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Naoumkina M, Hinchliffe DJ, Thyssen GN. Naturally colored cotton for wearable applications. FRONTIERS IN PLANT SCIENCE 2024; 15:1350405. [PMID: 38576792 PMCID: PMC10991814 DOI: 10.3389/fpls.2024.1350405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
Naturally colored cotton (NCC) offers an environmentally friendly fiber for textile applications. Processing white cotton fiber into textiles requires extensive energy, water, and chemicals, whereas processing of NCC skips the most polluting activity, scouring-bleaching and dyeing; therefore, NCC provides an avenue to minimize the harmful impacts of textile production. NCC varieties are suitable for organic agriculture since they are naturally insect and disease-resistant, salt and drought-tolerant. Various fiber shades, ranging from light green to tan and brown, are available in the cultivated NCC (Gossypium hirsutum L.) species. The pigments responsible for the color of brown cotton fiber are proanthocyanidins or their derivatives synthesized by the flavonoid pathway. Due to pigments, the NCC has excellent ultraviolet protection properties. Some brown cotton varieties exhibited superior thermal resistance of fiber that can be used to make fabrics with enhanced flame retardancy. Here, we review molecular mechanisms involved in the pigment production of brown cotton and challenges in breeding NCC varieties with a wide range of colors but without penalty in fiber quality. Also, we discuss opportunities for NCC with flame-retarding properties in textile applications.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience and Utilization Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), New Orleans, LA, United States
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Wang Y, Liao X, Shang W, Qin J, Xu X, Hu X. The secreted feruloyl esterase of Verticillium dahliae modulates host immunity via degradation of GhDFR. MOLECULAR PLANT PATHOLOGY 2024; 25:e13431. [PMID: 38353627 PMCID: PMC10866084 DOI: 10.1111/mpp.13431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Feruloyl esterase (ferulic acid esterase, FAE) is an essential component of many biological processes in both eukaryotes and prokaryotes. This research aimed to investigate the role of FAE and its regulation mechanism in plant immunity. We identified a secreted feruloyl esterase VdFAE from the hemibiotrophic plant pathogen Verticillium dahliae. VdFAE acted as an important virulence factor during V. dahliae infection, and triggered plant defence responses, including cell death in Nicotiana benthamiana. Deletion of VdFAE led to a decrease in the degradation of ethyl ferulate. VdFAE interacted with Gossypium hirsutum protein dihydroflavanol 4-reductase (GhDFR), a positive regulator in plant innate immunity, and promoted the degradation of GhDFR. Furthermore, silencing of GhDFR led to reduced resistance of cotton plants against V. dahliae. The results suggested a fungal virulence strategy in which a fungal pathogen secretes FAE to interact with host DFR and interfere with plant immunity, thereby promoting infection.
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Affiliation(s)
- Yajuan Wang
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency Production, Key Laboratory of Plant Protection Resources and Pest Integrated Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Xiwen Liao
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency Production, Key Laboratory of Plant Protection Resources and Pest Integrated Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Wenjing Shang
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency Production, Key Laboratory of Plant Protection Resources and Pest Integrated Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jun Qin
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency Production, Key Laboratory of Plant Protection Resources and Pest Integrated Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Xiangming Xu
- Pest & Pathogen Ecology, NIAB East MallingWest MallingUK
| | - Xiaoping Hu
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency Production, Key Laboratory of Plant Protection Resources and Pest Integrated Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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Identification and Functional Analysis of the Promoter of a Leucoanthocyanidin Reductase Gene from Gossypium hirsutum. Mol Biotechnol 2023; 65:645-654. [PMID: 36155889 DOI: 10.1007/s12033-022-00571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/15/2022] [Indexed: 10/14/2022]
Abstract
Leucoanthocyanidin reductase (LAR) is the critical enzyme in the synthesis pathway of proanthocyanidins, which are the primary pigments in brown cotton fibers. Our previous study has revealed significant differences in the expression levels of GhLAR1 between white and brown cotton fibers at 10 DPA. In this work, the expression pattern of the GhLAR1 gene was further studied, and the promoter of GhLAR1 (1780 bp) was isolated and characterized. Bioinformatic analysis indicated that GhLAR1 promoter contained many known light response elements and several defenses related to transcriptional factor-binding boxes, which may partially explain the response of the GhLAR1 to temperature, NaCl, and PEG treatments. Furthermore, GhLAR1 was preferentially and strongly expressed in fibers and flowers of cotton, and the expression levels in all tested tissues (especially fibers) of brown cotton were significantly higher than those in white cotton. Consistent with the expression analysis, the GhLAR1 promoter mainly drove GUS expression in epidermal trichomes and floral organs.
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Wang Z, Rehman A, Jia Y, Dai P, He S, Wang X, Li H, Wang L, Qayyum A, Peng Z, Du X. Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton. Gene 2023; 868:147374. [PMID: 36934785 DOI: 10.1016/j.gene.2023.147374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.
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Affiliation(s)
- Zhenzhen Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yinhua Jia
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Panhong Dai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Xiaoyang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China.
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
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Lv YP, Zhao G, Xie YF, Owusu AG, Wu Y, Gao JS. Transcriptome and Metabolome Profiling Unveil Pigment Formation Variations in Brown Cotton Lines (Gossypium hirsutum L.). Int J Mol Sci 2023; 24:ijms24065249. [PMID: 36982328 PMCID: PMC10049672 DOI: 10.3390/ijms24065249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
Naturally brown colored cotton (NBCC) is becoming increasingly popular due to its natural properties of coloration. However, poor fiber quality and color fading are key issues that are hindering the cultivation of naturally colored cotton. In this study, based on transcriptome and metabolome of 18 days post-anthesis (DPA), we compared the variations of pigment formation in two brown cotton fibers (DCF and LCF), with white cotton fiber (WCF) belonging to a near-isogenic line. A transcriptome study revealed a total of 15,785 differentially expressed genes significantly enriched in the flavonoid biosynthesis pathway. Furthermore, for flavonoid biosynthesis-related genes, such as flavonoid 3′5′-hydroxylase (F3′5′H), anthocyanidin synthase (ANS), anthocyanidin reductase (ANR), chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR), and chalcone isomerase (CHI), their expressions significantly increased in LCF compared with DCF and WCF. Moreover, transcription factors MYB and bHLH were significantly expressed in LCF and DCF. Most flavonoid-related metabolites (myricetin naringenin, catechin, epicatechin-epiafzelechin, and epigallocatechin) were found to be more highly up-regulated in LCF and DCF than WCF. These findings reveal the regulatory mechanism controlling different brown pigmentation in cotton fibers and elucidate the need for the proper selection of high-quality brown cotton fiber breeding lines for promising fiber quality and durable brown color pigmentation.
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Transcriptomic profiling analysis to identify genes associated with PA biosynthesis and insolubilization in the late stage of fruit development in C-PCNA persimmon. Sci Rep 2022; 12:19140. [PMID: 36352175 PMCID: PMC9646812 DOI: 10.1038/s41598-022-23742-4] [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: 04/14/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
PA-enhanced content causes astringency in persimmon fruit. PCNA persimmons can lose their astringency naturally and they become edible when still on the tree, which allows for conserves of physical and financial resources. C-PCNA persimmon originates in China. Its deastringency trait primarily depends on decreased PA biosynthesis and PA insolubilization at the late stage of fruit development. Although some genes and transcription factors that may be involved in the deastringency of C-PCNA persimmon have been reported, the expression patterns of these genes during the key deastringency stage are reported less. To investigate the variation in PA contents and the expression patterns of deastringency-related genes during typical C-PCNA persimmon 'Xiaoguo-tianshi' fruit development and ripening, PA content and transcriptional profiling were carried out at five late stages from 70 to 160 DAF. The combinational analysis phenotype, PA content, and DEG enrichment revealed that 120-140 DAF and 140-160 DAF were the critical phases for PA biosynthesis reduction and PA insolubilization, respectively. The expression of PA biosynthesis-associated genes indicated that the downregulation of the ANR gene at 140-160 DAF may be associated with PA biosynthesis and is decreased by inhibiting its precursor cis-flavan-3-ols. We also found that a decrease in acetaldehyde metabolism-associated ALDH genes and an increase in ADH and PDC genes might result in C-PCNA persimmon PA insolubilization. In addition, a few MYB-bHLH-WD40 (MBW) homologous transcription factors in persimmon might play important roles in persimmon PA accumulation. Furthermore, combined coexpression network analysis and phylogenetic analysis of MBW suggested that three putative transcription factors WD40 (evm.TU.contig1.155), MYB (evm.TU.contig8910.486) and bHLH (evm.TU.contig1398.203), might connect and co-regulate both PA biosynthesis and its insolubilization in C-PCNA persimmon. The present study elucidated transcriptional insights into PA biosynthesis and insolubilization during the late development stages based on the C-PCNA D. kaki genome (unpublished). Thus, we focused on PA content variation and the expression patterns of genes involved in PA biosynthesis and insolubilization. Our work has provided additional evidence on previous knowledge and a basis for further exploration of the natural deastringency of C-PCNA persimmon.
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Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks. Genes (Basel) 2022; 13:genes13060954. [PMID: 35741716 PMCID: PMC9222338 DOI: 10.3390/genes13060954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations.
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Wang Z, Zhang X, He S, Rehman A, Jia Y, Li H, Pan Z, Geng X, Gao Q, Wang L, Peng Z, Du X. Transcriptome Co-expression Network and Metabolome Analysis Identifies Key Genes and Regulators of Proanthocyanidins Biosynthesis in Brown Cotton. FRONTIERS IN PLANT SCIENCE 2022; 12:822198. [PMID: 35237281 PMCID: PMC8882990 DOI: 10.3389/fpls.2021.822198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/29/2021] [Indexed: 05/24/2023]
Abstract
Brown cotton fiber (BCF) is a unique raw material of naturally colored cotton (NCC). But characteristics of the regulatory gene network and metabolic components related to the proanthocyanidins biosynthesis pathway at various stages of its fiber development remain unclear. Here, the dynamic changes in proanthocyanidins biosynthesis components and transcripts in the BCF variety "Zong 1-61" and its white near-isogenic lines (NILs) "RT" were characterized at five fiber developmental stages (0, 5, 10, 15, and 20 days post-anthesis; DPA). Enrichment analysis of differentially expressed genes (DEGs), comparison of metabolome differences, and pathway enrichment analysis of a weighted gene correlation network analysis together revealed the dominant gene expression of flavonoid biosynthesis (FB), phenylpropanoid metabolisms, and some carbohydrate metabolisms at 15 or 20 DPA than white cotton. Eventually, 63 genes were identified from five modules putatively related to FB. Three R2R3-MYB and two bHLH transcription factors were predicted as the core genes. Further, GhANS, GhANR1, and GhUFGT2 were preliminarily regulated by GhMYB46, GhMYB6, and GhMYB3, respectively, according to yeast one-hybrid assays in vitro. Our findings provide an important transcriptional regulatory network of proanthocyanidins biosynthesis pathway and dynamic flavonoid metabolism profiles.
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Affiliation(s)
- Zhenzhen Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaomeng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hongge Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiong Gao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Biochemical and Expression Analyses Revealed the Involvement of Proanthocyanidins and/or Their Derivatives in Fiber Pigmentation of Gossypium stocksii. Int J Mol Sci 2022; 23:ijms23021008. [PMID: 35055193 PMCID: PMC8779443 DOI: 10.3390/ijms23021008] [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: 12/12/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
The wild cotton species Gossypium stocksii produces a brown fiber that provides a valuable resource for the color improvement of naturally colored cotton (NCC) fiber. However, the biochemical basis and molecular mechanism of its fiber pigmentation remain unclear. Herein, we analyzed the dynamics of proanthocyanidins (PAs) accumulation in developing the fiber of G. stocksii, which suggested a similar role of PAs and/or their derivatives in the fiber coloration of G. stocksii. In addition, comparative transcriptomics analyses revealed that the PA biosynthetic genes were expressed at higher levels and for a longer period in developing fibers of G. stocksii than G. arboreum (white fiber), and the transcription factors, such as TT8, possibly played crucial regulatory roles in regulating the PA branch genes. Moreover, we found that the anthocyanidin reductase (ANR) was expressed at a higher level than the leucoanthocyanidin reductases (LARs) and significantly upregulated during fiber elongation, suggesting a major role of ANR in PA synthesis in G. stocksii fiber. In summary, this work revealed the accumulation of PAs and the expression enhancement of PA biosynthetic genes in developing fibers of G. stocksii. We believe this work will help our understanding of the molecular mechanisms of cotton fiber coloration and further promote the future breeding of novel NCCs.
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Nogia P, Pati PK. Plant Secondary Metabolite Transporters: Diversity, Functionality, and Their Modulation. FRONTIERS IN PLANT SCIENCE 2021; 12:758202. [PMID: 34777438 PMCID: PMC8580416 DOI: 10.3389/fpls.2021.758202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/01/2021] [Indexed: 05/04/2023]
Abstract
Secondary metabolites (SMs) play crucial roles in the vital functioning of plants such as growth, development, defense, and survival via their transportation and accumulation at the required site. However, unlike primary metabolites, the transport mechanisms of SMs are not yet well explored. There exists a huge gap between the abundant presence of SM transporters, their identification, and functional characterization. A better understanding of plant SM transporters will surely be a step forward to fulfill the steeply increasing demand for bioactive compounds for the formulation of herbal medicines. Thus, the engineering of transporters by modulating their expression is emerging as the most viable option to achieve the long-term goal of systemic metabolic engineering for enhanced metabolite production at minimum cost. In this review article, we are updating the understanding of recent advancements in the field of plant SM transporters, particularly those discovered in the past two decades. Herein, we provide notable insights about various types of fully or partially characterized transporters from the ABC, MATE, PUP, and NPF families including their diverse functionalities, structural information, potential approaches for their identification and characterization, several regulatory parameters, and their modulation. A novel perspective to the concept of "Transporter Engineering" has also been unveiled by highlighting its potential applications particularly in plant stress (biotic and abiotic) tolerance, SM accumulation, and removal of anti-nutritional compounds, which will be of great value for the crop improvement program. The present study creates a roadmap for easy identification and a better understanding of various transporters, which can be utilized as suitable targets for transporter engineering in future research.
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Affiliation(s)
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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Tang Z, Fan Y, Zhang L, Zheng C, Chen A, Sun Y, Guo H, Wu J, Li T, Fan Y, Lian X, Guo H, Ma X, Chen H, Zeng F. Quantitative metabolome and transcriptome analysis reveals complex regulatory pathway underlying photoinduced fiber color formation in cotton. Gene 2020; 767:145180. [PMID: 33002572 DOI: 10.1016/j.gene.2020.145180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/29/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022]
Abstract
As an important plant single cell model and textile application materials, poorly known about fiber color formation in cotton, which is sensitively regulated by environmental signals. Our studies underline the importance of photo signal on sensitive fiber color formation and characterize fiber color early initiation (15 DPA) and late accumulated metabolites (45 DPA) in different lighting condition. The results revealed 236 differential metabolites between control and shading, of which phenylpropanoids metabolites accounted for 20%, including uncharacterized novel metabolites and pathways. Furthermore, the early initiation specific genes respond to the absence of light are highly correlated with phenylpropanoid metabolites related to pigmentation. The current study reveals the complex pathways involving early initiation regulation and late metabolic pathways. In addition, the collection composed of uncharacterized photoinduced metabolites and early initiation signaling/regulatory genes were identified, which are important resources for understanding fiber color formation. This report provides new insight into molecular regulatory and biochemical basis underlying photoinduced fiber color formation in cotton.
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Affiliation(s)
- Zhengmin Tang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yijie Fan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Congcong Zheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Aiyun Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yuxiao Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Haixia Guo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Jianfei Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Tongtong Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yupeng Fan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Xin Lian
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Huihui Guo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Haifeng Chen
- Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China
| | - Fanchang Zeng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
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Genetic Analysis of the Transition from Wild to Domesticated Cotton ( Gossypium hirsutum L.). G3-GENES GENOMES GENETICS 2020; 10:731-754. [PMID: 31843806 PMCID: PMC7003101 DOI: 10.1534/g3.119.400909] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F2 individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.
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Gao J, Shen L, Yuan J, Zheng H, Su Q, Yang W, Zhang L, Nnaemeka VE, Sun J, Ke L, Sun Y. Functional analysis of GhCHS, GhANR and GhLAR in colored fiber formation of Gossypium hirsutum L. BMC PLANT BIOLOGY 2019; 19:455. [PMID: 31664897 PMCID: PMC6819470 DOI: 10.1186/s12870-019-2065-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/02/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND The formation of natural colored fibers mainly results from the accumulation of different anthocyanidins and their derivatives in the fibers of Gossypium hirsutum L. Chalcone synthase (CHS) is the first committed enzyme of flavonoid biosynthesis, and anthocyanidins are transported into fiber cells after biosynthesis mainly by Anthocyanidin reductase (ANR) and Leucoanthocyanidin reductase (LAR) to present diverse colors with distinct stability. The biochemical and molecular mechanism of pigment formation in natural colored cotton fiber is not clear. RESULTS The three key genes of GhCHS, GhANR and GhLAR were predominantly expressed in the developing fibers of colored cotton. In the GhCHSi, GhANRi and GhLARi transgenic cottons, the expression levels of GhCHS, GhANR and GhLAR significantly decreased in the developing cotton fiber, negatively correlated with the content of anthocyanidins and the color depth of cotton fiber. In colored cotton Zongxu1 (ZX1) and the GhCHSi, GhANRi and GhLARi transgenic lines of ZX1, HZ and ZH, the anthocyanidin contents of the leaves, cotton kernels, the mixture of fiber and seedcoat were all changed and positively correlated with the fiber color. CONCLUSION The three genes of GhCHS, GhANR and GhLAR were predominantly expressed early in developing colored cotton fibers and identified to be a key genes of cotton fiber color formation. The expression levels of the three genes affected the anthocyanidin contents and fiber color depth. So the three genes played a crucial part in cotton fiber color formation and has important significant to improve natural colored cotton quality and create new colored cotton germplasm resources by genetic engineering.
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Affiliation(s)
- Jianfang Gao
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Li Shen
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Jingli Yuan
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Hongli Zheng
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Quansheng Su
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Weiguang Yang
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Liqing Zhang
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Vitalis Ekene Nnaemeka
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Jie Sun
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China
| | - Liping Ke
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
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Khan AQ, Li Z, Ahmed MM, Wang P, Zhang X, Tu L. Eriodictyol can modulate cellular auxin gradients to efficiently promote in vitro cotton fibre development. BMC PLANT BIOLOGY 2019; 19:443. [PMID: 31651240 PMCID: PMC6814110 DOI: 10.1186/s12870-019-2054-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/25/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Flavonoids have essential roles in flower pigmentation, fibre development and disease resistance in cotton. Previous studies show that accumulation of naringenin in developing cotton fibres significantly affects fibre growth. This study focused on determining the effects of the flavonoids naringenin, dihydrokaempferol, dihydroquerectin and eriodictyol on fibre development in an in vitro system. RESULTS 20 μM eriodictyol treatment produced a maximum fibre growth, in terms of fibre length and total fibre units. To gain insight into the associated transcriptional regulatory networks, RNA-seq analysis was performed on eriodictyol-treated elongated fibres, and computational analysis of differentially expressed genes revealed that carbohydrate metabolism and phytohormone signaling pathways were differentially modulated. Eriodictyol treatment also promoted the biosynthesis of quercetin and dihydroquerectin in ovules and elongating fibres through enhanced expression of genes encoding chalcone isomerase, chalcone synthase and flavanone 3-hydroxylase. In addition, auxin biosynthesis and signaling pathway genes were differentially expressed in eriodictyol-driven in vitro fibre elongation. In absence of auxin, eriodictyol predominantly enhanced fibre growth when the localized auxin gradient was disrupted by the auxin transport inhibitor, triiodobenzoic acid. CONCLUSION Eriodictyol was found to significantly enhance fibre development through accumulating and maintaining the temporal auxin gradient in developing unicellular cotton fibres.
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Affiliation(s)
- Anam Qadir Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
- Institute of Plant Breeding & Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University 430070, Wuhan, Hubei People’s Republic of China
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15
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Sun S, Xiong XP, Zhu Q, Li YJ, Sun J. Transcriptome Sequencing and Metabolome Analysis Reveal Genes Involved in Pigmentation of Green-Colored Cotton Fibers. Int J Mol Sci 2019; 20:E4838. [PMID: 31569469 PMCID: PMC6801983 DOI: 10.3390/ijms20194838] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
Green-colored fiber (GCF) is the unique raw material for naturally colored cotton textile but we know little about the pigmentation process in GCF. Here we compared transcriptomes and metabolomes of 12, 18 and 24 days post-anthesis (DPA) fibers from a green fiber cotton accession and its white-colored fiber (WCF) near-isogenic line. We found a total of 2047 non-redundant metabolites in GCF and WCF that were enriched in 80 pathways, including those of biosynthesis of phenylpropanoid, cutin, suberin, and wax. Most metabolites, particularly sinapaldehyde, of the phenylpropanoid pathway had a higher level in GCF than in WCF, consistent with the significant up-regulation of the genes responsible for biosynthesis of those metabolites. Weighted gene co-expression network analysis (WGCNA) of genes differentially expressed between GCF and WCF was used to uncover gene-modules co-expressed or associated with the accumulation of green pigments. Of the 16 gene-modules co-expressed with fiber color or time points, the blue module associated with G24 (i.e., GCF at 24 DPA) was of particular importance because a large proportion of its genes were significantly up-regulated at 24 DPA when fiber color was visually distinguishable between GCF and WCF. A total of 56 hub genes, including the two homoeologous Gh4CL4 that could act in green pigment biosynthesis, were identified among the genes of the blue module that are mainly involved in lipid metabolism, phenylpropanoid biosynthesis, RNA transcription, signaling, and transport. Our results provide novel insights into the mechanisms underlying pigmentation of green fibers and clues for developing cottons with stable green colored fibers.
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Affiliation(s)
- Shichao Sun
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Bei 5 Road, Shihezi 832003, China.
| | - Xian-Peng Xiong
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Bei 5 Road, Shihezi 832003, China.
| | - Qianhao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra 2601, Australia.
| | - Yan-Jun Li
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Bei 5 Road, Shihezi 832003, China.
| | - Jie Sun
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Bei 5 Road, Shihezi 832003, China.
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Yan Q, Wang Y, Li Q, Zhang Z, Ding H, Zhang Y, Liu H, Luo M, Liu D, Song W, Liu H, Yao D, Ouyang X, Li Y, Li X, Pei Y, Xiao Y. Up-regulation of GhTT2-3A in cotton fibres during secondary wall thickening results in brown fibres with improved quality. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1735-1747. [PMID: 29509985 PMCID: PMC6131414 DOI: 10.1111/pbi.12910] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 05/20/2023]
Abstract
Brown cotton fibres are the most widely used naturally coloured raw materials for the eco-friendly textile industry. Previous studies have indicated that brown fibre pigments belong to proanthocyanidins (PAs) or their derivatives, and fibre coloration is negatively associated with cotton productivity and fibre quality. To date, the molecular basis controlling the biosynthesis and accumulation of brown pigments in cotton fibres is largely unknown. In this study, based on expressional and transgenic analyses of cotton homologs of ArabidopsisPA regulator TRANSPARENT TESTA 2 (TT2) and fine-mapping of the cotton dark-brown fibre gene (Lc1), we show that a TT2 homolog, GhTT2-3A, controls PA biosynthesis and brown pigmentation in cotton fibres. We observed that GhTT2-3A activated GhbHLH130D, a homolog of ArabidopsisTT8, which in turn synergistically acted with GhTT2-3A to activate downstream PA structural genes and PA synthesis and accumulation in cotton fibres. Furthermore, the up-regulation of GhTT2-3A in fibres at the secondary wall-thickening stage resulted in brown mature fibres, and fibre quality and lint percentage were comparable to that of the white-fibre control. The findings of this study reveal the regulatory mechanism controlling brown pigmentation in cotton fibres and demonstrate a promising biotechnological strategy to break the negative linkage between coloration and fibre quality and/or productivity.
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Affiliation(s)
- Qian Yan
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Yi Wang
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Qian Li
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Zhengsheng Zhang
- College of Agronomy and Biological Science and TechnologySouthwest UniversityChongqingChina
| | - Hui Ding
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Yue Zhang
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Housheng Liu
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Ming Luo
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Dexin Liu
- College of Agronomy and Biological Science and TechnologySouthwest UniversityChongqingChina
| | - Wu Song
- Institute of Xinjiang Naturally‐Coloured CottonChina Coloured Cotton (Group) CompanyUrumchiXinjiang Uygur Autonomous RegionChina
| | - Haifeng Liu
- Institute of Xinjiang Naturally‐Coloured CottonChina Coloured Cotton (Group) CompanyUrumchiXinjiang Uygur Autonomous RegionChina
| | - Dan Yao
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Xufen Ouyang
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Yaohua Li
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Xin Li
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Yan Pei
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
| | - Yuehua Xiao
- Biotechnology Research CenterChongqing Key Laboratory of Application and Safety Control of Genetically Modified CropsSouthwest UniversityChongqingChina
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17
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Liu HF, Luo C, Song W, Shen H, Li G, He ZG, Chen WG, Cao YY, Huang F, Tang SW, Hong P, Zhao EF, Zhu J, He D, Wang S, Huo GY, Liu H. Flavonoid biosynthesis controls fiber color in naturally colored cotton. PeerJ 2018; 6:e4537. [PMID: 29682406 PMCID: PMC5910794 DOI: 10.7717/peerj.4537] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/06/2018] [Indexed: 12/28/2022] Open
Abstract
The existence of only natural brown and green cotton fibers (BCF and GCF, respectively), as well as poor fiber quality, limits the use of naturally colored cotton (Gossypium hirsutum L.). A better understanding of fiber pigment regulation is needed to surmount these obstacles. In this work, transcriptome analysis and quantitative reverse transcription PCR revealed that 13 and 9 phenylpropanoid (metabolic) pathway genes were enriched during pigment synthesis, while the differential expression of phenylpropanoid (metabolic) and flavonoid metabolic pathway genes occurred among BCF, GCF, and white cotton fibers (WCF). Silencing the chalcone flavanone isomerase gene in a BCF line resulted in three fiber phenotypes among offspring of the RNAi lines: BCF, almost WCF, and GCF. The lines with almost WCF suppressed chalcone flavanone isomerase, while the lines with GCF highly expressed the glucosyl transferase (3GT) gene. Overexpression of the Gh3GT or Arabidopsis thaliana 3GT gene in BCF lines resulted in GCF. Additionally, the phenylpropanoid and flavonoid metabolites of BCF and GCF were significantly higher than those of WCF as assessed by a metabolomics analysis. Thus, the flavonoid biosynthetic pathway controls both brown and green pigmentation processes. Like natural colored fibers, the transgenic colored fibers were weaker and shorter than WCF. This study shows the potential of flavonoid pathway modifications to alter cotton fibers’ color and quality.
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Affiliation(s)
- Hai-Feng Liu
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Cheng Luo
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Wu Song
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Haitao Shen
- Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Zhi-Gang He
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Wen-Gang Chen
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Yan-Yan Cao
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Fang Huang
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Shou-Wu Tang
- China Colored-cotton (Group) Co., Ltd., Urumqi, Xinjiang, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - En-Feng Zhao
- Translational Stem Cell Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jianbo Zhu
- Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Dajun He
- Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Shaoming Wang
- Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Guang-Ying Huo
- Translational Stem Cell Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hailiang Liu
- Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, Xinjiang, China.,Translational Stem Cell Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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Li PT, Wang M, Lu QW, Ge Q, Rashid MHO, Liu AY, Gong JW, Shang HH, Gong WK, Li JW, Song WW, Guo LX, Su W, Li SQ, Guo XP, Shi YZ, Yuan YL. Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and Chromosome Segment Substitution Lines from G. hirsutum × G. barbadense. BMC Genomics 2017; 18:705. [PMID: 28886694 PMCID: PMC5591532 DOI: 10.1186/s12864-017-4077-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton. Results In total, 15 RNA-seq libraries were constructed and sequenced separately, generating 705.433 million clean reads with mean GC content of 45.13% and average Q30 of 90.26%. Through multiple comparisons between libraries, 1801 differentially expressed genes (DEGs) were identified, of which the 902 up-regulated DEGs were mainly involved in cell wall organization and response to oxidative stress and auxin, while the 898 down-regulated ones participated in translation, regulation of transcription, DNA-templated and cytoplasmic translation based on GO annotation and KEGG enrichment analysis. Subsequently, STEM software was performed to explicate the temporal expression pattern of DEGs. Two peroxidases and four flavonoid pathway-related genes were identified in the “oxidation-reduction process”, which could play a role in fiber development and quality formation. Finally, the reliability of RNA-seq data was validated by quantitative real-time PCR of randomly selected 20 genes. Conclusions The present report focuses on the similarities and differences of transcriptome profiles between the two CSSLs and the recurrent parent CCRI36 and provides novel insights into the molecular mechanism of fiber development, and into further exploration of the feasible contribution of G. barbadense substitution segments to fiber quality formation, which will lay solid foundation for simultaneously improving fiber yield and quality of upland cotton through CSSLs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4077-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peng-Tao Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mi Wang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Quan-Wei Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Md Harun Or Rashid
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Ai-Ying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Ju-Wu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Hai-Hong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Wan-Kui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Jun-Wen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Wei-Wu Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Li-Xue Guo
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Wei Su
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.,College of Agriculture, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Shao-Qi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Xiao-Ping Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Yu-Zhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
| | - You-Lu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
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Lu N, Roldan M, Dixon RA. Characterization of two TT2-type MYB transcription factors regulating proanthocyanidin biosynthesis in tetraploid cotton, Gossypium hirsutum. PLANTA 2017; 246:323-335. [PMID: 28421329 DOI: 10.1007/s00425-017-2682-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/21/2017] [Indexed: 05/27/2023]
Abstract
Two TT2-type MYB transcription factors identified from tetraploid cotton are involved in regulating proanthocyanidin biosynthesis, providing new strategies for engineering condensed tannins in crops. Proanthocyanidins (PAs), also known as condensed tannins, are important secondary metabolites involved in stress resistance in plants, and are health supplements that help to reduce cholesterol levels. As one of the most widely grown crops in the world, cotton provides the majority of natural fabrics and is a supplemental food for ruminant animals. The previous studies have suggested that PAs present in cotton are a major contributor to fiber color. However, the biosynthesis of PAs in cotton still remains to be elucidated. AtTT2 (transparent testa 2) is a MYB family transcription factor from Arabidopsis that initiates the biosynthesis of PAs by inducing the expression of multiple genes in the pathway. In this study, we isolated two R2R3-type MYB transcription factors from Gossypium hirsutum that are homologous to AtTT2. Expression analysis showed that both genes were expressed at different levels in various cotton tissues, including leaf, seed coat, and fiber. Protoplast transactivation assays revealed that these two GhMYBs were able to activate promoters of genes encoding enzymes in the PA biosynthesis pathway, namely anthocyanidin reductase and leucoanthocyanidin reductase. Complementation experiments showed that both of the GhMYBs were able to recover the transparent testa seed coat phenotype of the Arabidopsis tt2 mutant by restoring PA biosynthesis. Ectopic expression of either of the two GhMYBs in Medicago truncatula hairy roots increased the contents of anthocyanins and PAs compared to control lines expressing the GUS gene, and expression levels of MtDFR, MtLAR, and MtANR were also elevated in lines expressing GhMYBs. Together, these data provide new insights into engineering condensed tannins in cotton.
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Affiliation(s)
- Nan Lu
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | | | - Richard A Dixon
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA.
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20
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Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, Yuan D, Zhang Q, Lindsey K, Zhang X. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 2017; 49:579-587. [PMID: 28263319 DOI: 10.1038/ng.3807] [Citation(s) in RCA: 269] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Abstract
Comparative population genomics offers an excellent opportunity for unraveling the genetic history of crop domestication. Upland cotton (Gossypium hirsutum) has long been an important economic crop, but a genome-wide and evolutionary understanding of the effects of human selection is lacking. Here, we describe a variation map for 352 wild and domesticated cotton accessions. We scanned 93 domestication sweeps occupying 74 Mb of the A subgenome and 104 Mb of the D subgenome, and identified 19 candidate loci for fiber-quality-related traits through a genome-wide association study. We provide evidence showing asymmetric subgenome domestication for directional selection of long fibers. Global analyses of DNase I-hypersensitive sites and 3D genome architecture, linking functional variants to gene transcription, demonstrate the effects of domestication on cis-regulatory divergence. This study provides new insights into the evolution of gene organization, regulation and adaptation in a major crop, and should serve as a rich resource for genome-based cotton improvement.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaolin Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xinhui Nie
- Key Laboratory of Oasis Eco-agriculture of the Xinjiang Production and Construction Corps, College of Agronomy, Shihezi University, Shihezi, China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiyan Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ling Min
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daojun Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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21
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Hinchliffe DJ, Condon BD, Thyssen G, Naoumkina M, Madison CA, Reynolds M, Delhom CD, Fang DD, Li P, McCarty J. The GhTT2_A07 gene is linked to the brown colour and natural flame retardancy phenotypes of Lc1 cotton (Gossypium hirsutum L.) fibres. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5461-5471. [PMID: 27567364 PMCID: PMC5049394 DOI: 10.1093/jxb/erw312] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Some naturally coloured brown cotton fibres from accessions of Gossypium hirsutum L. can be used to make textiles with enhanced flame retardancy (FR). Several independent brown fibre loci have been identified and mapped to chromosomes, but the underlying genes have not yet been identified, and the mechanism of lint fibre FR is not yet fully understood. In this study, we show that both the brown colour and enhanced FR of the Lc1 lint colour locus are linked to a 1.4Mb inversion on chromosome A07 that is immediately upstream of a gene with similarity to Arabidopsis TRANSPARENT TESTA 2 (TT2). As a result of the alternative upstream sequence, the transcription factor GhTT2_A07 is highly up-regulated in developing fibres. In turn, genes in the phenylpropanoid metabolic pathway are activated, leading to biosynthesis of proanthocyanidins and accumulation of inorganic elements. We show that enhanced FR and anthocyanin precursors appear in developing brown fibres well before the brown colour is detectible, demonstrating for the first time that the polymerized proanthocyanidins that constitute the brown colour are not the source of enhanced FR. Identifying the particular colourless metabolite that provides Lc1 cotton with enhanced FR could help minimize the use of synthetic chemical flame retardant additives in textiles.
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Affiliation(s)
- Doug J Hinchliffe
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Brian D Condon
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Gregory Thyssen
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Crista A Madison
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Michael Reynolds
- Cotton Chemistry and Utilization Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Christopher D Delhom
- Cotton Structure and Quality Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Ping Li
- Cotton Fiber Bioscience Research Unit, Southern Regional Research Center, Agricultural Research Service, USDA, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA
| | - Jack McCarty
- Genetics and Sustainable Agriculture Research Unit, Agricultural Research Service, USDA, Mississippi State, MS 39762, USA
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22
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De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq. PLoS One 2016; 11:e0150273. [PMID: 26943165 PMCID: PMC4778938 DOI: 10.1371/journal.pone.0150273] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 02/11/2016] [Indexed: 01/19/2023] Open
Abstract
Plantago ovata is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of P. ovata ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant. De novo assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of P. ovata using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in P. ovata.
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23
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Gao JS, Wu N, Shen ZL, Lv K, Qian SH, Guo N, Sun X, Cai YP, Lin Y. Molecular cloning, expression analysis and subcellular localization of a Transparent Testa 12 ortholog in brown cotton (Gossypium hirsutum L.). Gene 2016; 576:763-9. [DOI: 10.1016/j.gene.2015.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 10/16/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
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24
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Yan Q, Liu HS, Yao D, Li X, Chen H, Dou Y, Wang Y, Pei Y, Xiao YH. The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization. PLoS One 2015; 10:e0126558. [PMID: 25992947 PMCID: PMC4436304 DOI: 10.1371/journal.pone.0126558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/03/2015] [Indexed: 12/05/2022] Open
Abstract
Basic/helix-loop-helix (bHLH) proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum), a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors) maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062) showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.
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Affiliation(s)
- Qian Yan
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Hou-Sheng Liu
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Dan Yao
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Xin Li
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Han Chen
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Yang Dou
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Yi Wang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Yan Pei
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
| | - Yue-Hua Xiao
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Beibei, Chongqing, China
- * E-mail:
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