scholarly journals Novel insights into water-deficit-responsive mRNAs and lncRNAs during fiber development in Gossypium hirsutum

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Nan Wu ◽  
Jun Yang ◽  
Guoning Wang ◽  
Huifeng Ke ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Water Deficit ◽  
Cotton Fiber ◽  
Fiber Quality ◽  
Development Stage ◽  
Fiber Development ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Protein Coding ◽  
Fiber Cells ◽  
Response To Water

Abstract Background The fiber yield and quality of cotton are greatly and periodically affected by water deficit. However, the molecular mechanism of the water deficit response in cotton fiber cells has not been fully elucidated. Results In this study, water deficit caused a significant reduction in fiber length, strength, and elongation rate but a dramatic increase in micronaire value. To explore genome-wide transcriptional changes, fibers from cotton plants subjected to water deficit (WD) and normal irrigation (NI) during fiber development were analyzed by transcriptome sequencing. Analysis showed that 3427 mRNAs and 1021 long noncoding RNAs (lncRNAs) from fibers were differentially expressed between WD and NI plants. The maximum number of differentially expressed genes (DEGs) and lncRNAs (DERs) was identified in fibers at the secondary cell wall biosynthesis stage, suggesting that this is a critical period in response to water deficit. Twelve genes in cotton fiber were differentially and persistently expressed at ≥ five time points, suggesting that these genes are involved in both fiber development and the water-deficit response and could potentially be used in breeding to improve cotton resistance to drought stress. A total of 540 DEGs were predicted to be potentially regulated by DERs by analysis of coexpression and genomic colocation, accounting for approximately 15.76% of all DEGs. Four DERs, potentially acting as target mimics for microRNAs (miRNAs), indirectly regulated their corresponding DEGs in response to water deficit. Conclusions This work provides a comprehensive transcriptome analysis of fiber cells and a set of protein-coding genes and lncRNAs implicated in the cotton response to water deficit, significantly affecting fiber quality during the fiber development stage.

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

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 128 ◽  
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.

scholarly journals Identification of Candidate Genes Controlling Fiber Quality Traits in Upland Cotton Through Integration of Meta-QTL, Significant SNP and Transcriptomic Data

2020 ◽  
Author(s):  
XU Shudi ◽  
Zhenyuan Pan ◽  
Feifan Yin ◽  
Qingyong Yang ◽  
Zhongxu Lin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Cotton Fiber ◽  
Molecular Mechanisms ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Significant Snps ◽  
Fiber Development ◽  
Computational Technique ◽  
Quality Traits ◽  
Fiber Quality Traits

Abstract Background Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants. Results In our study, 884 QTL associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTL were identified, including 19 meta-QTL for fiber length (FL), 18 meta-QTL for fiber strength (FS), 11 meta-QTL for fiber uniformity (FU), 11 meta-QTL for fiber elongation (FE), and 15 meta-QTL for micronaire (MIC). Combined with 8589 significant SNPs associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development. Conclusions This study provides not only stable QTLs used for marker-assisted selection (MAS), but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

scholarly journals Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL, significant SNP and transcriptomic data

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Shudi XU ◽  
Zhenyuan PAN ◽  
Feifan YIN ◽  
Qingyong YANG ◽  
Zhongxu LIN ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Cotton Fiber ◽  
Molecular Mechanisms ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Fiber Development ◽  
Computational Technique ◽  
Quality Traits ◽  
Nucleotide Polymorphisms ◽  
Fiber Quality Traits

Abstract Background Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants. Results In our study, 884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTLs were identified, including 19 meta-QTLs for fiber length; 18 meta-QTLs for fiber strength; 11 meta-QTLs for fiber uniformity; 11 meta-QTLs for fiber elongation; and 15 meta-QTLs for micronaire. Combined with 8 589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression levels specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development. Conclusions This study provides not only stable QTLs used for marker-assisted selection, but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

scholarly journals Identification of Candidate Genes Controlling Fiber Quality Traits in Upland Cotton through Integration of Meta-QTL, Significant SNP and Transcriptomic Data

2020 ◽  
Author(s):  
XU Shudi ◽  
Zhenyuan Pan ◽  
Feifan Yin ◽  
Qingyong Yang ◽  
Zhongxu Lin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Cotton Fiber ◽  
Molecular Mechanisms ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Significant Snps ◽  
Fiber Development ◽  
Computational Technique ◽  
Quality Traits ◽  
Fiber Quality Traits

Abstract Background: Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants. Results: In our study, 884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTLs were identified, including 19 meta-QTLs for fiber length (FL); 18 meta-QTLs for fiber strength (FS); 11 meta-QTLs for fiber uniformity (FU); 11 meta-QTLs for fiber elongation (FE); and 15 meta-QTLs for micronaire (MIC). Combined with 8,589 significant SNPs associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression levels specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development. Conclusions: This study provides not only stable QTLs used for marker-assisted selection (MAS), but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

scholarly journals Hormones Performs a Crucial Role in the Regulation of Cotton Fiber Synthesis

2021 ◽  
Vol 2 (4) ◽  
pp. 9-25
Author(s):  
Muhammad Nouman Khalid ◽  
Keyword(s):  
Abscisic Acid ◽  
Cotton Fiber ◽  
Textile Industry ◽  
Single Cells ◽  
Critical Role ◽  
Fiber Development ◽  
Fiber Formation ◽  
Complete Analysis ◽  
Developmental Processes ◽  
Fiber Cells

Cotton is the world's most important source of renewable fiber, and it is largely utilized in the textile industry to make clothes. In contrast to the ovule epidermis, cotton fibers are single cells that have differentiated from it, making them an attractive model system for the study of polyploidization, production of cell wall and elongation of cell. Plant hormones, that are present in very small low quantities in the plant, play essential roles in a variety of developmental processes, and new research has found that hormones play a critical role in controlling cotton fiber formation, as well as other developmental processes. For example, it has been demonstrated that the exogenous administration of hormones can stimulate the start and development of fiber cells. However, there is currently a lack of a thorough knowledge of phytohormones that regulate the formation of fiber. This paper focuses on latest developments in the understanding of the roles of different phytohormones involved in fiber development, including brassinosteroid, gibberellin, cytokinin, auxin, ethylene and abscisic acid. This paper reviews the discovery of genes associated in hormone biosynthesis and signaling pathways, as well as the methods by which these phytohormones control the commencement and elongation of fiber cells in cotton. All of the hormones involved in fiber formation are beneficial; however, cytokinin and abscisic acid are detrimental. Auxin, gibberellin, brassinosteroid, ethylene, jasmonate, and strigolactones are among the hormones involved in fiber development. A complete analysis of the function of phytohormones in cotton fiber development is our goal.

scholarly journals Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiangtao Yang ◽  
Lihua Gao ◽  
Xiaojing Liu ◽  
Xiaochun Zhang ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gossypium Hirsutum ◽  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Fiber Development ◽  
Comparative Transcriptome

AbstractCotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

scholarly journals Identification of the Group III WRKY Subfamily and the Functional Analysis of GhWRKY53 in Gossypium hirsutum L.

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1235
Author(s):  
Dongjie Yang ◽  
Yuanyuan Liu ◽  
Hailiang Cheng ◽  
Qiaolian Wang ◽  
Limin Lv ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Cotton Fiber ◽  
Fiber Quality ◽  
Fiber Development ◽  
Amino Acid Sequences ◽  
Fiber Formation ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Gossypium Hirsutum L ◽  
Group Iii

WRKY transcription factors had multiple functions in plant secondary metabolism, leaf senescence, fruit ripening, adaptation to biotic and abiotic stress, and plant growth and development. However, knowledge of the group III WRKY subfamily in fiber development in upland cotton (Gossypium hirsutum L.) is largely absent. Previous studies have shown that there were 21 putative group III WRKY members in G. hirsutum L. These putative amino acid sequences from the III WRKY group were phylogenetically clustered into three clades. Multiple alignment, conservative motif analysis, and gene structure analysis showed that the members clustered together in the phylogenetic tree had similar motifs and gene structures. Expression pattern analysis revealed that variation in the expression levels of these genes in different tissues and fiber development stages. To better understand the functions of putative group III WRKY genes in G. hirsutum L., we selected the cotton fiber initiation-related gene GhWRKY53 for cloning and functional identification. The subcellular localization experiment of GhWRKY53 in Nicotiana tabacum leaves showed that it was located in the nucleus. The heterologous expression of GhWRKY53 in Arabidopsis thaliana could significantly increase the density of trichomes. Twelve proteins that interacted with GhWRKY53 were screened from the cotton fiber cDNA library by yeast two-hybrid experiment. This study findings lay a foundation for further research on the role of the GhWRKY53 during cotton fiber development and provide a new insight for further studying putative group III WRKY genes in G. hirsutum L. Our research results also provide vital information for the genetic mechanism of high-quality cotton fiber formation and essential genetic resources for cotton fiber quality improvement.

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