Characterization of Cotton ARF Factors and the Role of GhARF2b in Fiber Development

Abstract Background: Cotton fiber is a model system for studying plant cell development. At present, our understanding of cotton fiber development and the regulatory network is still primitive. Results: Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton G. hirsutum, which has 73 ARF genes, and its putative extent parental diploids G. arboreum and G. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in G. hirsutum ARF genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that GhARF2b, a homolog of the Arabidopsis AtARF2, was preferentially expressed in developing ovules and fibers. Overexpression of GhARF2b by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi of resulted in fewer but longer fiber. Conclusion: Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

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Characterization of cotton ARF factors and the role of GhARF2b in fiber development

BMC Genomics ◽

10.1186/s12864-021-07504-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiufang Zhang ◽

Junfeng Cao ◽

Chaochen Huang ◽

Zishou Zheng ◽

Xia Liu ◽

...

Keyword(s):

Cotton Fiber ◽

Target Genes ◽

Early Stage ◽

Fiber Development ◽

Auxin Response Factor ◽

Response Factor ◽

Auxin Response ◽

Cotton Fiber Development ◽

Cotton Species

AbstractBackgroundCotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored.ResultsHere, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cottonG. hirsutum, which has 73 ARF genes, and its putative extent parental diploidsG. arboreumandG. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that inG. hirsutum ARFgenes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate thatGhARF2b, a homolog of the ArabidopsisAtARF2, was preferentially expressed in developing ovules and fibers. Overexpression ofGhARF2bby a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes.ConclusionOur results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

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Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

Plants ◽

10.3390/plants9010128 ◽

2020 ◽

Vol 9 (1) ◽

pp. 128 ◽

Cited By ~ 5

Author(s):

Haron Salih ◽

Shoupu He ◽

Hongge Li ◽

Zhen Peng ◽

Xiongming Du

Keyword(s):

Transcription Factor ◽

Gene Family ◽

Cotton Fiber ◽

Metabolic Pathways ◽

Higher Plants ◽

Fiber Development ◽

Protein Family ◽

Sequencing Analysis ◽

Cotton Fiber Development ◽

Cotton Species

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.

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A Pivotal Role of Hormones in Regulating Cotton Fiber Development

Frontiers in Plant Science ◽

10.3389/fpls.2019.00087 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 14

Author(s):

Guanghui Xiao ◽

Peng Zhao ◽

Yu Zhang

Keyword(s):

Cotton Fiber ◽

Fiber Development ◽

Pivotal Role ◽

Cotton Fiber Development

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Cloning and characterization of a gene for an LRR receptor-like protein kinase associated with cotton fiber development

Molecular Genetics and Genomics ◽

10.1007/s00438-005-1115-z ◽

2005 ◽

Vol 273 (3) ◽

pp. 217-224 ◽

Cited By ~ 22

Author(s):

Yuan-Li Li ◽

Jie Sun ◽

Gui-Xian Xia

Keyword(s):

Protein Kinase ◽

Cotton Fiber ◽

Fiber Development ◽

Cotton Fiber Development

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Genome-Wide Analysis of AAT Genes and Their Expression Profiling during Fiber Development in Cotton

Plants ◽

10.3390/plants10112461 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2461

Author(s):

Dongjie Yang ◽

Yuanyuan Liu ◽

Hailiang Cheng ◽

Qiaolian Wang ◽

Limin Lv ◽

...

Keyword(s):

Cotton Fiber ◽

Biological Function ◽

Higher Plants ◽

Crop Improvement ◽

Fiber Development ◽

Maturity Stage ◽

Amino Acid Transporters ◽

Cotton Fiber Development ◽

Fiber Initiation ◽

Cotton Species

Amino acid transporters (AATs) are a kind of membrane proteins that mediate the transport of amino acids across cell membranes in higher plants. The AAT proteins are involved in regulating plant cell growth and various developmental processes. However, the biological function of this gene family in cotton fiber development is not clear. In this study, 190, 190, 101, and 94 full-length AAT genes were identified from Gossypiumhirsutum, G. barbadense, G. arboreum, and G. raimondii. A total of 575 AAT genes from the four cotton species were divided into two subfamilies and 12 clades based on phylogenetic analysis. The AAT genes in the four cotton species were distributed on all the chromosomes. All GhAAT genes contain multiple exons, and each GhAAT protein has multiple conserved motifs. Transcriptional profiling and RT qPCR analysis showed that four GhATT genes tend to express specifically at the fiber initiation stage. Eight genes tend to express specifically at the fiber elongation and maturity stage, and four genes tend to express specifically at the fiber initiation and elongation stages. Our results provide a solid basis for further elucidating the biological function of AAT genes related to cotton fiber development and offer valuable genetic resources for crop improvement in the future.

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The role of phytohormones in cotton fiber development

Russian Journal of Plant Physiology ◽

10.1134/s1021443710040023 ◽

2010 ◽

Vol 57 (4) ◽

pp. 462-468 ◽

Cited By ~ 6

Author(s):

Wenbin Liao ◽

Juan Zhang ◽

Nanfei Xu ◽

Ming Peng

Keyword(s):

Cotton Fiber ◽

Fiber Development ◽

Cotton Fiber Development

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Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development

Journal of Cotton Research ◽

10.1186/s42397-021-00099-z ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Senmiao FAN ◽

Aiying LIU ◽

Xianyan ZOU ◽

Zhen ZHANG ◽

Qun GE ◽

...

Keyword(s):

Gene Family ◽

Cotton Fiber ◽

Fiber Strength ◽

Expression Patterns ◽

Fiber Development ◽

Fiber Elongation ◽

Transcript Levels ◽

Cotton Fiber Development ◽

Conserved Sequence ◽

Cotton Species

Abstract Background Pectin is a key substance involved in cell wall development, and the galacturonosyltransferases (GAUTs) gene family is a critical participant in the pectin synthesis pathway. Systematic and comprehensive research on GAUTs has not been performed in cotton. Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to increase knowledge of the function of pectin in cotton fiber development. Results In this study, we have identified 131 GAUT genes in the genomes of four Gossypium species (G. raimondii, G. barbadense, G. hirsutum, and G. arboreum), and classified them as GAUT-A, GAUT-B and GAUT-C, which coding probable galacturonosyltransferases. Among them, the GAUT genes encode proteins GAUT1 to GAUT15. All GAUT proteins except for GAUT7 contain a conserved glycosyl transferase family 8 domain (H-DN-A-SVV-S-V-H-T-F). The conserved sequence of GAUT7 is PLN (phospholamban) 02769 domain. According to cis-elemet analysis, GAUT genes transcript levels may be regulated by hormones such as JA, GA, SA, ABA, Me-JA, and IAA. The evolution and transcription patterns of the GAUT gene family in different cotton species and the transcript levels in upland cotton lines with different fiber strength were analyzed. Peak transcript level of GhGAUT genes have been observed before 15 DPA. In the six materials with high fiber strength, the transcription of GhGAUT genes were concentrated from 10 to 15 DPA; while the highest transcript levels in low fiber strength materials were detected between 5 and 10 DPA. These results lays the foundation for future research on gene function during cotton fiber development. Conclusions The GAUT gene family may affect cotton fiber development, including fiber elongation and fiber thickening. In the low strength fiber lines, GAUTs mainly participate in fiber elongation, whereas their major effect on cotton with high strength fiber is related to both elongation and thickening.

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