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Molecular Regulation of Cotton Fiber Development: A Review. Int J Mol Sci 2022; 23:ijms23095004. [PMID: 35563394 PMCID: PMC9101851 DOI: 10.3390/ijms23095004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Cotton (Gossypium spp.) is an economically important natural fiber crop. The quality of cotton fiber has a substantial effect on the quality of cotton textiles. The identification of cotton fiber development-related genes and exploration of their biological functions will not only enhance our understanding of the elongation and developmental mechanisms of cotton fibers but also provide insights that could aid the cultivation of new cotton varieties with improved fiber quality. Cotton fibers are single cells that have been differentiated from the ovule epidermis and serve as a model system for research on single-cell differentiation, growth, and fiber production. Genes and fiber formation mechanisms are examined in this review to shed new light on how important phytohormones, transcription factors, proteins, and genes linked to fiber development work together. Plant hormones, which occur in low quantities, play a critically important role in regulating cotton fiber development. Here, we review recent research that has greatly contributed to our understanding of the roles of different phytohormones in fiber development and regulation. We discuss the mechanisms by which phytohormones regulate the initiation and elongation of fiber cells in cotton, as well as the identification of genes involved in hormone biosynthetic and signaling pathways that regulate the initiation, elongation, and development of cotton fibers.
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Prasad P, Khatoon U, Verma RK, Aalam S, Kumar A, Mohapatra D, Bhattacharya P, Bag SK, Sawant SV. Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:811655. [PMID: 35283936 PMCID: PMC8908376 DOI: 10.3389/fpls.2022.811655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Cotton fiber development is still an intriguing question to understand fiber commitment and development. At different fiber developmental stages, many genes change their expression pattern and have a pivotal role in fiber quality and yield. Recently, numerous studies have been conducted for transcriptional regulation of fiber, and raw data were deposited to the public repository for comprehensive integrative analysis. Here, we remapped > 380 cotton RNAseq data with uniform mapping strategies that span ∼400 fold coverage to the genome. We identified stage-specific features related to fiber cell commitment, initiation, elongation, and Secondary Cell Wall (SCW) synthesis and their putative cis-regulatory elements for the specific regulation in fiber development. We also mined Exclusively Expressed Transcripts (EETs) that were positively selected during cotton fiber evolution and domestication. Furthermore, the expression of EETs was validated in 100 cotton genotypes through the nCounter assay and correlated with different fiber-related traits. Thus, our data mining study reveals several important features related to cotton fiber development and improvement, which were consolidated in the "CottonExpress-omics" database.
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Affiliation(s)
- Priti Prasad
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Uzma Khatoon
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Rishi Kumar Verma
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shahre Aalam
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | - Ajay Kumar
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | | | | | - Sumit K. Bag
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samir V. Sawant
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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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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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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Salih H, Odongo MR, Gong W, He S, Du X. Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development. BMC PLANT BIOLOGY 2019; 19:400. [PMID: 31510939 PMCID: PMC6739942 DOI: 10.1186/s12870-019-2003-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/30/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND C2H2-zinc finger protein family is commonly found in the plant, and it is known as the key actors in the regulation of transcription and vital component of chromatin structure. A large number of the C2H2-zinc finger gene members have not been well characterized based on their functions and structure in cotton. However, in other plants, only a few C2H2-zinc finger genes have been studied. RESULTS In this work, we performed a comprehensive analysis and identified 386, 196 and 195 C2H2-zinc finger genes in Gossypium hirsutum (upland cotton), Gossypium arboreum and Gossypium raimondii, respectively. Phylogenetic tree analysis of the C2H2-zinc finger proteins encoding the C2H2-zinc finger genes were classified into seven (7) subgroups. Moreover, the C2H2-zinc finger gene members were distributed in all cotton chromosomes though with asymmetrical distribution patterns. All the orthologous genes were detected between tetraploid and the diploid cotton, with 154 orthologous genes pair detected between upland cotton and Gossypium arboreum while 165 orthologous genes were found between upland cotton and Gossypium raimondii. Synonymous (Ks) and non-synonymous (Ka) nucleotide substitution rates (Ka/Ks) analysis indicated that the cotton C2H2-zinc finger genes were highly influenced mainly by negative selection, which maintained their protein levels after the duplication events. RNA-seq data and RT-qPCR validation of the RNA seq result revealed differential expression pattern of some the C2H2-zinc finger genes at different stages of cotton fiber development, an indication that the C2H2-zinc finger genes play an important role in initiating and regulating fiber development in cotton. CONCLUSIONS This study provides a strong foundation for future practical genome research on C2H2-zinc finger genes in upland cotton. The expression levels of C2H2-zinc finger genes family is a pointer of their involvement in various biochemical and physiological functions which are directly related to cotton fiber development during initiation and elongation stages. This work not only provides a basis for determining the nominal role of the C2H2-zinc finger genes in fiber development but also provide valuable information for characterization of potential candidate genes involved in regulation of cotton fiber development.
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Affiliation(s)
- Haron Salih
- College of life sciences, Huazhong Agricultural University, Wuhan, 430070 Hubei China
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
- Zalingei University, Central Darfur, Sudan
| | - Magwanga Richard Odongo
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Salih H, Gong W, He S, Xia W, Odongo MR, Du X. Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development. BMC Genomics 2019; 20:661. [PMID: 31426741 PMCID: PMC6700839 DOI: 10.1186/s12864-019-5978-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/16/2019] [Indexed: 01/28/2023] Open
Abstract
Background Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development. Results In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development. Conclusion The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality. Electronic supplementary material The online version of this article (10.1186/s12864-019-5978-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.,Zalingei University, Central Darfur, Sudan
| | - Wenfang Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Wang Xia
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Magwanga Richard Odongo
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
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Salih H, Gong W, He S, Mustafa NS, Du X. Comparative transcriptome analysis of TUCPs in Gossypium hirsutum Ligon-lintless-1 mutant and their proposed functions in cotton fiber development. Mol Genet Genomics 2018; 294:23-34. [DOI: 10.1007/s00438-018-1482-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/21/2018] [Indexed: 02/08/2023]
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Salih H, Gong W, He S, Sun G, Sun J, Du X. Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum. BMC Genet 2016; 17:129. [PMID: 27613381 PMCID: PMC5017022 DOI: 10.1186/s12863-016-0436-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background MYB family proteins are one of the most abundant transcription factors in the cotton plant and play diverse roles in cotton growth and evolution. Previously, few studies have been conducted in upland cotton, Gossypium hirsutum. The recent release of the G. hirsutum genome sequence provides a great opportunity to identify and characterize the entire upland cotton MYB protein family. Results In this study, we undertook a comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during cotton fiber development. A total of 524 non-redundant cotton MYB genes, among 1986 MYB and MYB-related putative proteins, were identified and classified into four subfamilies including 1R-MYB, 2R-MYB, 3R-MYB, and 4R-MYB. Based on phylogenetic tree analysis, MYB transcription factors were divided into 16 subgroups. The results showed that the majority (69.1 %) of GhMYBs genes belong to the 2R-MYB subfamily in upland cotton. Conclusion Our comparative genomics analysis has provided novel insights into the roles of MYB transcription factors in cotton fiber development. These results provide the basis for a greater understanding of MYB regulatory networks and to develop new approaches to improve cotton fiber development. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0436-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haron Salih
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, 455000, China.,College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Zalingei University, Central Darfur, Sudan
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, 455000, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, 455000, China
| | - Gaofei Sun
- Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, China
| | - Junling Sun
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, 455000, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang, 455000, China.
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