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Ma J, Yang L, Dang Y, Shahzad K, Song J, Jia B, Wang L, Feng J, Wang N, Pei W, Wu M, Zhang X, Zhang J, Wu J, Yu J. Deciphering the dynamic expression network of fiber elongation and the functional role of the GhTUB5 gene for fiber length in cotton based on an introgression population of upland cotton. J Adv Res 2024:S2090-1232(24)00324-2. [PMID: 39106927 DOI: 10.1016/j.jare.2024.08.004] [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: 02/27/2024] [Revised: 07/02/2024] [Accepted: 08/02/2024] [Indexed: 08/09/2024] Open
Abstract
INTRODUCTION Interspecific introgression between Gossypium hirsutum and G. barbadense allows breeding cotton with outstanding fiber length (FL). However, the dynamic gene regulatory network of FL-related genes has not been characterized, and the functional mechanism through which the hub gene GhTUB5 mediates fiber elongation has yet to be determined. METHODS Coexpression analyses of 277 developing fiber transcriptomes integrated with QTL mapping using 250 introgression lines of different FL phenotypes were conducted to identify genes related to fiber elongation. The function of GhTUB5 was determined by ectopic expression of two TUB5 alleles in Arabidopsis and knockout of GhTUB5 in upland cotton. Yeast two-hybrid, split-luciferase and pull-down assays were conducted to screen for interacting proteins, and upstream genes were identified by yeast one-hybrid, dual-LUC and electrophoretic mobility shift assays. RESULTS The 32,612, 30,837 and 30,277 genes expressed at 5, 10 and 15 days postanthesis (dpa) were grouped into 19 distinct coexpression modules, and 988 genes in the MEblack module were enriched in the cell wall process and exhibited significant associations with FL. A total of 20 FL-QTLs were identified, each explaining 3.34-16.04 % of the phenotypic variance in the FL. Furthermore, several FL-QTLs contained 15 genes that were differentially expressed in the MEblack module including the tubulin beta gene (TUB5). Compared with the wild type, the overexpression of GhTUB5 and GbTUB5 in Arabidopsis suppressed root cell length but promoted cellulose synthesis. Knockout of GhTUB5 resulted in longer fiber lines. Protein-based experiments revealed that GhTUB5 interacts with GhZFP6. Additionally, GhTUB5 was directly activated by GhHD-ZIP7, a homeobox-leucine zipper transcription factor, and its paralogous gene was previously reported to mediate fiber elongation. CONCLUSION This study opens a new avenue to dissect functional mechanism of cotton fiber elongation. Our findings provide some molecular details on how GhTUB5 mediates the FL phenotype in cotton.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Liupeng Yang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuanyue Dang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Nuohan Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Man Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, USA.
| | - Jianyong Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China; Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China.
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Song Q, Gao W, Du C, Wang J, Zuo K. Cotton microtubule-associated protein GhMAP20L5 mediates fiber elongation through the interaction with the tubulin GhTUB13. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111545. [PMID: 36464024 DOI: 10.1016/j.plantsci.2022.111545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/30/2022] [Accepted: 11/27/2022] [Indexed: 05/26/2023]
Abstract
Targeting proteins for Xklp2 (TPX2s) comprise a class of MAPs that are essential for plant growth and development by regulating the dynamic changes of microtubules (MTs) and proper formation of cytoskeleton. However, the function of TPX2 proteins in cotton fiber development remains poorly understood. Here, we identified the function of a fiber elongation-specific TPX2 protein, GhMAP20L5, in cotton. Suppressed GhMAP20L5 gene expression in cotton (GhMAP20L5i) significantly reduced fiber elongation rate, fiber length and lint percentage. GhMAP20L5i fibers had thinner and looser secondary cell walls (SCW), and incompact helix twists. GhMAP20L5 specifically interacted with the tubulin GhTUB13 on the cytoskeleton. Gene coexpression analysis showed that GhMAP20L5 involved in multiple pathways related to cytoskeleton establishment and fiber cell wall formation and affected cellulase genes expressions. In summary, our results revealed that GhMAP20L5 is important for fiber development by regulating cytoskeleton establishment and the cellulose deposition in cotton.
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Affiliation(s)
- Qingwei Song
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wanting Gao
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuanhui Du
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Ren Y, Song Q, Shan S, Wang J, Ma S, Song Y, Ma L, Zhang G, Niu N. Genome-Wide Identification and Expression Analysis of TUA and TUB Genes in Wheat ( Triticum aestivum L.) during Its Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:3495. [PMID: 36559605 PMCID: PMC9785050 DOI: 10.3390/plants11243495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Microtubules play a fundamental role in plant development, morphogenesis, and cytokinesis; they are assembled from heterodimers containing an α-tubulin (TUA) and a β-tubulin (TUB) protein. However, little research has been conducted on the TUA and TUB gene families in hexaploid wheat (Triticum aestivum L.). In this study, we identified 15 TaTUA and 28 TaTUB genes in wheat. Phylogenetic analysis showed that 15 TaTUA genes were divided into two major subfamilies, and 28 TaTUB genes were divided into five major subfamilies. Mostly, there were similar motif compositions and exon-intron structures among the same subfamilies. Segmental duplication of genes (WGD/segmental) is the main process of TaTUA and TaTUB gene family expansion in wheat. It was found that TaTUA and TaTUB genes presented specific temporal and spatial characteristics based on the expression profiles of 17 tissues during wheat development using publicly available RNA-seq data. It was worth noting, via qRT-PCR, that two TaTUA and five TaTUB genes were highly expressed in fertile anthers compared to male sterility. These were quite different between physiological male sterile lines and S-type cytoplasmic male sterile lines at different stages of pollen development. This study offers fundamental information on the TUA and TUB gene families during wheat development and provides new insights for exploring the molecular mechanism of wheat male sterility.
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Affiliation(s)
- Yang Ren
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
- College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Qilu Song
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Sicong Shan
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Junwei Wang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Shoucai Ma
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yulong Song
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Lingjian Ma
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Gaisheng Zhang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Na Niu
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
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Lu R, Li Y, Zhang J, Wang Y, Zhang J, Li Y, Zheng Y, Li XB. The bHLH/HLH transcription factors GhFP2 and GhACE1 antagonistically regulate fiber elongation in cotton. PLANT PHYSIOLOGY 2022; 189:628-643. [PMID: 35226094 PMCID: PMC9157132 DOI: 10.1093/plphys/kiac088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/31/2022] [Indexed: 06/01/2023]
Abstract
Basic helix-loop-helix/helix-loop-helix (bHLH/HLH) transcription factors play important roles in cell elongation in plants. However, little is known about how bHLH/HLH transcription factors antagonistically regulate fiber elongation in cotton (Gossypium hirsutum). In this study, we report that two bHLH/HLH transcription factors, fiber-related protein 2 (GhFP2) and ACTIVATOR FOR CELL ELONGATION 1 (GhACE1), function in fiber development of cotton. GhFP2 is an atypical bHLH protein without the basic region, and its expression is regulated by brassinosteroid (BR)-related BRASSINAZOLE RESISTANT 1 (GhBZR1). Overexpression of GhFP2 in cotton hindered fiber elongation, resulting in shortened fiber length. In contrast, suppression of GhFP2 expression in cotton promoted fiber development, leading to longer fibers compared with the wild-type. GhFP2 neither contains a DNA-binding domain nor has transcriptional activation activity. Furthermore, we identified GhACE1, a bHLH protein that interacts with GhFP2 and positively regulates fiber elongation. GhACE1 could bind to promoters of plasma membrane intrinsic protein 2;7 (GhPIP2;7) and expansions 8 (GhEXP8) for directly activating their expression, but the interaction between GhFP2 and GhACE1 suppressed transcriptional activation of these target genes by GhACE1. Taken together, our results indicate that GhACE1 promotes fiber elongation by activating expressions of GhPIP2;7 and GhEXP8, but its transcription activation on downstream genes may be obstructed by BR-modulated GhFP2. Thus, our data reveal a key mechanism for fiber cell elongation through a pair of antagonizing HLH/bHLH transcription factors in cotton.
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Affiliation(s)
- Rui Lu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Jiao Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yao Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Jie Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yu Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yong Zheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
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Han G, Li Y, Yang Z, Wang C, Zhang Y, Wang B. Molecular Mechanisms of Plant Trichome Development. FRONTIERS IN PLANT SCIENCE 2022; 13:910228. [PMID: 35720574 PMCID: PMC9198495 DOI: 10.3389/fpls.2022.910228] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
- Dongying Institute, Shandong Normal University, Dongying, China
| | - Yuxia Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zongran Yang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chengfeng Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yuanyuan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
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Yu D, Li X, Li Y, Ali F, Li F, Wang Z. Dynamic roles and intricate mechanisms of ethylene in epidermal hair development in Arabidopsis and cotton. THE NEW PHYTOLOGIST 2022; 234:375-391. [PMID: 34882809 DOI: 10.1111/nph.17901] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Ethylene affects many aspects of plant growth and development, including root hairs and trichomes growth in Arabidopsis, as well as fiber development in cotton, though the underlying mechanism is unclear. In this article, we update the research progress associated with the main genes in ethylene biosynthesis and signaling pathway, and we propose a clear ethylene pathway based on genome-wide identification of homologues in cotton. Expression pattern analysis using transcriptome data revealed that some candidate genes may contribute to cotton fiber development through the ethylene pathway. Moreover, we systematically summarized the effects of ethylene on the development of epidermal hair and the underlying regulatory mechanisms in Arabidopsis. Based on the knowledge of ethylene-promoted cell differentiation, elongation, and development in different tissues or plants, we advised a possible regulatory network for cotton fiber development with ethylene as the hub. Importantly, we emphasized the roles of ethylene as an important node in regulating cotton vegetative growth, and stress resistance, and suggested utilizing multiple methods to subtly modify ethylene synthesis or signaling in a tissue or spatiotemporal-specific manner to clarify its exact effect on architecture, adaptability of the plant, and fiber development, paving the way for basic research and genetic improvement of the cotton crop.
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Affiliation(s)
- Daoqian Yu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaona Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Wang Y, Li Y, Gong SY, Qin LX, Nie XY, Liu D, Zheng Y, Li XB. GhKNL1 controls fiber elongation and secondary cell wall synthesis by repressing its downstream genes in cotton (Gossypium hirsutum). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:39-55. [PMID: 34796654 DOI: 10.1111/jipb.13192] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Cotton which produces natural fiber materials for the textile industry is one of the most important crops in the world. Class II KNOX proteins are often considered as transcription factors in regulating plant secondary cell wall (SCW) formation. However, the molecular mechanism of the KNOX transcription factor-regulated SCW synthesis in plants (especially in cotton) remains unclear in details so far. In this study, we show a cotton class II KNOX protein (GhKNL1) as a transcription repressor functioning in fiber development. The GhKNL1-silenced transgenic cotton produced longer fibers with thicker SCWs, whereas GhKNL1 dominant repression transgenic lines displayed the opposite fiber phenotype, compared with controls. Further experiments revealed that GhKNL1 could directly bind to promoters of GhCesA4-2/4-4/8-2 and GhMYB46 for modulating cellulose synthesis during fiber SCW development in cotton. On the other hand, GhKNL1 could also suppress expressions of GhEXPA2D/4A-1/4D-1/13A through binding to their promoters for regulating fiber elongation of cotton. Taken together, these data revealed GhKNL1 functions in fiber elongation and SCW formation by directly repressing expressions of its target genes related to cell elongation and cellulose synthesis. Thus, our data provide an effective clue for potentially improving fiber quality by genetic manipulation of GhKNL1 in cotton breeding.
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Affiliation(s)
- Yao Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Si-Ying Gong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Li-Xia Qin
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xiao-Ying Nie
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Dong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yong Zheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
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Guo AH, Su Y, Huang Y, Wang YM, Nie HS, Zhao N, Hua JP. QTL controlling fiber quality traits under salt stress in upland cotton (Gossypium hirsutum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:661-685. [PMID: 33386428 PMCID: PMC7843563 DOI: 10.1007/s00122-020-03721-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 10/31/2020] [Indexed: 05/04/2023]
Abstract
QTL for fiber quality traits under salt stress discerned candidate genes controlling fatty acid metabolism. Salinity stress seriously affects plant growth and limits agricultural productivity of crop plants. To dissect the genetic basis of response to salinity stress, a recombinant inbred line population was developed to compare fiber quality in upland cotton (Gossypium hirsutum L.) under salt stress and normal conditions. Based on three datasets of (1) salt stress, (2) normal growth, and (3) the difference value between salt stress and normal conditions, 51, 70, and 53 QTL were mapped, respectively. Three QTL for fiber length (FL) (qFL-Chr1-1, qFL-Chr5-5, and qFL-Chr24-4) were detected under both salt and normal conditions and explained 4.26%, 9.38%, and 3.87% of average phenotypic variation, respectively. Seven genes within intervals of two stable QTL (qFL-Chr1-1 and qFL-Chr5-5) were highly expressed in lines with extreme long fiber. A total of 35 QTL clusters comprised of 107 QTL were located on 18 chromosomes and exhibited pleiotropic effects. Thereinto, two clusters were responsible for improving five fiber quality traits, and 6 influenced FL and fiber strength (FS). The QTL with positive effect for fiber length exhibited active effects on fatty acid synthesis and elongation, but the ones with negative effect played passive roles on fatty acid degradation under salt stress.
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Affiliation(s)
- An-Hui Guo
- Laboratory of Cotton Genetics; Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian district, Beijing, 100193, China
| | - Ying Su
- Laboratory of Cotton Genetics; Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian district, Beijing, 100193, China
| | - Yi Huang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yu-Mei Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
| | - Hu-Shuai Nie
- Laboratory of Cotton Genetics; Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian district, Beijing, 100193, China
| | - Nan Zhao
- Laboratory of Cotton Genetics; Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian district, Beijing, 100193, China
| | - Jin-Ping Hua
- Laboratory of Cotton Genetics; Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian district, Beijing, 100193, China.
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Pei W, Song J, Wang W, Ma J, Jia B, Wu L, Wu M, Chen Q, Qin Q, Zhu H, Hu C, Lei H, Gao X, Hu H, Zhang Y, Zhang J, Yu J, Qu Y. Quantitative Trait Locus Analysis and Identification of Candidate Genes for Micronaire in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2021; 12:763016. [PMID: 34777444 PMCID: PMC8579039 DOI: 10.3389/fpls.2021.763016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/22/2021] [Indexed: 05/08/2023]
Abstract
Cotton is the most important fiber crop and provides indispensable natural fibers for the textile industry. Micronaire (MIC) is determined by fiber fineness and maturity and is an important component of fiber quality. Gossypium barbadense L. possesses long, strong and fine fibers, while upland cotton (Gossypium hirsutum L.) is high yielding with high MIC and widely cultivated worldwide. To identify quantitative trait loci (QTLs) and candidate genes for MIC in G. barbadense, a population of 250 backcross inbred lines (BILs), developed from an interspecific cross of upland cotton CRI36 × Egyptian cotton (G. barbadense) Hai7124, was evaluated in 9 replicated field tests. Based on a high-density genetic map with 7709 genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) markers, 25 MIC QTLs were identified, including 12 previously described QTLs and 13 new QTLs. Importantly, two stable MIC QTLs (qMIC-D03-2 on D03 and qMIC-D08-1 on D08) were identified. Of a total of 338 genes identified within the two QTL regions, eight candidate genes with differential expression between TM-1 and Hai7124 were identified. Our research provides valuable information for improving MIC in cotton breeding.
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Affiliation(s)
- Wenfeng Pei
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Jikun Song
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wenkui Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianjiang Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Luyao Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Qin Qin
- Western Agriculture Research Centre, Chinese Academy of Agricultural Sciences, Changji, China
| | - Haiyong Zhu
- Western Agriculture Research Centre, Chinese Academy of Agricultural Sciences, Changji, China
| | - Chengcheng Hu
- Western Agriculture Research Centre, Chinese Academy of Agricultural Sciences, Changji, China
| | - Hai Lei
- Seed Management Station, Department of Agriculture and Rural Affairs of Xinjiang, Urumqi, China
| | - Xuefei Gao
- Join Hope Seed Co., Ltd., Changji, China
| | - Haijun Hu
- Join Hope Seed Co., Ltd., Changji, China
| | - Yu Zhang
- Join Hope Seed Co., Ltd., Changji, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Jinfa Zhang,
| | - Jiwen Yu
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Jiwen Yu,
| | - Yanying Qu
- Engineering Research Centre of Cotton of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- Yanying Qu,
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10
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Comparative phosphoproteomic analysis of BR-defective mutant reveals a key role of GhSK13 in regulating cotton fiber development. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1905-1917. [PMID: 32632733 DOI: 10.1007/s11427-020-1728-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Brassinosteroid (BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1 (pag1), and its corresponding wild-type (ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage (10 days after pollination (DPA)) and secondary cell wall synthesis stage (20 DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs (GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor Gh_DNF_YB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.
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11
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Lei K, Liu A, Fan S, Peng H, Zou X, Zhen Z, Huang J, Fan L, Zhang Z, Deng X, Ge Q, Gong W, Li J, Gong J, Shi Y, Jiang X, Zhang S, Jia T, Zhang L, Yuan Y, Shang H. Identification of TPX2 Gene Family in Upland Cotton and Its Functional Analysis in Cotton Fiber Development. Genes (Basel) 2019; 10:E508. [PMID: 31277527 PMCID: PMC6678848 DOI: 10.3390/genes10070508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/16/2022] Open
Abstract
Microtubules (MTs) are of importance to fiber development. The Xklp2 (TPX2) proteins as a class of microtubule-associated proteins (MAPs) play a key role in plant growth and development by regulating the dynamic changes of microtubules (MTs). However, the mechanism underlying this is unknown. The interactions between TPX2 proteins and tubulin protein, which are the main structural components, have not been studied in fiber development of upland cotton. Therefore, a genome-wide analysis of the TPX2 family was firstly performed in Gossypiumhirsutum L. This study identified 41 GhTPX2 sequences in the assembled G. hirsutum genome by a series of bioinformatic methods. Generally, this gene family is phylogenetically grouped into six subfamilies, and 41 G. hirsutum TPX2 genes (GhTPX2s) are distributed across 21 chromosomes. A heatmap of the TPX2 gene family showed that homologous GhTPX2 genes, GhWDLA2/7 and GhWDLA4/9, have large differences in expression levels between two upland cotton recombinant inbred lines (69307 and 69362) that are different in fiber quality at 15 and 20 days post anthesis. The relative data indicate that these four genes are down-regulated under oryzalin, which causes microtubule depolymerization, as determined via qRT-PCR. A subcellular localization experiment suggested that GhWDLA2 and GhWDLA7 are localized to the microtubule cytoskeleton, and GhWDLA4 and GhWDLA9 are only localized to the nucleus. However, only GhWDLA7 between GhWDLA2 and GhWDLA7 interacted with GhTUA2 in the yeast two-hybrid assay. These results lay the foundation for further function study of the TPX2 gene family.
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Affiliation(s)
- Kang Lei
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Huo Peng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xianyan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhang Zhen
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Jinyong Huang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Liqiang Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhibin Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Shuya Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Lipeng Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
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12
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Morello L, Pydiura N, Galinousky D, Blume Y, Breviario D. Flax tubulin and CesA superfamilies represent attractive and challenging targets for a variety of genome- and base-editing applications. Funct Integr Genomics 2019; 20:163-176. [PMID: 30826923 DOI: 10.1007/s10142-019-00667-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Flax is both a valuable resource and an interesting model crop. Despite a long history of flax genetic transformation only one transgenic linseed cultivar has been so far registered in Canada. Implementation and use of the genome-editing technologies that allow site-directed modification of endogenous genes without the introduction of foreign genes might improve this situation. Besides its potential for boosting crop yields, genome editing is now one of the best tools for carrying out reverse genetics and it is emerging as an especially versatile tool for studying basic biology. A complex interplay between the flax tubulin family (6 α-, 14 β-, and 2 γ-tubulin genes), the building block of microtubules, and the CesA (15-16 genes), the subunit of the multimeric cellulose-synthesizing complex devoted to the oriented deposition of the cellulose microfibrils is fundamental for the biosynthesis of the cell wall. The role of the different members of each family in providing specificities to the assembled complexes in terms of structure, dynamics, activity, and interaction remains substantially obscure. Genome-editing strategies, recently shown to be successful in flax, can therefore be useful to unravel the issue of functional redundancy and provide evidence for specific interactions between different members of the tubulin and CesA gene families, in relation to different phase and mode of cell wall biosynthesis.
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Affiliation(s)
- Laura Morello
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy
| | - Nikolay Pydiura
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine
| | - Dmitry Galinousky
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Akademicheskaya St. 27, 220072, Minsk, Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine.
| | - Diego Breviario
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy.
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13
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Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis. Genes (Basel) 2019; 10:genes10020119. [PMID: 30736327 PMCID: PMC6410125 DOI: 10.3390/genes10020119] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 01/28/2023] Open
Abstract
Upland cotton (Gossypium hirsutum) is grown for its elite fiber. Understanding differential gene expression patterns during fiber development will help to identify genes associated with fiber quality. In this study, we used two recombinant inbred lines (RILs) differing in fiber quality derived from an intra-hirsutum population to explore expression profiling differences and identify genes associated with high-quality fiber or specific fiber-development stages using RNA sequencing. Overall, 72/27, 1137/1584, 437/393, 1019/184, and 2555/1479 differentially expressed genes were up-/down-regulated in an elite fiber line (L1) relative to a poor-quality fiber line (L2) at 10, 15, 20, 25, and 30 days post-anthesis, respectively. Three-hundred sixty-three differentially expressed genes (DEGs) between two lines were colocalized in fiber strength (FS) quantitative trait loci (QTL). Short Time-series Expression Miner (STEM) analysis discriminated seven expression profiles; gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were performed to identify difference in function between genes unique to L1 and L2. Co-expression network analysis detected five modules highly associated with specific fiber-development stages, especially for high-quality fiber tissues. The hub genes in each module were identified by weighted gene co-expression network analysis. Hub genes encoding actin 1, Rho GTPase-activating protein with PAK-box, TPX2 protein, bHLH transcription factor, and leucine-rich repeat receptor-like protein kinase were identified. Correlation networks revealed considerable interaction among the hub genes, transcription factors, and other genes.
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14
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Gavazzi F, Pigna G, Braglia L, Gianì S, Breviario D, Morello L. Evolutionary characterization and transcript profiling of β-tubulin genes in flax (Linum usitatissimum L.) during plant development. BMC PLANT BIOLOGY 2017; 17:237. [PMID: 29221437 PMCID: PMC5721616 DOI: 10.1186/s12870-017-1186-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/29/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Microtubules, polymerized from alpha and beta-tubulin monomers, play a fundamental role in plant morphogenesis, determining the cell division plane, the direction of cell expansion and the deposition of cell wall material. During polarized pollen tube elongation, microtubules serve as tracks for vesicular transport and deposition of proteins/lipids at the tip membrane. Such functions are controlled by cortical microtubule arrays. Aim of this study was to first characterize the flax β-tubulin family by sequence and phylogenetic analysis and to investigate differential expression of β-tubulin genes possibly related to fibre elongation and to flower development. RESULTS We report the cloning and characterization of the complete flax β-tubulin gene family: exon-intron organization, duplicated gene comparison, phylogenetic analysis and expression pattern during stem and hypocotyl elongation and during flower development. Sequence analysis of the fourteen expressed β-tubulin genes revealed that the recent whole genome duplication of the flax genome was followed by massive retention of duplicated tubulin genes. Expression analysis showed that β-tubulin mRNA profiles gradually changed along with phloem fibre development in both the stem and hypocotyl. In flowers, changes in relative tubulin transcript levels took place at anthesis in anthers, but not in carpels. CONCLUSIONS Phylogenetic analysis supports the origin of extant plant β-tubulin genes from four ancestral genes pre-dating angiosperm separation. Expression analysis suggests that particular tubulin subpopulations are more suitable to sustain different microtubule functions such as cell elongation, cell wall thickening or pollen tube growth. Tubulin genes possibly related to different microtubule functions were identified as candidate for more detailed studies.
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Affiliation(s)
- Floriana Gavazzi
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Gaia Pigna
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Luca Braglia
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Silvia Gianì
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Laura Morello
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
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15
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MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development. Sci Rep 2017; 7:44454. [PMID: 28327647 PMCID: PMC5361117 DOI: 10.1038/srep44454] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/08/2017] [Indexed: 12/24/2022] Open
Abstract
The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield.
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16
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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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17
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Characterization and putative post-translational regulation of α- and β-tubulin gene families in Salix arbutifolia. Sci Rep 2016; 6:19258. [PMID: 26753794 PMCID: PMC4709717 DOI: 10.1038/srep19258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/10/2015] [Indexed: 11/08/2022] Open
Abstract
Microtubules, which are composed of heterodimers of α-tubulin (TUA) and β-tubulin (TUB) proteins, are closely associated with cellulose microfibril deposition and play pivotal roles in plant secondary cell wall development. In the present study, we identified eight TUA and twenty TUB genes in willow (Salix arbutifolia). Quantitative real-time PCR analysis showed that the small number of TUA gene family members relative to that of TUBs was complemented by a higher transcript copy number for each TUA gene, which is essential to the maintenance of the tubulin 1:1 heterodimer assembly. In Salix, five of eight TUAs were determined to be unusual because these contained a C-terminal methionine acid, leucine acid, glutamic acid, and glutamine acid, instead of the more typical tyrosine residue, which in turn generated the hypothesis of post-translational modifications (PTMs) that included deleucylation, demethiolation, deglutamynation, and deaspartylation. These PTMs are responsible for the removal of additional amino acid residues from TUAs prior to detyrosination, which is the first step of C-terminal PTMs. The additional PTMs of the TUA gene family might be responsible for the formation of different tubulin heterodimers that may have diverse functions for the adaptation of the woody perennial growth for Salix.
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18
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Liang W, Fang L, Xiang D, Hu Y, Feng H, Chang L, Zhang T. Transcriptome Analysis of Short Fiber Mutant Ligon lintless-1 (Li1) Reveals Critical Genes and Key Pathways in Cotton Fiber Elongation and Leaf Development. PLoS One 2015; 10:e0143503. [PMID: 26600249 PMCID: PMC4658197 DOI: 10.1371/journal.pone.0143503] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/05/2015] [Indexed: 01/12/2023] Open
Abstract
For efficient spinning and superior fabric production, long fiber length is a desired trait for cotton production. To unveil the molecular basis of the cotton fiber length regulation, a short fiber mutant, Ligon lintless-1 (Li1), is selected to compare with its corresponding wild type (WT). Li1 is a monogenic dominant cotton mutant causing extremely short fibers (<6mm) on mature seeds with visible pleiotropic effects on vegetative growth and development. In this research, we compared the transcriptome of fiber bearing ovules at 1 DPA, 3 DPA, 8 DPA and leaf between Li1 mutant and WT. A total of 7,852 differentially expressed genes (DEGs) were detected in ovules and leaves, which mainly participated in sugar, secondary metabolite and lipid metabolism pathways based on KEGG analysis. The common DEGs at 1 DPA and 3 DPA were involved in the responses to endogenous stimulus, signal transduction and long-chain fatty acid biosynthesis. For 3 DPA, 8 DPA and leaf, the common DEGs were involved in the responses to auxin and receptor kinases related pathway. Further analysis showed that 37 genes involved in very-long-chain fatty acid biosynthesis were suppressed in Li1 mutant during fiber fast elongation development. Most of the DEGs involved in cell wall metabolism, such cellulose synthase, expansin family, and glycosyl hydrolase were differentially expressed at 3 DPA and 8 DPA. Our results provide new insights into the mechanisms of fiber elongation, and offer novel genes as potential objects for fiber length improvement.
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Affiliation(s)
- Wenhua Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, the Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, the Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dan Xiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, the Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, the Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, the Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lijing Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, the Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, the Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
- * E-mail:
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Biotechnological aspects of cytoskeletal regulation in plants. Biotechnol Adv 2015; 33:1043-62. [DOI: 10.1016/j.biotechadv.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 03/03/2015] [Accepted: 03/09/2015] [Indexed: 11/23/2022]
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Jiang Y, Ding M, Cao Y, Yang F, Zhang H, He S, Dai H, Hao H, Rong J. Genetic fine mapping and candidate gene analysis of the Gossypium hirsutum Ligon lintless-1 (Li1) mutant on chromosome 22(D). Mol Genet Genomics 2015; 290:2199-211. [PMID: 26037218 DOI: 10.1007/s00438-015-1070-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
Abstract
Ligon lintless-1 (Li1) is a Gossypium hirsutum mutant that is controlled by a dominant gene that arrests the development of cotton fiber after anthesis. Two F2 mapping populations were developed from mutant (Li1 × H7124) F1 plants in 2012 and 2013; each was composed of 142 and 1024 plants, respectively. Using these populations, Li1 was mapped to a 0.3-cM region in which nine single-strand conformation polymorphism markers co-segregated with the Li1 locus. In the published G. raimondii genome, these markers were mapped to a region of about 1.2 Mb (the Li1 region) and were separated by markers that flanked the Li1 locus in the genetic map, dividing the Li1 region into three segments. Thirty-six genes were annotated by the gene prediction software FGENESH (Softberry) in the Li1 region. Twelve genes were candidates of Li1, while the remaining 24 genes were identified as transposable elements, DNA/RNA polymerase superfamily or unknown function genes. Among the 12 candidate genes, those encoding ribosomal protein s10, actin protein, ATP synthase, and beta-tubulin 5 were the most-promising candidates of the Li1 mutant because the function of these genes is closely related to fiber development. High-throughput RNA sequencing and quantitative PCR revealed that these candidate genes had obvious differential gene expression between mutant and wild-type plants at the fiber elongation stage, strengthening the inference that they could be the most likely candidate gene of the Li1 mutant phenotype.
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Affiliation(s)
- Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
| | - Yuefen Cao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
| | - Fen Yang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
| | - Hua Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
| | - Shae He
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
| | - Huaqin Dai
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
| | - Huanfeng Hao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China. .,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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21
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Fang L, Tian R, Li X, Chen J, Wang S, Wang P, Zhang T. Cotton fiber elongation network revealed by expression profiling of longer fiber lines introgressed with different Gossypium barbadense chromosome segments. BMC Genomics 2014; 15:838. [PMID: 25273845 PMCID: PMC4190578 DOI: 10.1186/1471-2164-15-838] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 09/24/2014] [Indexed: 12/24/2022] Open
Abstract
Background Cotton fiber, a highly elongated, thickened single cell of the seed epidermis, is a powerful cell wall research model. Fiber length, largely determined during the elongation stage, is a key property of fiber quality. Several studies using expressed sequence tags and microarray analysis have identified transcripts that accumulate preferentially during fiber elongation. To further show the mechanism of fiber elongation, we used Digital Gene Expression Tag Profiling to compare transcriptome data from longer fiber chromosome introgressed lines (CSILs) containing segments of various Gossypium barbadense chromosomes with data from its recurrent parent TM-1 during fiber elongation (from 5 DPA to 20 DPA). Results A large number of differentially expressed genes (DEGs) involved in carbohydrate, fatty acid and secondary metabolism, particularly cell wall biosynthesis, were highly upregulated during the fiber elongation stage, as determined by functional enrichment and pathway analysis. Furthermore, DEGs related to hormone responses and transcription factors showed upregulated expression levels in the CSILs. Moreover, metabolic and regulatory network analysis indicated that the same pathways were differentially altered, and distinct pathways exhibited altered gene expression, in the CSILs. Interestingly, mining of upregulated DEGs in the introgressed segments of these CSILs based on D-genome sequence data showed that these lines were enriched in glucuronosyltransferase, inositol-1, 4, 5-trisphosphate 3-kinase and desulfoglucosinolate sulfotransferase activity. These results were similar to the results of transcriptome analysis. Conclusions This report provides an integrative network about the molecular mechanisms controlling fiber length, which are mainly tied to carbohydrate metabolism, cell wall biosynthesis, fatty acid metabolism, secondary metabolism, hormone responses and Transcription factors. The results of this study provide new insights into the critical factors associated with cell elongation and will facilitate further research aimed at understanding the mechanisms underlying cotton fiber elongation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-838) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
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Yang Z, Zhang C, Yang X, Liu K, Wu Z, Zhang X, Zheng W, Xun Q, Liu C, Lu L, Yang Z, Qian Y, Xu Z, Li C, Li J, Li F. PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation. THE NEW PHYTOLOGIST 2014; 203:437-448. [PMID: 24786710 DOI: 10.1111/nph.12824] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/22/2014] [Indexed: 05/19/2023]
Abstract
Cotton (Gossypium hirsutum) is the major source of natural textile fibers. Brassinosteroids (BRs) play crucial roles in regulating fiber development. The molecular mechanisms of BRs in regulating fiber elongation, however, are poorly understood. pagoda1 (pag1) was identified via an activation tagging genetic screen and characterized by genome walking and brassinolide (BL) supplementation. RNA-Seq analysis was employed to elucidate the mechanisms of PAG1 in regulating fiber development. pag1 exhibited dwarfism and reduced fiber length due to significant inhibition of cell elongation and expansion. BL treatment rescued its growth and fiber elongation. PAG1 encodes a homolog of Arabidopsis CYP734A1 that inactivates BRs via C-26 hydroxylation. RNA-Seq analyses showed that the constitutive expression of PAG1 downregulated the expression of genes involved in very-long-chain fatty acids (VLCFA) biosynthesis, ethylene-mediated signaling, response to cadmium, cell wall development, cytoskeleton organization and cell growth. Our results demonstrate that PAG1 plays crucial roles in regulating fiber development via controlling the level of endogenous bioactive BRs, which may affect ethylene signaling cascade by mediating VLCFA. Therefore, BR may be a critical regulator of fiber elongation, a role which may in turn be linked to effects on VLCFA biosynthesis, ethylene and cadmium signaling, cell wall- and cytoskeleton-related gene expression.
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Affiliation(s)
- Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaojie Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhixia Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wu Zheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qingqing Xun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Chuanliang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoen Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuyuan Qian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhenzhen Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Changfeng Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Parrotta L, Cresti M, Cai G. Accumulation and post-translational modifications of plant tubulins. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:521-7. [PMID: 24112714 DOI: 10.1111/plb.12104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/08/2013] [Indexed: 05/03/2023]
Abstract
The microtubular cytoskeleton of plant cells provides support for several functions (including the anchoring of proteins, assembly of the mitotic spindle, cytoplasmic streaming and construction of cell walls). Both α- and β-tubulins are encoded through multigene families that are differentially expressed in different organs and tissues. To increase the variability of expression, both protein subunits are subjected to post-translational modifications, which could contribute to the assembly of specific microtubule structures. This review aims to highlight the role of specific post-translational modifications of tubulin in plant cells. We initially describe the expression and accumulation of α- and β-tubulin isoforms in different plants and at different stages of plant development. Second, we discuss the different types of post-translational modifications that, by adding or removing specific functional groups, increase the isoform heterogeneity and functional variability of tubulin. Modifications are proposed to form a 'code' that can be read by proteins interacting with microtubules. Therefore, the subpopulations of microtubules may bind to different associated proteins (motor and non-motor), thus creating the physical support for various microtubule functions.
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Affiliation(s)
- L Parrotta
- Dipartimento Scienze della Vita, Università di Siena, Siena, Italy
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24
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Breviario D, Gianì S, Morello L. Multiple tubulins: evolutionary aspects and biological implications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:202-18. [PMID: 23662651 DOI: 10.1111/tpj.12243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 05/05/2023]
Abstract
Plant tubulin is a dimeric protein that contributes to formation of microtubules, major intracellular structures that are involved in the control of fundamental processes such as cell division, polarity of growth, cell-wall deposition, intracellular trafficking and communications. Because it is a structural protein whose function is confined to the role of microtubule formation, tubulin may be perceived as an uninteresting gene product, but such a perception is incorrect. In fact, tubulin represents a key molecule for studying fundamental biological issues such as (i) microtubule evolution (also with reference to prokaryotic precursors and the formation of cytomotive filaments), (ii) protein structure with reference to the various biochemical features of members of the FstZ/tubulin superfamily, (iii) isoform variations contributed by the existence of multi-gene families and various kinds of post-translational modifications, (iv) anti-mitotic drug interactions and mode of action, (v) plant and cell symmetry, as determined using a series of tubulin mutants, (vi) multiple and sophisticated mechanisms of gene regulation, and (vii) intron molecular evolution. In this review, we present and discuss many of these issues, and offer an updated interpretation of the multi-tubulin hypothesis.
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Affiliation(s)
- Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, 20133 Milano, Italy.
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Soto-Cerda BJ, Diederichsen A, Ragupathy R, Cloutier S. Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types. BMC PLANT BIOLOGY 2013; 13:78. [PMID: 23647851 PMCID: PMC3656786 DOI: 10.1186/1471-2229-13-78] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 04/26/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. RESULTS Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (F(ST) = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r²) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. CONCLUSIONS Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.
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Affiliation(s)
- Braulio J Soto-Cerda
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9, Canada
- Present address: Agriaquaculture Nutritional Genomic Center, CGNA, Genomics and Bioinformatics Unito, Km 10 Camino Cajón-Vilcún, INIA Temuco, Chile
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatchewan, SK S7N 0X2, Canada
| | - Raja Ragupathy
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9, Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9, Canada
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Liu K, Sun J, Yao L, Yuan Y. Transcriptome analysis reveals critical genes and key pathways for early cotton fiber elongation in Ligon lintless-1 mutant. Genomics 2012; 100:42-50. [PMID: 22576057 DOI: 10.1016/j.ygeno.2012.04.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 04/24/2012] [Accepted: 04/26/2012] [Indexed: 12/13/2022]
Abstract
Fiber length is a key determinant of cotton yield and quality. Using a monogenic dominant cotton mutant Ligon lintless-1 with extremely short fibers, we employed microarray technology and quantitative real time PCR to compare transcriptomes of Li(1) and the normal wild-type TM-1, the results showed that only a few genes differentially expressed in 0 days postanthesis (DPA) ovules and 3 DPA fibers, whereas 577 transcripts differentially expressed in 6 DPA fibers. 6 DPA is probably a key phase determining fiber elongation. Gene ontology analyses showed such processes as response to stimulus, signal transduction, and lipid metabolism were readjusted by the mutant gene. Pathway studio analysis indicated that auxin signaling and sugar signaling pathways play major roles in modulation of early fiber elongation. This work provides new insight into the mechanisms of fiber development, and offers novel genes as potential objects for genetic manipulation to achieve improvement of fiber properties.
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Affiliation(s)
- Kang Liu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One 2011; 6:e22758. [PMID: 21829504 PMCID: PMC3145671 DOI: 10.1371/journal.pone.0022758] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 06/29/2011] [Indexed: 11/22/2022] Open
Abstract
Background Cotton fiber is the world's leading natural fiber used in the manufacture of textiles. Gossypium is also the model plant in the study of polyploidization, evolution, cell elongation, cell wall development, and cellulose biosynthesis. G. barbadense L. is an ideal candidate for providing new genetic variations useful to improve fiber quality for its superior properties. However, little is known about fiber development mechanisms of G. barbadense and only a few molecular resources are available in GenBank. Methodology and Principal Findings In total, 10,979 high-quality expressed sequence tags (ESTs) were generated from a normalized fiber cDNA library of G. barbadense. The ESTs were clustered and assembled into 5852 unigenes, consisting of 1492 contigs and 4360 singletons. The blastx result showed 2165 unigenes with significant similarity to known genes and 2687 unigenes with significant similarity to genes of predicted proteins. Functional classification revealed that unigenes were abundant in the functions of binding, catalytic activity, and metabolic pathways of carbohydrate, amino acid, energy, and lipids. The function motif/domain-related cytoskeleton and redox homeostasis were enriched. Among the 5852 unigenes, 282 and 736 unigenes were identified as potential cell wall biosynthesis and transcription factors, respectively. Furthermore, the relationships among cotton species or between cotton and other model plant systems were analyzed. Some putative species-specific unigenes of G. barbadense were highlighted. Conclusions/Significance The ESTs generated in this study are from the first large-scale EST project for G. barbadense and significantly enhance the number of G. barbadense ESTs in public databases. This knowledge will contribute to cotton improvements by studying fiber development mechanisms of G. barbadense, establishing a breeding program using marker-assisted selection, and discovering candidate genes related to important agronomic traits of cotton through oligonucleotide array. Our work will also provide important resources for comparative genomics, polyploidization, and genome evolution among Gossypium species.
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Zhao PM, Wang LL, Han LB, Wang J, Yao Y, Wang HY, Du XM, Luo YM, Xia GX. Proteomic identification of differentially expressed proteins in the Ligon lintless mutant of upland cotton (Gossypium hirsutum L.). J Proteome Res 2010; 9:1076-87. [PMID: 19954254 DOI: 10.1021/pr900975t] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Cotton fiber is an ideal model for studying plant cell elongation. To date, the underlying mechanisms controlling fiber elongation remain unclear due to their high complexity. In this study, a comparative proteomic analysis between a short-lint fiber mutant (Ligon lintless, Li(1)) and its wild-type was performed to identify fiber elongation-related proteins. By 2-DE combined with local EST database-assisted MS/MS analysis, 81 differentially expressed proteins assigned to different functional categories were identified from Li(1) fibers, of which 54 were down-regulated and 27 were up-regulated. Several novel aspects regarding cotton fiber elongation can be illustrated from our data. First, over half of the down-regulated proteins were newly identified at the protein level, which is mainly involved in protein folding and stabilization, nucleocytoplasmic transport, signal transduction, and vesicular-mediated transport. Second, a number of cytoskeleton-related proteins showed a remarkable decrease in protein abundance in the Li(1) fibers. Accordingly, the architecture of actin cytoskeleton was severely deformed and the microtubule organization was moderately altered, accompanied with dramatic disruption of vesicle trafficking. Third, the expression of several proteins involved in unfolded protein response (UPR) was activated in Li(1) fibers, indicating that the deficiency of fiber cell elongation was related to ER stress. Collectively, these findings significantly advanced our understanding of the mechanisms associated with cotton fiber elongation.
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Affiliation(s)
- Pi-Ming Zhao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Aberrant Expression of Critical Genes during Secondary Cell Wall Biogenesis in a Cotton Mutant, Ligon Lintless-1 (Li-1). Comp Funct Genomics 2010:659301. [PMID: 20148073 PMCID: PMC2817544 DOI: 10.1155/2009/659301] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 09/16/2009] [Accepted: 10/09/2009] [Indexed: 11/17/2022] Open
Abstract
Over ninety percent of the value of cotton comes from its fiber; however, the genetic mechanisms governing fiber development are poorly understood. Due to their biochemical and morphological diversity in fiber cells cotton fiber mutants have been useful in examining fiber development; therefore, using the Ligon Lintless (Li-1) mutant, a monogenic dominant cotton mutant with very short fibers, we employed the high throughput approaches of microarray technology and real time PCR to gain insights into what genes were critical during the secondary cell wall synthesis stage. Comparative transcriptome analysis of the normal TM-1 genotype and the near isogenic Li-1 revealed that over 100 transcripts were differentially expressed at least 2-fold during secondary wall biogenesis, although the genetic profile of the expansion phase showed no significant differences in the isolines. Of particular note, we identified three candidate gene families-expansin, sucrose synthase, and tubulin-whose expression in Li-1 deviates from normal expression patterns of its parent, TM-1. These genes may contribute to retarded growth of fibers in Li-1 since they are fiber-expressed structural and metabolic genes. This work provides more details into the mechanisms of fiber development, and suggests the Li gene is active during the later stages of fiber development.
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Fan L, Shi WJ, Hu WR, Hao XY, Wang DM, Yuan H, Yan HY. Molecular and biochemical evidence for phenylpropanoid synthesis and presence of wall-linked phenolics in cotton fibers. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2009; 51:626-37. [PMID: 19566641 DOI: 10.1111/j.1744-7909.2009.00840.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The mature cotton (Gossypium hirsutum L.) fiber is a single cell with a typically thickened secondary cell wall. The aim of this research was to use molecular, spectroscopic and chemical techniques to investigate the possible occurrence of previously overlooked accumulation of phenolics during secondary cell wall formation in cotton fibers. Relative quantitative reverse transcription-polymerase chain reaction analysis showed that GhCAD6 and GhCAD1 were predominantly expressed among seven gene homologs, only GhCAD6 was up-regulated during secondary wall formation in cotton fibers. Phylogenic analysis revealed that GhCAD6 belonged to Class I and was proposed to have a major role in monolignol biosynthesis, and GhCAD1 belonged to Class III and was proposed to have a compensatory mechanism for monolignol biosynthesis. Amino acid sequence comparison showed that the cofactor binding sites of GhCADs were highly conserved with high similarity and identity to bona fide cinnamyl alcohol dehydrogenases. The substrate binding site of GhCAD1 is different from GhCAD6. This difference was confirmed by the different catalytic activities observed with the enzymes. Cell wall auto-fluorescence, Fourier transform infrared spectroscopy (FTIR), high-performance liquid chromatography (HPLC) and chemical analyses confirmed that phenolic compounds were bound to the cell walls of mature cotton fibers. Our findings may suggest a potential for genetic manipulation of cotton fiber properties, which are of central importance to agricultural, cotton processing and textile industries.
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Affiliation(s)
- Ling Fan
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
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