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Transcriptome Profiling, Molecular Biological, and Physiological Studies Reveal a Major Role for Ethylene in Cotton Fiber Cell Elongation

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TLDR
The results indicate that ethylene plays a major role in promoting cotton fiber elongation and may promote cell elongation by increasing the expression of sucrose synthase, tubulin, and expansin genes.
Abstract
Upland cotton (Gossypium hirsutum) produces the most widely used natural fibers, yet the regulatory mechanisms governing fiber cell elongation are not well understood. Through sequencing of a cotton fiber cDNA library and subsequent microarray analysis, we found that ethylene biosynthesis is one of the most significantly upregulated biochemical pathways during fiber elongation. The 1-Aminocyclopropane-1-Carboxylic Acid Oxidase1-3 (ACO1-3) genes responsible for ethylene production were expressed at significantly higher levels during this growth stage. The amount of ethylene released from cultured ovules correlated with ACO expression and the rate of fiber growth. Exogenously applied ethylene promoted robust fiber cell expansion, whereas its biosynthetic inhibitor l-(2-aminoethoxyvinyl)-glycine (AVG) specifically suppressed fiber growth. The brassinosteroid (BR) biosynthetic pathway was modestly upregulated during this growth stage, and treatment with BR or its biosynthetic inhibitor brassinazole (BRZ) also promoted or inhibited, respectively, fiber growth. However, the effect of ethylene treatment was much stronger than that of BR, and the inhibitory effect of BRZ on fiber cells could be overcome by ethylene, but the AVG effect was much less reversed by BR. These results indicate that ethylene plays a major role in promoting cotton fiber elongation. Furthermore, ethylene may promote cell elongation by increasing the expression of sucrose synthase, tubulin, and expansin genes.

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Journal ArticleDOI

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

TL;DR: A web server, KOBAS 2.0, is reported, which annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations, which allows for both ID mapping and cross-species sequence similarity mapping.
Journal ArticleDOI

KOBAS server: a web-based platform for automated annotation and pathway identification

TL;DR: The usability of the KOBAS server is demonstrated by finding statistically enriched pathways in a set of upregulated genes in Alzheimer's Disease (AD) hippocampal cornu ammonis 1 (CA1) and the server can be accessed at .
References
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Journal ArticleDOI

Cluster analysis and display of genome-wide expression patterns

TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Journal ArticleDOI

A direct approach to false discovery rates

TL;DR: The calculation of the q‐value is discussed, the pFDR analogue of the p‐value, which eliminates the need to set the error rate beforehand as is traditionally done, and can yield an increase of over eight times in power compared with the Benjamini–Hochberg FDR method.
Journal ArticleDOI

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

TL;DR: This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments.
Book

Biochemistry & Molecular Biology of Plants

TL;DR: This edition of Biochemistry & Molecular Biology of Plants holds a unique place in the plant sciences literature as it provides the only comprehensive, authoritative, integrated single volume book in this essential field of study.
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