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Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development

Gossypium hirsutum and Gossypium barbadense are the widely cultivated tetraploid cottons around the world, which evolved great differences in the fiber yield and quality due to the independent domestication process. To reveal the genetic basis of the difference, we integrated 90 samples from ten tim...

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Autores principales: Zhang, Juncheng, Mei, Huan, Lu, Hejun, Chen, Rui, Hu, Yan, Zhang, Tianzhen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022538/
https://www.ncbi.nlm.nih.gov/pubmed/35463423
http://dx.doi.org/10.3389/fpls.2022.864529
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author Zhang, Juncheng
Mei, Huan
Lu, Hejun
Chen, Rui
Hu, Yan
Zhang, Tianzhen
author_facet Zhang, Juncheng
Mei, Huan
Lu, Hejun
Chen, Rui
Hu, Yan
Zhang, Tianzhen
author_sort Zhang, Juncheng
collection PubMed
description Gossypium hirsutum and Gossypium barbadense are the widely cultivated tetraploid cottons around the world, which evolved great differences in the fiber yield and quality due to the independent domestication process. To reveal the genetic basis of the difference, we integrated 90 samples from ten time points during the fiber developmental period for investigating the dynamics of gene expression changes associated with fiber in G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 and acc. 3-79. Globally, 44,484 genes expressed in all three cultivars account for 61.14% of the total genes. About 61.39% (N = 3,412) of the cotton transcription factors were involved in fiber development, which consisted of 58 cotton TF families. The differential analysis of intra- and interspecies showed that 3 DPA had more expression changes. To discover the genes with temporally changed expression profiles during the whole fiber development, 1,850 genes predominantly expressed in G. hirsutum and 1,050 in G. barbadense were identified, respectively. Based on the weighted gene co-expression network and time-course analysis, several candidate genes, mainly involved in the secondary cell wall synthesis and phytohormones, were identified in this study, underlying possibly the transcriptional regulation and molecular mechanisms of the fiber quality differences between G. barbadense and G. hirsutum. The quantitative real-time PCR validation of the candidate genes was consistent with the RNA-seq data. Our study provides a strong rationale for the analysis of gene function and breeding of high-quality cotton.
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spelling pubmed-90225382022-04-22 Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development Zhang, Juncheng Mei, Huan Lu, Hejun Chen, Rui Hu, Yan Zhang, Tianzhen Front Plant Sci Plant Science Gossypium hirsutum and Gossypium barbadense are the widely cultivated tetraploid cottons around the world, which evolved great differences in the fiber yield and quality due to the independent domestication process. To reveal the genetic basis of the difference, we integrated 90 samples from ten time points during the fiber developmental period for investigating the dynamics of gene expression changes associated with fiber in G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 and acc. 3-79. Globally, 44,484 genes expressed in all three cultivars account for 61.14% of the total genes. About 61.39% (N = 3,412) of the cotton transcription factors were involved in fiber development, which consisted of 58 cotton TF families. The differential analysis of intra- and interspecies showed that 3 DPA had more expression changes. To discover the genes with temporally changed expression profiles during the whole fiber development, 1,850 genes predominantly expressed in G. hirsutum and 1,050 in G. barbadense were identified, respectively. Based on the weighted gene co-expression network and time-course analysis, several candidate genes, mainly involved in the secondary cell wall synthesis and phytohormones, were identified in this study, underlying possibly the transcriptional regulation and molecular mechanisms of the fiber quality differences between G. barbadense and G. hirsutum. The quantitative real-time PCR validation of the candidate genes was consistent with the RNA-seq data. Our study provides a strong rationale for the analysis of gene function and breeding of high-quality cotton. Frontiers Media S.A. 2022-04-05 /pmc/articles/PMC9022538/ /pubmed/35463423 http://dx.doi.org/10.3389/fpls.2022.864529 Text en Copyright © 2022 Zhang, Mei, Lu, Chen, Hu and Zhang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Zhang, Juncheng
Mei, Huan
Lu, Hejun
Chen, Rui
Hu, Yan
Zhang, Tianzhen
Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development
title Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development
title_full Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development
title_fullStr Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development
title_full_unstemmed Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development
title_short Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development
title_sort transcriptome time-course analysis in the whole period of cotton fiber development
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022538/
https://www.ncbi.nlm.nih.gov/pubmed/35463423
http://dx.doi.org/10.3389/fpls.2022.864529
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