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Molecular Insights into Cotton Fiber Gene Regulation
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Molecular Insights into Cotton Fiber Gene Regulation

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 1772

Special Issue Editors

Prof. Dr. Yuxian Zhu

E-Mail Website
Guest Editor
1. Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
2. College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: mechanism of cotton fiber cell elongation; functional mechanism of plant hormones; regulation mechanism of gene expression
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Fuguang Li

E-Mail Website
Guest Editor
Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455004, China
Interests: cotton transformation; cotton breeding; genetic improvement; cotton resistance; cotton stress tolerance

Special Issue Information

Dear Colleagues,

Cotton is an irreplaceable economic crop domesticated by human beings for its extremely elongated fibers, with a central role in the world’s textile industry. Since the quality of cotton fiber cells directly determines its economic value, enhancing fiber quality is always the primary task in cotton breeding practices. In recent years, many fiber quality-related genes, QTLs and biochemical pathways have been identified and proposed. For example, several major QTLs were found to be associated with fiber length and quality improvement via cotton genome sequencing projects. Moreover, a lack of favorable allelic diversity in most cotton cultivars, which is recognized as the bottleneck for fiber quality enhancement, was overcome by introgression of exotic donors, i.e., from members of other Gossypium genera. In the future, scientists may incorporate more diploid genes or loci to improve the quality of Upland cotton fibers. This Special Issue of Plants will focus on and highlight the functional regulatory mechanisms that underlie fiber cell elongation, the evolution of genes involved in the specific linear cell growth mode, as well as control of cell wall biosynthesis and other related aspects.

Prof. Dr. Yuxian Zhu
Prof. Dr. Fuguang Li
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cotton fiber
  • plant hormone
  • elongation
  • cell wall growth
  • molecular regulation
  • QTLs
  • introgression

Published Papers (5 papers)

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Research

12 pages, 1554 KiB  
Article
Actively Expressed Intergenic Genes Generated by Transposable Element Insertions in Gossypium hirsutum Cotton
by Yongzhuo Guan, Mingao Zhou, Congyu Zhang, Zixuan Han, Yinbao Zhang, Zhiguo Wu and Yuxian Zhu
Plants 2024, 13(15), 2079; https://doi.org/10.3390/plants13152079 (registering DOI) - 26 Jul 2024
Abstract
The genomes and annotated genes of allotetraploid cotton Gossypium hirsutum have been extensively studied in recent years. However, the expression, regulation, and evolution of intergenic genes (ITGs) have not been completely deciphered. In this study, we identified a novel set of actively expressed [...] Read more.
The genomes and annotated genes of allotetraploid cotton Gossypium hirsutum have been extensively studied in recent years. However, the expression, regulation, and evolution of intergenic genes (ITGs) have not been completely deciphered. In this study, we identified a novel set of actively expressed ITGs in G. hirsutum cotton, through transcriptome profiling based on deep sequencing data, as well as chromatin immunoprecipitation, followed by sequencing (ChIP-seq) of histone modifications and how the ITGs evolved. Totals of 17,567 and 8249 ITGs were identified in G. hirsutum and Gossypium arboreum, respectively. The expression of ITGs in G. hirsutum was significantly higher than that in G. arboreum. Moreover, longer exons were observed in G. hirsutum ITGs. Notably, 42.3% of the ITGs from G. hirsutum were generated by the long terminal repeat (LTR) insertions, while their proportion in genic genes was 19.9%. The H3K27ac and H3K4me3 modification proportions and intensities of ITGs were equivalent to genic genes. The H3K4me1 modifications were lower in ITGs. Additionally, evolution analyses revealed that the ITGs from G. hirsutum were mainly produced around 6.6 and 1.6 million years ago (Mya), later than the pegged time for genic genes, which is 7.0 Mya. The characterization of ITGs helps to elucidate the evolution of cotton genomes and shed more light on their biological functions in the transcriptional regulation of eukaryotic genes, along with the roles of histone modifications in speciation and diversification. Full article
(This article belongs to the Special Issue Molecular Insights into Cotton Fiber Gene Regulation)
12 pages, 3988 KiB  
Article
GhMAX2 Contributes to Auxin-Mediated Fiber Elongation in Cotton (Gossypium hirsutum)
by Zailong Tian, Haijin Qin, Baojun Chen, Zhaoe Pan, Yinhua Jia, Xiongming Du and Shoupu He
Plants 2024, 13(15), 2041; https://doi.org/10.3390/plants13152041 - 25 Jul 2024
Viewed by 229
Abstract
Strigolactones (SLs) represent a new group of phytohormones that play a pivotal role in the regulation of plant shoot branching and the development of adventitious roots. In cotton (Gossypium hirsutum, Gh), SLs play a crucial role in the regulation of [...] Read more.
Strigolactones (SLs) represent a new group of phytohormones that play a pivotal role in the regulation of plant shoot branching and the development of adventitious roots. In cotton (Gossypium hirsutum, Gh), SLs play a crucial role in the regulation of fiber cell elongation and secondary cell wall thickness. However, the underlying molecular mechanisms of SL signaling involved in fiber cell development are largely unknown. In this study, we report two SL-signaling genes, GhMAX2-3 and GhMAX2-6, which positively regulate cotton fiber elongation. Further protein—protein interaction and degradation assays showed that the repressor of the auxin cascade GhIAA17 serves as a substrate for the F-box E3 ligase GhMAX2. The in vivo ubiquitination assay suggested that GhMAX2-3 and GhMAX2-6 ubiquitinate GhIAA17 and coordinately degrade GhIAA17 with GhTIR1. The findings of this investigation offer valuable insights into the roles of GhMAX2-mediated SL signaling in cotton and establish a solid foundation for future endeavors aimed at optimizing cotton plant cultivation. Full article
(This article belongs to the Special Issue Molecular Insights into Cotton Fiber Gene Regulation)
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15 pages, 5300 KiB  
Article
Integrative Transcriptomic and Metabolic Analyses Reveal That Flavonoid Biosynthesis Is the Key Pathway Regulating Pigment Deposition in Naturally Brown Cotton Fibers
by Shandang Shi, Rui Tang, Xiaoyun Hao, Shouwu Tang, Wengang Chen, Chao Jiang, Mengqian Long, Kailu Chen, Xiangxiang Hu, Quanliang Xie, Shuangquan Xie, Zhuang Meng, Asigul Ismayil, Xiang Jin, Fei Wang, Haifeng Liu and Hongbin Li
Plants 2024, 13(15), 2028; https://doi.org/10.3390/plants13152028 - 24 Jul 2024
Viewed by 249
Abstract
Brown cotton is a major cultivar of naturally colored cotton, and brown cotton fibers (BCFs) are widely utilized as raw materials for textile industry production due to their advantages of being green and dyeing-pollution-free. However, the mechanisms underlying the pigmentation in fibers are [...] Read more.
Brown cotton is a major cultivar of naturally colored cotton, and brown cotton fibers (BCFs) are widely utilized as raw materials for textile industry production due to their advantages of being green and dyeing-pollution-free. However, the mechanisms underlying the pigmentation in fibers are still poorly understood, which significantly limits their extensive applications in related fields. In this study, we conducted a multidimensional comparative analysis of the transcriptomes and metabolomes between brown and white fibers at different developmental periods to identify the key genes and pathways regulating the pigment deposition. The transcriptomic results indicated that the pathways of flavonoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched regulatory pathways, especially in the late development periods of fiber pigmentation; furthermore, the genes distributed in the pathways of PAL, CHS, F3H, DFR, ANR, and UFGT were identified as significantly up-regulated genes. The metabolic results showed that six metabolites, namely (−)-Epigallocatechin, Apiin, Cyanidin-3-O-glucoside, Gallocatechin, Myricetin, and Poncirin, were significantly accumulated in brown fibers but not in white fibers. Integrative analysis of the transcriptomic and metabolomic data demonstrated a possible regulatory network potentially regulating the pigment deposition, in which three MYB transcription factors promote the expression levels of flavonoid biosynthesis genes, thereby inducing the content increase in (−)-Epigallocatechin, Cyanidin-3-O-glucoside, Gallocatechin, and Myricetin in BCFs. Our findings provide new insights into the pigment deposition mechanism in BCFs and offer references for genetic engineering and breeding of colored cotton materials. Full article
(This article belongs to the Special Issue Molecular Insights into Cotton Fiber Gene Regulation)
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14 pages, 3422 KiB  
Article
Sphingosine Promotes Fiber Early Elongation in Upland Cotton
by Li Wang, Changyin Jin, Wenqing Zhang, Xueting Mei, Hang Yu, Man Wu, Wenfeng Pei, Jianjiang Ma, Bingbing Zhang, Ming Luo and Jiwen Yu
Plants 2024, 13(14), 1993; https://doi.org/10.3390/plants13141993 - 21 Jul 2024
Viewed by 287
Abstract
Sphingolipids play an important role in cotton fiber development, but the regulatory mechanism is largely unclear. We found that serine palmitoyltransferase (SPT) enzyme inhibitors, myriocin and sphingosine (dihydrosphingosine (DHS) and phytosphingosine (PHS)), affected early fiber elongation in cotton, and we performed a sphingolipidomic [...] Read more.
Sphingolipids play an important role in cotton fiber development, but the regulatory mechanism is largely unclear. We found that serine palmitoyltransferase (SPT) enzyme inhibitors, myriocin and sphingosine (dihydrosphingosine (DHS) and phytosphingosine (PHS)), affected early fiber elongation in cotton, and we performed a sphingolipidomic and transcriptomic analysis of control and PHS-treated fibers. Myriocin inhibited fiber elongation, while DHS and PHS promoted it in a dose–effect manner. Using liquid chromatography–tandem mass spectrometry (LC–MS/MS), we found that contents of 22 sphingolipids in the PHS-treated fibers for 10 days were changed, of which the contents of 4 sphingolipids increased and 18 sphingolipids decreased. The transcriptome analysis identified 432 differentially expressed genes (238 up-regulated and 194 down-regulated) in the PHS-treated fibers. Among them, the phenylpropanoid biosynthesis pathway is the most significant enrichment. The expression levels of transcription factors such as MYB, ERF, LBD, and bHLH in the fibers also changed, and most of MYB and ERF were up-regulated. Auxin-related genes IAA, GH3 and BIG GRAIN 1 were up-regulated, while ABPs were down-regulated, and the contents of 3 auxin metabolites were decreased. Our results provide important sphingolipid metabolites and regulatory pathways that influence fiber elongation. Full article
(This article belongs to the Special Issue Molecular Insights into Cotton Fiber Gene Regulation)
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14 pages, 5157 KiB  
Article
GhFAD3-4 Promotes Fiber Cell Elongation and Cell Wall Thickness by Increasing PI and IP3 Accumulation in Cotton
by Huiqin Wang, Mengyuan Fan, Yongcui Shen, Hanxuan Zhao, Shuangshuang Weng, Zhen Chen and Guanghui Xiao
Plants 2024, 13(11), 1510; https://doi.org/10.3390/plants13111510 - 30 May 2024
Viewed by 436
Abstract
The omega-3 fatty acid desaturase enzyme gene FAD3 is responsible for converting linoleic acid to linolenic acid in plant fatty acid synthesis. Despite limited knowledge of its role in cotton growth, our study focused on GhFAD3-4, a gene within the FAD3 family, [...] Read more.
The omega-3 fatty acid desaturase enzyme gene FAD3 is responsible for converting linoleic acid to linolenic acid in plant fatty acid synthesis. Despite limited knowledge of its role in cotton growth, our study focused on GhFAD3-4, a gene within the FAD3 family, which was found to promote fiber elongation and cell wall thickness in cotton. GhFAD3-4 was predominantly expressed in elongating fibers, and its suppression led to shorter fibers with reduced cell wall thickness and phosphoinositide (PI) and inositol triphosphate (IP3) levels. Transcriptome analysis of GhFAD3-4 knock-out mutants revealed significant impacts on genes involved in the phosphoinositol signaling pathway. Experimental evidence demonstrated that GhFAD3-4 positively regulated the expression of the GhBoGH3B and GhPIS genes, influencing cotton fiber development through the inositol signaling pathway. The application of PI and IP6 externally increased fiber length in GhFAD3-4 knock-out plants, while inhibiting PI led to a reduced fiber length in GhFAD3-4 overexpressing plants. These findings suggest that GhFAD3-4 plays a crucial role in enhancing fiber development by promoting PI and IP3 biosynthesis, offering the potential for breeding cotton varieties with superior fiber quality. Full article
(This article belongs to the Special Issue Molecular Insights into Cotton Fiber Gene Regulation)
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