miRNA collection from G. hirsutum accession and G. barbadense accession using large-scale RNA-seq and small RNA-seq datasets incorporated into a user-friendly database, CoNCRAtlas. This database provides a wide range and depth of lncRNA and miRNA annotation based on the systematic integration of extensive annotations such as expression patterns derived from transcriptome data analysis in thousands of samples, as well as multi-omics annotations. We assume this comprehensive resource will accelerate evolutionary and functional studies in ncRNAs and inform future breeding programs for cotton improvement. CoNCRAtlas is accessible at http://www.nipgr.ac.in/CoNCRAtlas/.
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Affiliation(s)
- Ajeet Singh
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Postdoctoral Associate, Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Vivek AT
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Kanika Gupta
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shruti Sharma
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
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6
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Liu Z, Sun Z, Ke H, Chen B, Gu Q, Zhang M, Wu N, Chen L, Li Y, Meng C, Wang G, Wu L, Zhang G, Ma Z, Zhang Y, Wang X. Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton. Int J Mol Sci 2023; 24:ijms24098293. [PMID: 37175999 PMCID: PMC10179096 DOI: 10.3390/ijms24098293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Comparative transcriptome analysis of fiber tissues between Gossypium barbadense and Gossypium hirsutum could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in G. barbadense, which showed four distinct expression patterns (I-IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between G. barbadense and G. hirsutum. Subsequently, we overexpressed GbAAR3 and GbTWS1, two of the 42 candidate genes, in Arabidopsis plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I-V) in G. barbadense. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their G. hirsutum orthologs, and the genotyping and phenotyping of a BC3F5 population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between G. barbadense and G. hirsutum and provide novel alternative genes for fiber quality improvement.
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Affiliation(s)
- Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Man Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Nan Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liting Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yanbin Li
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
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7
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Xie X, Jin J, Wang C, Lu P, Li Z, Tao J, Cao P, Xu Y. Investigating nicotine pathway-related long non-coding RNAs in tobacco. Front Genet 2023; 13:1102183. [PMID: 36744176 PMCID: PMC9892058 DOI: 10.3389/fgene.2022.1102183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with low or no protein-coding ability, which play essential roles in various biological processes in plants. Tobacco is an ideal model plant for studying nicotine biosynthesis and metabolism, and there is little research on lncRNAs in this field. Therefore, how to take advantage of the mature tobacco system to profoundly investigate the lncRNAs involved in the nicotine pathway is intriguing. By exploiting 549 public RNA-Seq datasets of tobacco, 30,212 lncRNA candidates were identified, including 24,084 large intervening non-coding RNAs (lincRNAs), 5,778 natural antisense transcripts (NATs) and 350 intronic non-coding RNAs (incRNAs). Compared with protein-coding genes, lncRNAs have distinct properties in terms of exon number, sequence length, A/U content, and tissue-specific expression pattern. lincRNAs showed an asymmetric evolutionary pattern, with a higher proportion (68.71%) expressed from the Nicotiana sylvestris (S) subgenome. We predicted the potential cis/trans-regulatory effects on protein-coding genes. One hundred four lncRNAs were detected as precursors of 30 known microRNA (miRNA) family members, and 110 lncRNAs were expected to be the potential endogenous target mimics for 39 miRNAs. By combining the results of weighted gene co-expression network analysis with the differentially expressed gene analysis of topping RNA-seq data, we constructed a sub-network containing eight lncRNAs and 25 nicotine-related coding genes. We confirmed that the expression of seven lncRNAs could be affected by MeJA treatment and may be controlled by the transcription factor NtMYC2 using a quantitative PCR assay and gene editing. The results suggested that lncRNAs are involved in the nicotine pathway. Our findings further deepened the understanding of the features and functions of lncRNAs and provided new candidates for regulating nicotine biosynthesis in tobacco.
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Chen L, Shen E, Zhao Y, Wang H, Wilson I, Zhu QH. The Conservation of Long Intergenic Non-Coding RNAs and Their Response to Verticillium dahliae Infection in Cotton. Int J Mol Sci 2022; 23:ijms23158594. [PMID: 35955726 PMCID: PMC9368808 DOI: 10.3390/ijms23158594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) have been demonstrated to be vital regulators of diverse biological processes in both animals and plants. While many lincRNAs have been identified in cotton, we still know little about the repositories and conservativeness of lincRNAs in different cotton species or about their role in responding to biotic stresses. Here, by using publicly available RNA-seq datasets from diverse sources, including experiments of Verticillium dahliae (Vd) infection, we identified 24,425 and 17,713 lincRNAs, respectively, in Gossypium hirsutum (Ghr) and G. barbadense (Gba), the two cultivated allotetraploid cotton species, and 6933 and 5911 lincRNAs, respectively, in G. arboreum (Gar) and G. raimondii (Gra), the two extant diploid progenitors of the allotetraploid cotton. While closely related subgenomes, such as Ghr_At and Gba_At, tend to have more conserved lincRNAs, most lincRNAs are species-specific. The majority of the synthetic and transcribed lincRNAs (78.2%) have a one-to-one orthologous relationship between different (sub)genomes, although a few of them (0.7%) are retained in all (sub)genomes of the four species. The Vd responsiveness of lincRNAs seems to be positively associated with their conservation level. The major functionalities of the Vd-responsive lincRNAs seem to be largely conserved amongst Gra, Ghr, and Gba. Many Vd-responsive Ghr-lincRNAs overlap with Vd-responsive QTL, and several lincRNAs were predicted to be endogenous target mimicries of miR482/2118, with a pair being highly conserved between Ghr and Gba. On top of the confirmation of the feature characteristics of the lincRNAs previously reported in cotton and other species, our study provided new insights into the conservativeness and divergence of lincRNAs during cotton evolution and into the relationship between the conservativeness and Vd responsiveness of lincRNAs. The study also identified candidate lincRNAs with a potential role in disease response for functional characterization.
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Affiliation(s)
- Li Chen
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
| | - Enhui Shen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China;
| | - Yunlei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Hongmei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
- Correspondence:
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9
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Li W, Hu X, Huang X. Long intergenic non-protein coding RNA 847 promotes laryngeal squamous cell carcinoma progression through the microRNA-181a-5p/zinc finger E-box binding homeobox 2 axis. Bioengineered 2022; 13:9987-10000. [PMID: 35435130 PMCID: PMC9161931 DOI: 10.1080/21655979.2022.2062531] [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] [Indexed: 01/03/2023] Open
Abstract
The present study is targeted at investigating the effects of long intergenic non-protein coding RNA 847 (LINC00847) on the malignant biological behaviors of laryngeal squamous cell carcinoma (LSCC) cells, and the mechanisms. Quantitative real-time PCR and Western blotting were conducted for detecting the expressions of LINC00847, microRNA-181a-5p (miR-181a-5p) and zinc finger E-box binding homeobox 2 (ZEB2) in LSCC cell lines and tissue samples. BrdU, cell counting kit-8, scratch wound healing, Transwell and flow cytometry assays were utilized for detecting cell proliferation, migration, invasion, and cell cycle progression. Dual-luciferase reporter gene, RNA binding protein immunoprecipitation (RIP), and RNA pull-down assays were utilized to investigate the interaction among LINC00847, miR-181a-5p, and ZEB2. The subcellular location of LINC00847 was determined by RNA fluorescence in situ hybridization (RNA-FISH) assay. Tumor growth was evaluated using a xenograft model of nude mice. It was revealed that LINC00847 expression was increased in LSCC tissues, and its high expression was associated with lymph node metastasis and poor differentiation. LINC00847 was mainly located in the cytoplasm of LSCC cells, and LINC00847 overexpression promoted LSCC cell proliferation, migration, invasion, and accelerated the cell cycle progression while knocking down LINC00847 had the opposite effects in vitro and inhibited the tumor growth in vivo. LINC00847 directly targeted miR-181a-5p and negatively modulated miR-181a-5p expression. ZEB2 was a target gene of miR-181a-5p, and was positively and indirectly modulated by LINC00847. Our data suggest that LINC00847 promotes LSCC progression by regulating the miR-181a-5p/ZEB2 axis.
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Affiliation(s)
- Wei Li
- Department of Otolaryngology, Ezhou Central Hospital, Hubei, Ezhou Province, P.R. China
| | - Xionghui Hu
- Department of Otolaryngology, Tongxiang First People’s Hospital, Jiaxing, Zhejiang Province, P.R. China
| | - Xiaolin Huang
- Department of Otolaryngology, Ezhou Central Hospital, Hubei, Ezhou Province, P.R. China
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Identification of long non-coding RNAs in Verticillium dahliae following inoculation of cotton. Microbiol Res 2022; 257:126962. [PMID: 35042052 DOI: 10.1016/j.micres.2022.126962] [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: 05/23/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 11/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, these functions have not been assessed in Verticillium dahliae, a soil-borne fungal pathogen that causes devastating wilt diseases in many crops. The discovery and identity of novel lncRNAs and their association with virulence may contribute to an increased understanding of the regulation of virulence in V. dahliae. Here, we identified a total of 352 lncRNAs in V. dahliae. The lncRNAs were transcribed from all V. dahliae chromosomes, typically with shorter open reading frames, lower GC content, and fewer exons than protein-coding genes. In addition, 308 protein-coding genes located within 10 kb upstream and 10 kb downstream of lncRNAs were identified as neighboring genes, and which were considered as potential targets of lncRNA. These neighboring genes encode products involved in development, stress responses, and pathogenicity of V. dahliae, such as transcription factors (TF), kinase, and members of the secretome. Furthermore, 47 lncRNAs were significantly differentially expressed in V. dahliae following inoculation of susceptible cotton (Gossyoiumhisutum) cultivar Junmian No.1, suggesting that lncRNAs may be involved in the regulation of virulence in V. dahliae. Moreover, correlations in expression patterns between lncRNA and their neighboring genes were detected. Expression of lncRNA012077 and its neighboring gene was up-regulated 6 h following inoculation of cotton, while the expression of lncRNA007722 was down-regulated at 6 h but up-regulated at 24 h, in a pattern opposite to that of its neighboring gene. Overexpression of lncRNA012077 in wild-type strain (Vd991) enhanced its virulence on cotton while overexpression of lncRNA009491 reduced virulence. Identification of novel lncRNAs and their association with virulence may provide new targets for disease control.
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11
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Wang L, Han J, Lu K, Li M, Gao M, Cao Z, Zhao T, Chen X, Tao X, Chen Q, Guan X. Functional examination of lncRNAs in allotetraploid Gossypium hirsutum. BMC Genomics 2021; 22:443. [PMID: 34120591 PMCID: PMC8201905 DOI: 10.1186/s12864-021-07771-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. RESULTS We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. CONCLUSIONS Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.
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Affiliation(s)
- Luyao Wang
- Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China
- College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China
| | - Jin Han
- College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China
| | - Menglin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China
| | - Zeyi Cao
- College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China
| | - Xue Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, China.
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China.
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Building 11, Yonyou Industrial Park, Yazhou District, Hainan Province, 572025, Sanya, China.
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12
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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Wang L, Wang G, Long L, Altunok S, Feng Z, Wang D, Khawar KM, Mujtaba M. Understanding the role of phytohormones in cotton fiber development through omic approaches; recent advances and future directions. Int J Biol Macromol 2020; 163:1301-1313. [PMID: 32679330 DOI: 10.1016/j.ijbiomac.2020.07.104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/27/2020] [Accepted: 07/09/2020] [Indexed: 01/13/2023]
Abstract
Cotton is among the most important fiber crops for the textile-based industry, thanks to its cellulose-rich mature fibers. The fiber initiation and elongation are one of the best models for deciphering mechanisms of single-cell differentiation and growth, that also target of fiber development programs. During the last couple of decades, high yielding omics approaches (genomics, transcriptomics, and proteomics), have helped in the identification of several genes and gene products involved in fiber development along with functional relationship to phytohormones. For example, MYB transcription factor family and Sus gene family have been evidenced by controlling cotton fiber initiation. Most importantly, the biosynthesis, responses, and transporting of phytohormones is documented to participate in the initiation of cotton fibers. Herein, in this review, the reliable genetic evidence by manipulating the above genes in cotton have been summarized to describe the relationships among key phytohormones, transcription factors, proteins, and downstream fiber growth-related genes such as Sus. The effect of other important factors such as ROS, fatty acid metabolism, and actin (globular multi-functional proteins) over fiber development has also been discussed. The challenges and deficiencies in the research of cotton fiber development have been mentioned along with a future perspective to discover new crucial genes using multiple omics analysis.
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Affiliation(s)
- Lichen Wang
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Guifeng Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei 430070, China; Shandong Cotton Production Technical Guidance Station, Jinan, Shandong 250100, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan 475004, China
| | - Sumeyye Altunok
- Institute of Biotechnology, Ankara University, 06110 Ankara, Turkey
| | - Zongqin Feng
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Depeng Wang
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Khalid Mahmood Khawar
- Department of Field Crops, Faculty of Agriculture, Ankara University, 06100 Ankara, Turkey
| | - Muhammad Mujtaba
- Institute of Biotechnology, Ankara University, 06110 Ankara, Turkey.
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Patel JD, Huang X, Lin L, Das S, Chandnani R, Khanal S, Adhikari J, Shehzad T, Guo H, Roy-Zokan EM, Rong J, Paterson AH. The Ligon lintless -2 Short Fiber Mutation Is Located within a Terminal Deletion of Chromosome 18 in Cotton. PLANT PHYSIOLOGY 2020; 183:277-288. [PMID: 32102829 PMCID: PMC7210651 DOI: 10.1104/pp.19.01531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/28/2020] [Indexed: 05/06/2023]
Abstract
Extreme elongation distinguishes about one-fourth of cotton (Gossypium sp.) seed epidermal cells as "lint" fibers, useful for the textile industry, from "fuzz" fibers (<5 mm). Ligon lintless-2 (Li 2 ), a dominant mutation that results in no lint fiber but normal fuzz fiber, offers insight into pathways and mechanisms that differentiate spinnable cotton from its progenitors. A genetic map developed using 1,545 F2 plants showed that marker CISP15 was 0.4 cM from Li 2 , and "dominant" simple sequence repeat (SSR) markers (i.e. with null alleles in the Li 2 genotype) SSR7 and SSR18 showed complete linkage with Li 2 Nonrandom distribution of markers with null alleles suggests that the Li 2 phenotype results from a 176- to 221-kb deletion of the terminal region of chromosome 18 that may have been masked in prior pooled-sample mapping strategies. The deletion includes 10 genes with putative roles in fiber development. Two Glycosyltransferase Family 1 genes showed striking expression differences during elongation of wild-type versus Li 2 fiber, and virus-induced silencing of these genes in the wild type induced Li 2 -like phenotypes. Further, at least 7 of the 10 putative fiber development genes in the deletion region showed higher expression in the wild type than in Li 2 mutants during fiber development stages, suggesting coordinated regulation of processes in cell wall development and cell elongation, consistent with the hypothesis that some fiber-related quantitative trait loci comprise closely spaced groups of functionally diverse but coordinately regulated genes.
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Affiliation(s)
- Jinesh D Patel
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Xianzhong Huang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
- Plant Genomics Laboratory, College of Life Sciences, Shihezi University, 832003 Shihezi, China
| | - Lifeng Lin
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Sayan Das
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Rahul Chandnani
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, 2713 Doha, Qatar
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Eileen M Roy-Zokan
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Junkang Rong
- Zhejiang A&F University, Linan, Hangzhou 311300, Zhejiang, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
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Salih H, He S, Li H, Peng Z, Du X. Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development. PLANTS (BASEL, SWITZERLAND) 2020; 9:E128. [PMID: 31968683 PMCID: PMC7020184 DOI: 10.3390/plants9010128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/17/2022]
Abstract
The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.
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Affiliation(s)
- Haron Salih
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China; (H.S.); (S.H.); (H.L.); (Z.P.)
- Department of Crop Science, College of Agriculture, Zalingei University, P.O. BOX 6, Central Darfur, Sudan
| | - Shoupu He
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China; (H.S.); (S.H.); (H.L.); (Z.P.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
| | - Hongge Li
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China; (H.S.); (S.H.); (H.L.); (Z.P.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
| | - Zhen Peng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China; (H.S.); (S.H.); (H.L.); (Z.P.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
| | - Xiongming Du
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China; (H.S.); (S.H.); (H.L.); (Z.P.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
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