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Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii

Cotton is one of the major industrial crops that supply natural fibers and oil for industries. This study was conducted to understand the mechanism of delayed gland morphogenesis in seeds of Gossypium bickii. In this study, we compared glandless seeds of G. bickii with glanded seeds of Gossypium arb...

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Autores principales: Ali, Mushtaque, Cheng, Hailiang, Soomro, Mahtab, Shuyan, Li, Bilal Tufail, Muhammad, Nazir, Mian Faisal, Feng, Xiaoxu, Zhang, Youping, Dongyun, Zuo, Limin, Lv, Wang, Qiaolian, Song, Guoli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290383/
https://www.ncbi.nlm.nih.gov/pubmed/32357512
http://dx.doi.org/10.3390/genes11050472
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author Ali, Mushtaque
Cheng, Hailiang
Soomro, Mahtab
Shuyan, Li
Bilal Tufail, Muhammad
Nazir, Mian Faisal
Feng, Xiaoxu
Zhang, Youping
Dongyun, Zuo
Limin, Lv
Wang, Qiaolian
Song, Guoli
author_facet Ali, Mushtaque
Cheng, Hailiang
Soomro, Mahtab
Shuyan, Li
Bilal Tufail, Muhammad
Nazir, Mian Faisal
Feng, Xiaoxu
Zhang, Youping
Dongyun, Zuo
Limin, Lv
Wang, Qiaolian
Song, Guoli
author_sort Ali, Mushtaque
collection PubMed
description Cotton is one of the major industrial crops that supply natural fibers and oil for industries. This study was conducted to understand the mechanism of delayed gland morphogenesis in seeds of Gossypium bickii. In this study, we compared glandless seeds of G. bickii with glanded seeds of Gossypium arboreum. High-throughput sequencing technology was used to explore and classify the expression patterns of gland-related genes in seeds and seedlings of cotton plants. Approximately 131.33 Gigabases of raw data from 12 RNA sequencing samples with three biological replicates were generated. A total of 7196 differentially-expressed genes (DEGs) were identified in all transcriptome data. Among them, 3396 genes were found up-regulated and 3480 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to identify different functions between genes unique to glandless imbibed seeds and glanded seedlings. Co-expression network analysis revealed four modules that were identified as highly associated with the development of glandless seeds. Here the hub genes in each module were identified by weighted gene co-expression network analysis (WGCNA). In total, we have selected 13 genes involved in transcription factors, protein and MYB-related functions, that were differentially expressed in transcriptomic data and validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). These selected genes may play an important role for delayed gland morphogenesis. Our study provides comprehensive insight into the key genes related to glandless traits of seeds and plants, and can be further exploited by functional and molecular studies.
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spelling pubmed-72903832020-06-15 Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii Ali, Mushtaque Cheng, Hailiang Soomro, Mahtab Shuyan, Li Bilal Tufail, Muhammad Nazir, Mian Faisal Feng, Xiaoxu Zhang, Youping Dongyun, Zuo Limin, Lv Wang, Qiaolian Song, Guoli Genes (Basel) Article Cotton is one of the major industrial crops that supply natural fibers and oil for industries. This study was conducted to understand the mechanism of delayed gland morphogenesis in seeds of Gossypium bickii. In this study, we compared glandless seeds of G. bickii with glanded seeds of Gossypium arboreum. High-throughput sequencing technology was used to explore and classify the expression patterns of gland-related genes in seeds and seedlings of cotton plants. Approximately 131.33 Gigabases of raw data from 12 RNA sequencing samples with three biological replicates were generated. A total of 7196 differentially-expressed genes (DEGs) were identified in all transcriptome data. Among them, 3396 genes were found up-regulated and 3480 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to identify different functions between genes unique to glandless imbibed seeds and glanded seedlings. Co-expression network analysis revealed four modules that were identified as highly associated with the development of glandless seeds. Here the hub genes in each module were identified by weighted gene co-expression network analysis (WGCNA). In total, we have selected 13 genes involved in transcription factors, protein and MYB-related functions, that were differentially expressed in transcriptomic data and validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). These selected genes may play an important role for delayed gland morphogenesis. Our study provides comprehensive insight into the key genes related to glandless traits of seeds and plants, and can be further exploited by functional and molecular studies. MDPI 2020-04-26 /pmc/articles/PMC7290383/ /pubmed/32357512 http://dx.doi.org/10.3390/genes11050472 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ali, Mushtaque
Cheng, Hailiang
Soomro, Mahtab
Shuyan, Li
Bilal Tufail, Muhammad
Nazir, Mian Faisal
Feng, Xiaoxu
Zhang, Youping
Dongyun, Zuo
Limin, Lv
Wang, Qiaolian
Song, Guoli
Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
title Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
title_full Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
title_fullStr Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
title_full_unstemmed Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
title_short Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
title_sort comparative transcriptomic analysis to identify the genes related to delayed gland morphogenesis in gossypium bickii
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290383/
https://www.ncbi.nlm.nih.gov/pubmed/32357512
http://dx.doi.org/10.3390/genes11050472
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